Vanquish Pumps C, Pumps F (VC-PXX, VF-PXX) - Operating Manual

thermoscientific
Vanquish
Pumps C, Pumps F
VC-Pxx, VF-Pxx
Operating Manual
4820.4405-EN Revision 5.1 • May 2023
*4820.4405-EN-5.1*
Copyright © 2023 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Manual
The hardware descriptions in this manual revision refer to devices: VC-P10-A-01, VC-P20-A-01,
VC-P21-A-01, VC-P32-A-01, VC-P33-A-01, VC-P40-A-01, VF-P10-A-01, VF-P20-A, VF-P32-A-01.
Trademarks
Acrobat, Adobe, and Adobe Reader are trademarks of Adobe Systems Incorporated.
Microsoft and Windows are trademarks of Microsoft Corporation.
MP35N is a trademark of SPS Technologies.
PharMed is a trademark of Saint-Gobain Performance Plastics.
Torx is a trademark of Acument Intellectual Properties, LLC.
All other trademarks are property of Thermo Fisher Scientific and its subsidiaries.
Disclaimer
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to
use in the product operation. The document is copyright protected; any reproduction of the
whole or any part of this document is strictly prohibited, except with the written authorization
of Thermo Fisher Scientific Inc.
This manual is provided "as is." The contents of this manual are subject to being changed,
without notice, in future revisions.
Thermo Fisher Scientific Inc. makes no representations that this document is complete,
accurate, or error-free. Thermo Fisher Scientific Inc. assumes no responsibility and will not be
liable for any errors, omissions, damage, or loss that might result from any use of this document,
even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a
purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale.
The Terms and Conditions of Sale shall govern all conflicting information between the two
documents.
Printed manual version only

Printed in Germany on 100% chlorine-free bleached, high-white paper that is produced in an
environmentally friendly process, leading to a paper profile of zero CO2 emissions.
Manufacturer's address
Dionex Softron GmbH, Part of Thermo Fisher Scientific, Dornierstrasse 4, D-82110 Germering
Contacting Us
Contacting Us
There are several ways to contact us:
Ordering Information
For ordering information or sales support for HPLC products, contact
your local Thermo Fisher Scientific sales organization. For contact
information, go to Contact Us on http://www.thermofisher.com.
Technical Assistance
For technical support for HPLC products, contact your local Thermo
Fisher Scientific support organization. For contact information, go to
Contact Us on http://www.thermofisher.com.
Pumps C, Pumps F ( VC-Pxx, VF-Pxx) Page 3

Operating Manual
Contacting Us
Page 4 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)

Operating Manual
Contents
Contents
1 Using this Manual....................................................................... 11
1.1 About this Manual ............................................................................................... 12
1.2 Conventions ......................................................................................................... 13
1.2.1 Conventions for Safety Messages ............................................................ 13
1.2.2 Special Notices ......................................................................................... 13
1.2.3 Typographical Conventions ...................................................................... 14
1.3 Reference Documentation................................................................................... 15
2 Safety ......................................................................................... 17

2.1 Safety Symbols and Signal Words ........................................................................ 18
2.1.1 Safety Symbols and Signal Words in this Manual..................................... 18
2.1.2 Observing this Manual ............................................................................. 18
2.1.3 Safety Symbols on the Device .................................................................. 19
2.1.4 Rating Plate .............................................................................................. 19
2.2 Intended Use........................................................................................................ 20
2.3 Safety Precautions ............................................................................................... 21
2.3.1 General Safety Information...................................................................... 21
2.3.2 Qualification of the Personnel ................................................................. 22
2.3.3 Personal Protective Equipment................................................................ 22
2.3.4 Electrical Safety Precautions .................................................................... 23
2.3.5 General Residual Hazards......................................................................... 24
2.3.6 In Case of Emergency ............................................................................... 25
2.4 Solvent and Additive Information ........................................................................ 26
2.4.1 General Compatibility .............................................................................. 26
2.4.2 Piston Seal Compatibility.......................................................................... 26
2.4.3 Allowed pH Ranges................................................................................... 27
2.4.4 Allowed Concentrations ........................................................................... 28
2.4.5 Further Information ................................................................................. 28
2.5 Compliance Information ...................................................................................... 29
3 Device Overview......................................................................... 31

3.1 Pump Features ..................................................................................................... 32
3.2 Operating Principle .............................................................................................. 33
3.3 Interior Components............................................................................................ 34
3.4 Piston Seal Wash System ..................................................................................... 35

Operating Manual
Contents
3.5 Purge/Sensor Unit................................................................................................ 36

3.6 Mixing System...................................................................................................... 37
3.7 Leak Detection ..................................................................................................... 38
3.8 Operation............................................................................................................. 39
4 Unpacking .................................................................................. 41

4.1 Unpacking ............................................................................................................ 42
4.2 Scope of Delivery ................................................................................................. 44
5 Installation ................................................................................. 45

5.1 Safety Guidelines for Installation ......................................................................... 46
5.2 Installing the Device............................................................................................. 47
5.3 Site Requirements................................................................................................ 49
5.3.1 Power Considerations .............................................................................. 49
5.3.2 Power Cord............................................................................................... 50
5.3.3 Condensation ........................................................................................... 50
5.4 Accessing the Interior Components ..................................................................... 51
5.5 Setting Up the Hardware ..................................................................................... 52
5.5.1 System Arrangement................................................................................ 52
5.5.2 Connecting the Device ............................................................................. 53
5.5.3 Connecting the Power Cord ..................................................................... 54
5.6 Setting Up the Flow Connections......................................................................... 55
5.6.1 General Information and Guidelines........................................................ 55
5.6.2 Guiding Capillaries and Tubing Through the System................................ 56
5.6.3 Connecting Fittings, Capillaries, and Tubing ............................................ 57
5.6.4 Guiding Liquids to Waste ......................................................................... 62
5.6.5 Connecting the Solvent Lines ................................................................... 63
5.6.6 Installing Solvent Shut-Off Valves ............................................................ 67
5.7 Seal Wash System ................................................................................................ 69
5.7.1 Choosing the Seal Wash Liquid ................................................................ 69
5.7.2 Setting Up the Seal Wash System ............................................................ 70
5.7.3 Flushing the Seal Wash System ................................................................ 76
5.8 Connecting the Pump and Autosampler .............................................................. 78
5.9 Turning On the Device ......................................................................................... 79
5.10 Setting Up the Device in the Software ................................................................. 80

Operating Manual
Contents
6 Operation................................................................................... 81
6.1 Introduction to this Chapter ................................................................................ 82
6.2 Safety Guidelines for Operation........................................................................... 83
6.3 Control Elements ................................................................................................. 84
6.3.1 Keypad...................................................................................................... 84
6.3.2 Status Indicators....................................................................................... 86
6.4 Power On/Off Control.......................................................................................... 89
6.5 Use of Solvents and Additives.............................................................................. 90
6.6 Preparing the Device for Operation..................................................................... 92
6.7 Important Operating Parameters ........................................................................ 94
6.8 Purging the Pump .............................................................................................. 100
6.8.1 Automatic Purging.................................................................................. 101
6.8.2 Manual Purging ...................................................................................... 102
6.9 Optimizing the Performance of the Device........................................................ 107
6.9.1 General Guidelines ................................................................................. 107
6.9.2 Installing Solvent Shut-Off Valves .......................................................... 107
6.10 Shutting Down the Device ................................................................................. 110
6.10.1 Short-Term Shutdown (Interruption of Operation) ............................... 110
6.10.2 Long-Term Shutdown............................................................................. 111
6.10.3 Restart after Long-Term Shutdown........................................................ 113
7 Maintenance and Service ......................................................... 115

7.1 Introduction to Maintenance and Service ......................................................... 116
7.2 Safety Guidelines for Maintenance and Service ................................................ 117
7.3 General Rules for Maintenance and Service...................................................... 119
7.4 Routine and Preventive Maintenance ............................................................... 120
7.4.1 Internal Maintenance............................................................................. 120
7.4.2 Maintenance Plan .................................................................................. 120
7.4.3 Flushing the Pump to Avoid Contamination .......................................... 122
7.4.4 Flushing the Pump with Persistent Contamination Only ....................... 123
7.4.5 Cleaning or Decontaminating the Device............................................... 124
7.4.6 Predictive Performance.......................................................................... 125
7.5 Seal Wash System .............................................................................................. 127
7.5.1 Testing the Seal Wash System for Leakage ............................................ 128
7.5.2 Replacing the Seal Wash Lines ............................................................... 129
7.5.3 Replacing the Seal Wash Detector ......................................................... 132

Operating Manual
Contents
7.6 Pump Head......................................................................................................... 134

7.6.1 Overview of Pump Head Parts ............................................................... 135
7.6.2 Replacing the Pump Head ...................................................................... 136
7.6.3 Replacing the Pistons ............................................................................. 142
7.6.4 Cleaning the Piston................................................................................. 144
7.6.5 Replacing the Piston Seals or Support Ring............................................ 145
7.6.6 Recommendations for New Piston Seals................................................ 149
7.6.7 Replacing the Seal Wash Seals ............................................................... 151
7.6.8 Replacing the Pump Head Seals ............................................................. 154
7.6.9 Testing the Piston Seals for Leakage ...................................................... 156
7.7 Check Valves ...................................................................................................... 159
7.7.1 Replacing the Inlet Check Valves............................................................ 159
7.7.2 Replacing the Outlet Check Valves......................................................... 161
7.7.3 Cleaning the Check Valves...................................................................... 164
7.8 Mixing System.................................................................................................... 166
7.8.1 Testing the Static Mixer for Permeability............................................... 166
7.8.2 Replacing the Static Mixer or Capillary Mixer ........................................ 167
7.9 Solvent Lines and Solvent Line Filters ................................................................ 169
7.9.1 Emptying the Solvent Lines .................................................................... 169
7.9.2 Replacing Solvent Lines .......................................................................... 170
7.9.3 Replacing the Solvent Line Filter ............................................................ 173
7.10 Replacing the Purge Valve Knob ........................................................................ 175
7.11 Testing the Pump for Leakage (General Test).................................................... 177
7.11.1 Automatic Testing .................................................................................. 177
7.11.2 Manual Testing....................................................................................... 178
7.12 Replacing the Main Power Fuses ....................................................................... 181
7.13 Updating the Device Firmware .......................................................................... 183
7.14 Replacing the Doors ........................................................................................... 185
7.15 Transporting or Shipping the Device.................................................................. 187
7.15.1 Preparing the Device for Transport........................................................ 187
7.15.2 Transporting the Device to a New Location ........................................... 188
7.15.3 Shipping the Device................................................................................ 189
7.16 Replacing the Slide-In Module ........................................................................... 190
7.16.1 Removing the Slide-In Module ............................................................... 190
7.16.2 Returning the Slide-In Module ............................................................... 192
7.16.3 Installing the Slide-In Module ................................................................ 192
7.16.4 Setting Up the Slide-In Module .............................................................. 194

Operating Manual
Contents
8 Troubleshooting ....................................................................... 197

8.1 General Information about Troubleshooting..................................................... 198
8.2 Messages............................................................................................................ 200
8.3 Testing the Pump for Leakage............................................................................ 209
8.4 Resolving Liquid Leaks........................................................................................ 210
8.5 Pressure Issues or Shifts in Retention Time ....................................................... 211
8.5.1 Pressure Not Zero with Open Purge Valve............................................. 211
8.5.2 Checking the Compression Values ......................................................... 211
8.5.3 Testing the Static Mixer for Permeability............................................... 213
8.6 Removing Persistent Air Bubbles ....................................................................... 214
9 Pump-Specific Information ....................................................... 215

9.1 Introduction to this Chapter .............................................................................. 216
9.2 Quaternary Pump and Dual Pump ..................................................................... 217
9.2.1 Interior Components (Quaternary Pump).............................................. 218
9.2.2 Interior Components (Dual Pump) ......................................................... 219
9.2.3 Operating Principle................................................................................. 221
9.2.4 Dwell Volume of the Pump .................................................................... 222
9.2.5 Setting the Solvent Composition............................................................ 223
9.2.6 Synchronizing the Injection Time with the Pump Strokes...................... 224
9.2.7 Dual Pump Specifics ............................................................................... 225
9.3 Binary Pump....................................................................................................... 228
9.3.1 Interior Components .............................................................................. 228
9.3.3 Dwell Volume of the Pump .................................................................... 231
9.3.4 Setting the Solvent Composition............................................................ 232
9.4 Isocratic Pump ................................................................................................... 233
9.4.1 Interior Components .............................................................................. 233
10 Modifying the Pump for Specific Applications........................... 235

10.1 Gradient Delay Volume, Dwell Volume and Ripple............................................ 236
10.1.1 Available Mixing Systems ....................................................................... 237
10.1.2 Exchanging the Mixing System............................................................... 239
10.2 Normal-Phase Compatible Solvents and Additives............................................ 249

Operating Manual
Contents
11 Specifications ........................................................................... 251

11.1 Performance Specifications ............................................................................... 252
11.1.1 Quaternary Pump and Dual Pump ......................................................... 252
11.1.2 Binary Pump ........................................................................................... 254
11.1.3 Isocratic Pump........................................................................................ 256
11.2 Physical Specifications ....................................................................................... 258
12 Accessories, Consumables and Replacement Parts ................... 259

12.1 General Information .......................................................................................... 260
12.2 Ship Kit ............................................................................................................... 261
12.2.1 Binary Pump ........................................................................................... 261
12.2.2 Dual Pump .............................................................................................. 263
12.2.3 Isocratic Pump........................................................................................ 264
12.2.4 Quaternary Pump................................................................................... 265
12.3 Optional Accessories.......................................................................................... 267
12.3.1 Optional Accessories (Miscellaneous).................................................... 267
12.3.2 Optional Mixing Systems and Inline Filters ............................................ 268
12.4 Consumables and Replacement Parts................................................................ 270
12.4.1 Maintenance Kits ................................................................................... 270
12.4.2 Pump Heads and Components............................................................... 274
12.4.3 Solvents and Wash Systems ................................................................... 277
12.4.4 Mixing Systems....................................................................................... 279
12.4.5 Miscellaneous Parts ............................................................................... 279
12.4.6 Interface Cables and Power Cords ......................................................... 280
13 Appendix.................................................................................. 281
13.1 Compliance Information .................................................................................... 282
13.1.1 Declarations of Conformity .................................................................... 282
13.1.2 WEEE Compliance .................................................................................. 283
13.1.3 FCC Compliance...................................................................................... 283
13.1.4 Manual Release History.......................................................................... 284
13.2 Digital I/O ........................................................................................................... 285
Index ........................................................................................ 287

Operating Manual
1 • Using this Manual
1 Using this Manual

This chapter provides information about this manual, the conventions
used throughout the manual, and the reference documentation that is
available in addition to this manual.

Operating Manual
1.1 About this Manual

This manual describes the functional features and operating principle of
your Vanquish™ device and provides instructions for installation, set up,
start up, shut down, operation, maintenance and troubleshooting.
This manual also contains safety messages, precautionary statements,

and special notices. Follow these properly to prevent personal injury,
damage to the device, or loss of data.
Note the following:
• The device configuration may vary; therefore, not all descriptions

necessarily apply to your particular device.
• If some detail applies to only one model or variant, the model or

variant is identified by name.
• Illustrations in this manual are provided for basic understanding.

They can vary from the actual model of the device or component.
However, this does not influence the descriptions. No claims can be
derived from the illustrations in this manual.
• The pump is also referred to as device in this manual. If some detail

applies to only one pump type or model, the type or model is
identified by name.
The descriptions in this manual assume that the device is installed in the
Vanquish system stack. If this is not the case, additional hardware is
required and must be ordered separately. The information in this
manual applies correspondingly.

Operating Manual
1.2 Conventions
This section describes the conventions that are used throughout this
manual.
1.2.1 Conventions for Safety Messages

The safety messages and precautionary statements in this manual
appear as follows:
• Safety messages or precautionary statements that apply to the

entire manual and all procedures in this manual are grouped in the
Safety chapter.
• Safety messages or precautionary statements that apply to an entire

section or to multiple procedures in a section appear at the
beginning of the section to which they apply.
• Safety messages that apply to only a particular section or procedure

appear in the section or procedure to which they apply. They appear
different from the main flow of text.
Safety messages are often preceded by an alert symbol and/or alert
word. The alert word appears in uppercase letters and in bold type.
Make sure that you understand and follow all safety messages
presented in this manual.
1.2.2 Special Notices

Special notices and informational notes in this manual appear different
from the main flow of text. They appear in boxes and a note label
identifies them. The label text appears in uppercase letters and in bold
type.
NOTICE
Highlights information necessary to prevent damage to the device or
invalid test results.
TIP Highlights information of general interest or helpful information that

can make a task easier or optimize the performance of the device.

Operating Manual
1.2.3 Typographical Conventions

These typographical conventions apply to the descriptions in this
manual:
Data Input and Output

The following appears in bold type:
• Input that you enter by the keyboard or that you select with the
mouse
• Buttons that you click on the screen
• Commands that you enter by the keyboard
• Names of, for example, dialog boxes, properties, and parameters

For brevity, long expressions and paths appear in the condensed form,
for example: Click File > Save as.
References and Messages
• References to additional documentation appear italicized.
• Messages that appear on the screen are identified by quotation

marks.
Viewpoint
If not otherwise stated, the expressions left and right in this manual
always refer to the viewpoint of a person that is facing the device from
the front.
Particularly Important Words

Particularly important words in the main flow of text appear italicized.
Electronic Manual Version (PDF)

The electronic version (PDF) of the manual contains numerous links that
you can click to go to other locations within the manual. These include:
• Table of contents entries
• Index entries
• Cross-references (in blue text)

Operating Manual
1.3 Reference Documentation

In addition to this operating manual, other documentation is available
for reference.
Hardware Documentation
Additional hardware documentation includes the following:
• Operating manuals for the other modules of the Vanquish system
• Vanquish System Operating Manual
• Instrument Installation Qualification Operating Instructions
Thermo Fisher Scientific provides up-to-date operating manuals as PDF
(Portable Document Format) files that you can access from our customer
manuals web site. To open and read the PDF files, Adobe™ Reader™ or
Adobe™ Acrobat™ is required.
Go to the following web site: www.thermofisher.com/HPLCmanuals
Software Documentation
Additional software documentation includes the following:
• Chromeleon™ Help and documents

The Chromeleon Help provides extensive information and
comprehensive reference material for all aspects of the software.
In addition, the following documentation is available (availability
depends on the software version):
• Installation Guide
For basic information about device installation and configuration,
refer to the Installation Guide.
• Instrument Configuration Manager Help

For specific information about a certain device, refer to the
Instrument Configuration Manager Help. In Chromeleon 7, devices
are called modules.
• Quick Start Guide

For information about the main elements of the user interface and
step-by-step guidance through the most important workflows, refer
to the Quick Start Guide.
• Reference Card
For a concise overview of the most important workflows, refer to
the Reference Card.
TIP The Chromeleon Help and documents are included in the software
shipment.

Operating Manual
Third-Party Documentation
Refer also to the user documentation provided by the manufacturers of
third-party components and materials, for example, Safety Data Sheets
(SDSs).

Operating Manual
2 • Safety
2 Safety
This chapter provides general and specific safety information and
informs about the intended use of the device.

Operating Manual
2 • Safety
2.1 Safety Symbols and Signal Words

2.1.1 Safety Symbols and Signal Words in this Manual
This manual contains safety messages to prevent injury of the persons
using the device.
The safety symbols and signal words in this manual include the
following:
Always be aware of the safety information. Do not proceed until you

have fully understood the information and consider the consequences of
what you are doing.
CAUTION
Indicates a hazardous situation that, if not avoided, could result in minor
or moderate injury.
WARNING
Indicates a hazardous situation that, if not avoided, could result in
serious injury.
2.1.2 Observing this Manual

Observe the following:
• Before installing or operating the device, read this manual carefully

to be familiar with the device and this manual. The manual contains
important information with regard to user safety as well as use and
care of the device.
• Always keep the manual near the device for quick reference.
• Save this manual and pass it on to any subsequent user.
Read, understand, and comply with all safety messages and

precautionary statements presented in this manual.

Operating Manual
2 • Safety
2.1.3 Safety Symbols on the Device

The table lists the safety symbols that appear on the device or on labels
affixed to the device. Follow the safety notices in this manual to prevent
the risk of operator injury or damage to the device.
Symbol Description
Indicates a potential hazard. Refer to this manual to avoid the risk of

personal injury and/or to prevent damage to the device.
— Power supply is on
Ο Power supply is off
Indicates alternating current.
2.1.4 Rating Plate

The rating plate is present on the device near the electrical connections.
The rating plate indicates the serial number, part number, module
name, revision number (if any), and the line and fuse rating.
TIP An additional type label on the leak tray of the device indicates the
module name, serial number, part number, and revision number (if any).
To facilitate device identification, have the information from this label
available when communicating with Thermo Fisher Scientific.

Operating Manual
2 • Safety
2.2 Intended Use

The device is intended to be part of the Vanquish system.
The intended use of the Vanquish system is to analyze mixtures of

compounds in sample solutions.
The device is for use by qualified personnel and in laboratory

environment only.
The device and Vanquish system are intended to be used as General

Laboratory Equipment (GLE).
They are not intended for use in diagnostic procedures.
Laboratory Practice
Thermo Fisher Scientific recommends that the laboratory in which the
Vanquish system is used follow best practices for LC analyses. This
includes among others:
• Using appropriate standards
• Regularly running calibration
• Establishing shelf life limits and following them for all consumables
used with the system
• Running the system according to the laboratory's verified and

validated 'lab developed test' protocol

Operating Manual
2 • Safety
2.3 Safety Precautions

2.3.1 General Safety Information
All users must observe the general safety information presented in this
section and all specific safety messages and precautionary statements
elsewhere in this manual during all phases of installation, operation,
troubleshooting, maintenance, shutdown, and transport of the device.
If the device is used in a manner not specified by Thermo Fisher

Scientific, the protection provided by the device could be impaired.
• Operate the device only within its technical specifications.
• Use only the replacement parts and additional components, options,
and peripherals specifically authorized and qualified for the device
by Thermo Fisher Scientific.
• Perform only the procedures that are described in this operating
manual and in supporting documents for the device. Follow all
instructions step by step and use the tools recommended for the
procedure.
• Open the enclosure of the device and other components only if
specifically instructed to do so in this manual.
• Thermo Fisher Scientific cannot be held liable for any damage,
material or otherwise, resulting from inappropriate or improper use
of the device. If there is any question regarding appropriate usage,
contact Thermo Fisher Scientific before proceeding.
Safety Standard
This device is a Safety Class I instrument (provided with terminal for
protective grounding). The device has been manufactured and tested
according to international safety standards.

Operating Manual
2 • Safety
2.3.2 Qualification of the Personnel

Observe the information below on the proper qualification of the
personnel installing and/or operating the device.
Installation
Only skilled personnel are permitted to install the device and to

establish the electrical connections according to the appropriate
regulations.
• Thermo Fisher Scientific recommends always having service
personnel certified by Thermo Fisher Scientific perform the
installation (for brevity, referred to as Thermo Fisher Scientific
service engineer).
• If a person other than a Thermo Fisher Scientific service engineer
installs and sets up the module, the installer is responsible for
ensuring the safety of the module and system.
General Operation
The device is designed to be operated only by trained and qualified

personnel in a laboratory environment.
All users must know the hazards presented by the device and the
substances they are using. All users should observe the related Safety
Data Sheets (SDSs).
2.3.3 Personal Protective Equipment

Wear personal protective equipment and follow good laboratory
practice to protect you from hazardous substances. The appropriate
equipment depends on the hazard. For advice on the hazards and the
equipment required for the substances you are using, refer to the
material handling and safety data sheet provided by the vendor.
An eyewash facility and a sink should be available nearby. If any

substance contacts your skin or eyes, wash the affected area and seek
medical attention.
Protective Clothing
To protect you from chemical splashes, harmful liquids, or other
contamination, put on appropriate protective clothing, such as a lab
coat.

Operating Manual
2 • Safety
Protective Eyewear
To prevent liquids from striking your eyes, put on appropriate protective
eyewear, such as safety glasses with side shields. If there is a risk of
splashing liquids, put on goggles.
Gloves
To protect you from harmful liquids and avoid personal injury during
maintenance or service, put on appropriate protective gloves.
2.3.4 Electrical Safety Precautions
WARNING—Electric Shock or Damage to the Device

High voltages are present inside the device that could cause an electric
shock or damage to the device.
• Do not make any changes to the electrical or grounding connections.
• If you suspect any kind of electrical damage, disconnect the power
cord and contact Thermo Fisher Scientific Technical Support for
assistance.
• Do not open the housing or remove protective panels unless
specifically instructed to do so in this manual.
• Do not place liquid reservoirs directly upon the device. Liquid might
leak into the device and get into contact with electronic components
causing a short circuit. Instead, place liquid reservoirs in the solvent
rack that is available for the Vanquish system.

Operating Manual
2 • Safety
2.3.5 General Residual Hazards

Pay attention to the following general residual hazards when working
with the device:
WARNING—Hazardous Substances
Solvents, mobile phases, samples, and reagents might contain toxic,
carcinogenic, mutagenic, infectious, or otherwise harmful substances.
The handling of these substances can pose health and safety risks.
• Be sure that you know the properties of all substances that you are
using. Avoid exposure to harmful substances. If you have any doubt
about a substance, handle the substance as if it is potentially
harmful.
• Wear personal protective equipment as required by the hazard and
follow good laboratory practice.
• Reduce the volume of substances to the minimum volume required
for sample analysis.
• Avoid handling of solvent reservoirs above head height.
• Do not operate the device in a potentially flammable environment.
• Avoid accumulation of harmful substances. Make sure that the
installation site is well ventilated.
• Dispose of hazardous waste in an environmentally safe manner that
is consistent with local regulations. Follow a regulated, approved
waste disposal program.
WARNING—Biohazard
Biohazardous material, for example microorganisms, cell cultures,
tissues, body fluids, and other biological agents can transmit infectious
diseases. To avoid infections with these agents:
• Assume that all biological substances are at least potentially
infectious.
• Wear personal protective equipment as required by the hazard and
follow good laboratory practice.
• Dispose of biohazardous waste in an environmentally safe manner
that is consistent with local regulations. Follow a regulated,
approved waste disposal program.

Operating Manual
2 • Safety
WARNING—Self-Ignition of Solvents
Solvents with a self-ignition temperature below 150 °C might ignite
when in contact with a hot surface (for example, due to leakage in the
chromatography system).
Avoid the use of these solvents.
WARNING—Hazardous Vapors
Mobile phases and samples might contain volatile or flammable
solvents. The handling of these substances can pose health and safety
risks.
• Avoid accumulation of these substances. Make sure that the
installation site is well ventilated.
• Avoid open flames and sparks.
• Do not operate the device in the presence of flammable gases or
fumes.
CAUTION—Allergic Reaction
Some capillaries in the system are made of MP35N™, a nickel/cobalt-
based alloy. Individuals with sensitivity to nickel/cobalt may show an
allergic reaction from skin contact.
CAUTION—Sparking due to Electrostatic Discharge

Liquid flowing through capillaries can generate static electricity. This
effect is particularly present with insulating capillaries and non-
conductive solvents (for example, pure acetonitrile). Discharge of
electrostatic energy might lead to sparking, which could constitute a fire
hazard.
Prevent the generation of static electricity near the chromatography
system.
2.3.6 In Case of Emergency
WARNING—Safety Hazard
In case of emergency, disconnect the device from the power line.

Operating Manual
2 • Safety
2.4 Solvent and Additive Information

2.4.1 General Compatibility
To protect optimal functionality of the Vanquish system, observe these
recommendations on the use of solvents and additives:
• The system must be used with reversed-phase (RP) compatible

solvents and additives only.
• Use only solvents and additives that are compatible with all parts in
the flow path.
• Anhydrous methanol may lead to stress failures in titanium surfaces,

especially when formic acid or TFA is added to the mixture. Thermo
Fisher Scientific recommends adding 3% of water to prevent this.
TIP In a Vanquish Core system, normal-phase (NP) compatible solvents

and additives may be used if the system modules have been modified
for NP applications. Refer to the Vanquish System Operating Manual.
2.4.2 Piston Seal Compatibility

The table provides information about the piston seals used in the pumps
and their solvent compatibility.
Pump Piston Seals
VC‑pumps except The pumps are shipped with UHMW-PE piston seals. Using
VC‑P21 and VC‑P33 tetrahydrofuran, ketones, or ammonium hydroxide as
solvents can damage the seals.
In rare cases, a shortened lifetime of reversed-phase
(UHMW-PE) piston seals has been observed with high pH,
ammonium hydroxide containing mobile phases and
prolonged exposure.
Under harsh conditions, consider replacing the UHMW-PE
piston seals with carbon-fiber filled PTFE piston seals.
Consider the following:
• With the piston seals, also replace the seal wash seals
(part no. 6040.0306, containing 2 seals for use as both,
piston seal and seal wash seal).
• Install new pistons. Exchanging the piston seals but
keeping the pistons that were used with the UHMW-PE
piston seals may impair the seal life of the PTFE seals.
• Note that slightly increased abrasion may be observed
with these seals, depending on the application. Consider
testing the permeability of the static mixer regularly at
short intervals.

Operating Manual
2 • Safety
Pump Piston Seals
VC‑P21 and VC‑P33 The pumps are shipped with carbon-fiber filled PTFE piston
pumps seals. Slightly increased abrasion may be observed with
these seals, depending on the application. Consider testing
the permeability of the static mixer regularly at short
intervals.
VF‑pumps The pumps are shipped with UHMW-PE piston seals. Using
tetrahydrofuran, ketones, or ammonium hydroxide as
solvents can damage the seals.
In rare cases, a shortened lifetime of reversed-phase
(UHMW-PE) piston seals has been observed with high pH,
ammonium hydroxide containing mobile phases and
prolonged exposure.
Under harsh conditions, consider replacing the UHMW-PE
piston seals with carbon-fiber filled PTFE piston seals.
Consider the following:
• With the piston seals, also replace the seal wash seals
(part no. 6040.0306, containing 2 seals for use as both,
piston seal and seal wash seal).
• Install new pistons. Exchanging the piston seals but
keeping the pistons that were used with the UHMW-PE
piston seals may impair the seal life of the PTFE seals.
• In addition, note the following:
¨ Slightly increased abrasion may be observed with the
PTFE seals, depending on the application. Consider
testing the permeability of the static mixer regularly at
short intervals.
¨ The pump should not be operated with pressures
higher than 70 MPa.
¨ The pump is no longer biocompatible.
2.4.3 Allowed pH Ranges

Allowed pH ranges (standard system configuration):
System Allowed Remarks

(Standard pH ranges
Configuration)
Vanquish Core 1-13 • pH value of 2 (Vanquish Horizon/Flex): Short-term

use only. The application time should be as short
Vanquish 2-12
as possible. Flush the system thoroughly after
Horizon
these applications.
Vanquish Flex
• pH value of 1-2 (Vanquish Core): The application
time should be as short as possible. Flush the
system thoroughly after these applications.
• pH values higher than 9.5 with optical detectors:
Avoid using mobile phases with a pH value higher
than 9.5 together with optical detectors. This can
impair the functionality and optical performance
of the detector flow cell.

Operating Manual
2 • Safety
2.4.4 Allowed Concentrations

Allowed concentrations (standard system configuration):
System Chloride Buffer Remarks

(Standard
Configuration)
Vanquish Core 0.1 mol/L 1 mol/L or High chloride concentration: The

or less less application time should be as
short as possible. Flush the
Vanquish Horizon 1 mol/L or -
system thoroughly after these
Vanquish Flex less
applications.
2.4.5 Further Information

• For details about the materials that are used in the analytical flow
path of the device, see the Specifications chapter in this manual. For
information about the materials that are used in the flow path of the
other modules in the Vanquish system, refer to the Specifications
chapter in the Operating Manual for the modules.
• Observe the general guidelines and recommendations on the use of

solvents and additives in the chromatography system (see Use of
Solvents and Additives (} page 90)).
• Refer also to the Operating Manuals for all modules in the Vanquish
system. They may provide additional guidelines and information.
NOTICE
If the system configuration includes a non-standard detector, for
example, a charged aerosol detector or refractive index detector, refer
to the Operating Manual for the detector for specific recommendations
regarding solvents and additives.

Operating Manual
2 • Safety
2.5 Compliance Information

Thermo Fisher Scientific performs complete testing and evaluation of its
products to ensure full compliance with applicable domestic and
international regulations. When the device is delivered to you, it meets
all pertinent electromagnetic compatibility (EMC) and safety standards
as described in this manual.
Changes that you make to the device may void compliance with one or
more of these EMC and safety standards. Changes to the device include
replacing a part or adding components, options, or peripherals not
specifically authorized and qualified for the product by Thermo Fisher
Scientific. To ensure continued compliance with EMC and safety
standards, replacement parts and additional components, options, and
peripherals must be ordered from Thermo Fisher Scientific or one of its
authorized representatives.
The device has been shipped from the manufacturing site in a safe
condition.
See also
2 Compliance Information (} page 282)

Operating Manual
2 • Safety

Operating Manual
3 • Device Overview
3 Device Overview
This chapter introduces you to the device and the main components.

Operating Manual
3.1 Pump Features

The pump comprises the following features:
Main Features
• Serial dual-piston pump with electronic compressibility

compensation (SmartFlow™) for precise and virtually pulse-free flow
• Floating piston design for compensation of small mechanical

tolerances within the specification and thus enhanced robustness of
the pump
• Active piston seal wash system for high lifetime of pistons and piston
seals
The piston seal wash system keeps the pistons wet and rinses the
piston seals automatically. This prevents crystallization and particle
deposits on the piston surfaces and seals, which may damage the
components.
• Built-in vacuum degasser for enhanced flow stability and best

detector sensitivity (all pumps except isocratic pump)
• Mixing system with capillary mixer and static mixer for smoother
baselines
With the isocratic pump, the mixing system serves as inline filter.
• Easy access to the user-serviceable components
• Easy maintenance because the pump remains in the Vanquish

system stack
For specifications, see Performance Specifications (} page 252).
Special Pump Features
• Binary pump
Solvent selector "2 from 6" for increased flexibility
• Dual pump
The dual pump combines two ternary pumps in a single enclosure.

Operating Manual
3.2 Operating Principle

General Information
The pump is a serial dual-piston pump with electronic compressibility
compensation for precise and virtually pulse-free flow.
The pump head comprises a working cylinder and an equilibration

cylinder that are connected in series. Thus, the solvent passes both
cylinders successively. To achieve continuous delivery, the working
cylinder delivers while the equilibration cylinder is filled simultaneously.
The equilibration cylinder serves as the reservoir and delivers while the
working cylinder performs the intake stroke.
When delivering compressible liquids without controlled pre-

compression, pulsation increases along with the increasing working
pressure because part of the delivery stroke is required for compressing
the liquid in the working cylinder. Pulsation during the pre-compression
phase is reduced to a minimum by velocity modulation of the drive.
Highly constant delivery is ensured by a patented secondary control
system (automatic compressibility compensation). Independent of the
operating pressure, the flow rate of the solvent (after expansion to
atmospheric pressure) is always kept constant.
Pump-Specific Information
• Pumps with vacuum degasser

The vacuum degasser enhances the flow stability and allows best
detector sensitivity by continuously removing dissolved gasses that
may be trapped in the solvents.
• Pumps with mixing system

The mixing system ensures smoother baselines by combining and
premixing the solvent streams in the capillary mixer and improving
the mixing quality further in the static mixer.
• For pump-specific pictures that illustrate how the pump operates,

see Pump-Specific Information (} page 215).

Operating Manual
3.3 Interior Components

The user-accessible components of the pump are located directly behind
the front doors.
For pump-specific pictures that provide an overview of the interior

components, see Pump-Specific Information (} page 215).

Operating Manual
3.4 Piston Seal Wash System

To keep the pistons wet and rinse the piston seals, the pump has an
active piston seal wash system (seal wash system). Piston seal washing
prolongs the lifetime of the pistons and seals by preventing
crystallization and particle deposits on the piston surfaces and seals,
which may otherwise damage the pistons and seals.
The picture shows the flow path through the seal wash system.
Figure 1: Flow path through the seal wash system (left: isocratic pump,
quaternary pump; right: binary pump, dual pump)
No. Description
1 Seal wash line from autosampler

2 Seal wash pump (peristaltic pump)
3 Peristaltic tubing (PharMed™ tubing)
4 Pump heads
5 Seal wash detector (drop detector)
6 To waste

Operating Manual
3.5 Purge/Sensor Unit

The purge/sensor unit comprises the purge valve and the system
pressure sensor.
Figure 2: Purge/sensor unit (example, here in binary pump)
No. Description
1a Isocratic pump, dual pump, quaternary pump: Capillary from the pump head
Binary pump: Capillary from the right pump head
1b Binary pump only: Capillary from the left pump head
2 System pressure sensor
3 Capillary mixer
4 Purge outlet
5 Purge valve knob
Binary Pump
With the binary pump, the purge/sensor unit also combines the solvent
streams from the pump heads.

Operating Manual
3.6 Mixing System

The pump is shipped with a mixing system, comprising the following
mixers:
• Capillary mixer
In the capillary mixer, the solvent streams delivered by the pump are
combined and premixed.
• Static mixer
The static mixer improves the mixing quality.
Mixing with capillary mixer and static mixer results in smoother
baselines.
The pump is shipped with the following mixing system:
Pump Mixing System
Binary VC-pump Mixing system, volume 400 µL, comprising:

Quaternary pump • Capillary mixer, volume: 50 µL
Dual pump • Static mixer, volume: 350 µL
The dual pump has two mixing systems.
Binary VF-pump Mixing system, volume 200 µL, comprising:
Isocratic pump • Capillary mixer, volume: 50 µL
• Static mixer, volume: 150 µL
With the isocratic pump, the mixing system serves as
inline filter.
For pump-specific pictures, see the Interior Components sections in Pump-Specific
Information (} page 215).
TIP Mixing systems with other volumes are available as an option (see
Gradient Delay Volume, Dwell Volume and Ripple (} page 236)).

Operating Manual
3.7 Leak Detection

Leaks are a potential safety issue.
The leak sensor inside the device monitors the device for liquid leaks
from the flow connections. The liquid is collected in the leak tray and
guided to the drain port. From the drain port, the liquid is discharged to
waste through the drain system of the Vanquish system.
When the leak sensor detects leakage, the status indicators change to
red and beeping starts to alert you. Follow the instructions in this
manual to find and eliminate the source for the leakage.
If leakage is not resolved after 3 minutes, the pump stops the flow.

Operating Manual
3.8 Operation
The device is designed to be operated from a computer configured with
the Chromeleon Chromatography Data System (CDS). The Chromeleon
software provides complete instrument control, data acquisition, and
data management.
For a basic description of instrument control and automated sample

analysis with the Chromeleon software, refer to the Vanquish System
Operating Manual. Details on control and operation of the device are
available in the Chromeleon Help.
TIP The device can be operated also with other data systems, such as
Thermo ScientificTM XcaliburTM. In this case, installation of additional
software is required in addition to the data system software. For details,
contact the Thermo Fisher Scientific sales organization.
A keypad is available inside the device, allowing you to perform certain

basic functions directly from the device.

Operating Manual

Operating Manual
4 • Unpacking
4 Unpacking
This chapter provides information for unpacking the device and informs
you about the scope of delivery.

Operating Manual
4 • Unpacking
4.1 Unpacking
Damaged Packaging, Defective on Arrival
Inspect the shipping container for signs of external damage and, after
unpacking, inspect the device for any signs of mechanical damage that
might have occurred during shipment.
If you suspect that the device may have been damaged during shipment,
immediately notify the incoming carrier and Thermo Fisher Scientific
about the damage. Shipping insurance will compensate for the damage
only if reported immediately.
Unpacking the Device
CAUTION—Heavy Load, Bulky Device

The device is too heavy or bulky for one person alone to handle safely.
To avoid personal injury or damage to the device, observe the following
guidelines:
• Physical handling of the device, including lifting or moving, requires
a team effort of two persons.
• A team effort is in particular required when lifting the device into
the system stack or when removing it.
• Use the carrying handles that were shipped with the device to move
or transport the device. Never move or lift the device by the front
doors. This will damage the doors or the device.
Tools required
Screwdriver, TorxTM T20
Follow these steps
1. Place the shipping container on the floor and open it.
2. Remove the ship kit from the shipping container.
3. Remove the device from the shipping container: Grasp the device by
the carrying handles. Slowly and carefully, lift the device out of the
shipping container.

Operating Manual
4 • Unpacking
Figure 3: Carrying handles on the device
No. Component
1 Carrying handles
2 Attachment screw (one on each carrying handle)
4. Place the device on a stable surface.
5. If applicable:
Remove any additional packing material. Leave any protective films
attached to the surfaces of the device until it is properly positioned
in the system stack.
6. Transport the device by the carrying handles to the installation site,

if it is not already there, and place it in the system stack (see System
Arrangement (} page 52)).
7. On each carrying handle, loosen the attachment screw until the

carrying handle is moveable in the rail. Do not remove the screws
from the carrying handles completely.
8. Slide off the carrying handles from the rails towards the rear of the
device.
Figure 4: Sliding off the carrying handle from the left rail
TIP Keep the shipping container, the carrying handles with the
attachment screws, and all packing material. These items will be needed
if the device is transported to a new location or shipped.
9. Some surfaces including the doors of the device are covered by a

protective film during shipment. Remove the protective film from all
surfaces as applicable.

Operating Manual
4 • Unpacking
4.2 Scope of Delivery

The following items are included in the delivery:
• Pump
• Ship Kit
• Operating manual (downloadable from customer manual web site)
• Power cord
For information on contents of the ship kit or reordering parts, see
Accessories, Consumables and Replacement Parts (} page 259).

Operating Manual
5 • Installation
5 Installation
This chapter specifies the requirements for the installation site and
describes how to set up, install, and configure the device in the Vanquish
system and in the chromatography software.

Operating Manual
5 • Installation
5.1 Safety Guidelines for Installation

Pay attention to the following safety guidelines:
Observe all warning messages and precautionary statements presented

in Safety Precautions (} page 21).

guidelines:
CAUTION—Electric Shock or Damage to the Device

After the power to the device is turned off, the device is still energized
as long as the power cord is connected. Repair work on the device while
the device is connected to power could lead to personal injury.
• Always unplug the power cord before starting repair work inside the
device.
• If you were instructed to remove any housing covers or panels, do
not connect the power cord to the device while the cover or panels
are removed.

Operating Manual
5 • Installation
5.2 Installing the Device

A Thermo Fisher Scientific service engineer installs and sets up the
Vanquish system, including all modules and options or parts shipped
with them. The service engineer checks that the installation is correct
and that the Vanquish system and modules operate as specified. The
engineer also demonstrates the basic operation and main features.
If personnel other than a Thermo Fisher Scientific service engineer

installs the device, follow the steps below.
NOTICE
The device is part of the Vanquish system. Therefore, follow the order
for installing the system modules as described in the Vanquish System
Operating Manual.
1. Pay attention to the safety guidelines and observe all site

requirements. See Safety Guidelines for Installation (} page 46) and
Site Requirements (} page 49).
2. Set up the device hardware. See Setting Up the Hardware

(} page 52).
3. Set up the flow connections. See Setting Up the Flow Connections

(} page 55).
4. Turn on the device. See Turning On the Device (} page 79).
TIP
Before turning on the power to a Vanquish system module for the first
time, verify that the chromatography software is installed on the data
system computer. When the power is turned on, the required USB
drivers are automatically found and the Windows™ operating system
can detect the device.
5. Set up the device in the software. See Setting Up the Device in the
Software (} page 80).
6. Recommended:
Perform Instrument Installation Qualification.
In the Chromeleon software, a wizard is available to guide you
through the qualification process. On the Chromeleon 7 Console:
Click Tools > Instrument Qualification > Installation Qualification.
Follow the instructions in the Instruments Installation Qualification
Operating Instructions. The manual provides information about the
required materials and detailed instructions.

Operating Manual
5 • Installation
NOTICE
If the device is operated with another data system, refer to the
documentation for the software that you are using and/or perform the
qualification manually. The Instruments Installation Qualification
Operating Instructions provide information about the parameters to be
adapted and the required settings.
7. Recommended: Perform Operational Qualification.

The qualification kit includes all materials required for the
qualification and detailed instructions.
Moving the Device after Installation

If you have to move the device after it has been set up and installed in
the Vanquish system, prepare the device for transport and move it to
the new location. Follow the instructions in Transporting or Shipping the
Device (} page 187).

Operating Manual
5 • Installation
5.3 Site Requirements

The operating environment is important to ensure optimal performance
of the device.
This section provides important requirements for the installation site.

Note the following:
• Operate the device only under appropriate laboratory conditions.
• The device is intended to be part of the Vanquish system. Observe

the site requirements for the Vanquish system as stated in the
Vanquish System Operating Manual.
• For specifications, see Specifications (} page 251) and the

Specifications sections in the Operating Manuals for the other
modules in the Vanquish system.
• For general residual hazards, see General Residual Hazards

(} page 24).
5.3.1 Power Considerations

The power supply of the device has wide-ranging capability, accepting
any line voltage in the range specified for the device.

Connecting the device to a line voltage higher or lower than specified
could result in personal injury or damage to the device.
Connect the device to the specified line voltage only.

Operating Manual
5 • Installation
5.3.2 Power Cord

The power cords are designed to match the wall socket requirements of
the country in which they are used. The end of the power cords that
plugs into the power socket on the device is identical for all power cords.
The end of the power cords that plugs into the wall socket is different.
WARNING—Electric Shock or Damage to the Device

• Never use a power cord other than the power cords provided by
Thermo Fisher Scientific for the device.
• Only use a power cord that is designed for the country in which you
use the device.
• Do not use extension cords.
• Never plug the power cord to a power socket that is shared with
other equipment (for example, multiple sockets).
• Operate the device only from a power outlet that has a protective
ground connection.
• In case of emergency, it must be possible to reach the power cord
easily at any time to disconnect the device from the power line.
WARNING—Electric Shock or Damage to a Product

Misuse of the power cords could cause personal injury or damage the
instrument. Use the power cords provided by Thermo Fisher Scientific
only for the purpose for which they are intended. Do not use them for
any other purpose, for example, for connecting other instruments.
5.3.3 Condensation
NOTICE—Condensation in the device can damage the electronics.

• When using, shipping, or storing the device, avoid or minimize
conditions that can lead to a build-up of condensation in the device.
For example, avoid significant or fast changes in environmental
conditions.
• If you suspect that condensation is present, allow the device to
warm up to room temperature. This may take several hours. Wait
until the condensation is gone completely before connecting the
device to the power line.

Operating Manual
5 • Installation
5.4 Accessing the Interior Components

To access the interior components in the device, open the front doors.
To allow easy access from the front, the user-accessible components and
flow connections in the device are located directly behind the doors.
Figure 5: Opening the front doors

Operating Manual
5 • Installation
5.5 Setting Up the Hardware

This section describes how to set up the hardware and provides
information about the device connectors and cables.
5.5.1 System Arrangement

The device is part of the Vanquish system. The system modules are
typically arranged in a system stack, with the arrangement depending on
the system configuration.
Figure 6: Vanquish system, standard configuration (example)
No. Description
1 Solvent Rack
2 Detector
3 Autosampler
4 Pump
5 System Base
6 Column Compartment
For instructions on how to set up the system stack, refer to the Vanquish
System Operating Manual.

Operating Manual
5 • Installation
5.5.2 Connecting the Device

Device Connectors
The following connectors are provided on the device:
Figure 7: Electrical connectors and device connectors on the pump
No. Description
1 Rating plate (example), indicating the serial number, part number, module
name, revision number (if any), and the line and fuse rating
2 Main power switch (on/off control)
3 Fuse holder
4 Power-inlet connector
5 System Interlink port
Allows power on/off control for the device from the Vanquish system base
and device communication
6 Digital I/O ports (Dig I/O)
Allow exchange of digital signals with external instruments
Each digital I/O port provides one input, one relay output, and one
bidirectional input/output. For connection and pin assignment information,
see Digital I/O (} page 285).
7 USB hub ("A" type connector)
Allows connection to other modules in the Vanquish system
8 USB (Universal Serial Bus) port ("B" type connector)
Allows connection to other modules in the Vanquish system or the
computer on which the data management system is installed, such as the
Chromeleon software
TIP Thermo Fisher Scientific recommends using the USB ports only as
described above. If the USB ports are used for any other purpose,
Thermo Fisher Scientific cannot ensure proper functionality.

Operating Manual
5 • Installation
Follow these steps
NOTICE
• Never use defective communication cables. If you suspect that a
cable is defective, replace the cable.
• To ensure trouble-free operation, use only the cables provided by
Thermo Fisher Scientific for connecting the device.
1. Place the device in the system as required by the system

configuration. For details, refer to the Vanquish System Operating
Manual.
2. Connect the required interface cables to the device. For information

about how to connect the device to other modules in the Vanquish
system or to the chromatography data system computer, refer to
the Vanquish System Operating Manual.
3. Connect the power cord (see Connecting the Power Cord

(} page 54)).
5.5.3 Connecting the Power Cord
NOTICE
Condensation in a device can damage the electronics.
• Before connecting the devices to the power line, be sure that no
condensation is present in the devices.
• If you suspect that condensation is present, allow the device to
warm up to room temperature slowly. Wait until the condensation is
completely gone before proceeding.
1. Verify that the power switch on the device is set to OFF.
2. Connect the power cord to the power inlet connector on the device.
3. Connect the free end of the power cord to an appropriate power

source.

Operating Manual
5 • Installation
5.6 Setting Up the Flow Connections

This section describes how to set up the flow connections to and from
the device and additional flow connections, if required.
5.6.1 General Information and Guidelines

The pump is shipped from the manufacturing site with the flow
connections installed between the interior components.
When setting up flow connections, follow these rules and

recommendations:
Flow connections can be filled with hazardous substances. Observe the

warning messages and precautionary statements presented in Safety
Precautions (} page 21).
• Dirty components can contaminate the chromatography system.

Contamination leads to poor performance of the modules and entire
system or can even cause damage to the modules and system.
Therefore:
¨ Always wear appropriate gloves.
¨ Place the components only on a clean, lint-free surface.
¨ Keep your tools clean.
¨ Use only lint-free cloth for cleaning.
• For installation instructions and guidelines and for handling

recommendations, see Connecting Fittings, Capillaries, and Tubing
(} page 57).
NOTICE
When you install devices or components to the system, always flush
them to waste before connecting them in the system flow path. To flush
the Vanquish modules, follow the instructions in the Vanquish System
Operating Manual.
TIP Components or connections in the flow path to other system

modules may be closed with plugs to protect the component or
connection during transport.
When you remove the plugs to connect the device in the system, keep
the plugs. You may need them to close the connections again, for
example, for future transport.

Operating Manual
5 • Installation
Follow these steps

To set up the additional flow connections and complete the installation,
follow these steps:
1. Connect the pump to the drain system (see Guiding Liquids to Waste
(} page 62)).
2. Connect the solvent lines (see Connecting the Solvent Lines

(} page 63)).
3. Set up the seal wash system (see Seal Wash System (} page 69)).
4. Connect the pump to the autosampler (see Connecting the Pump

and Autosampler (} page 78)).
5.6.2 Guiding Capillaries and Tubing Through the System

Flow connections between the modules of the Vanquish system are
guided through either the tubing chase in the devices or the guide holes
or capillary clips of the devices.
Tubing Chase with Tubing Guides

To guide certain tubes and lines from the top module to the bottom
module in the Vanquish system stack, the stackable modules have a
tubing chase on the inside right. The tubing chase provides four tubing
guides.
Each guide can hold up to three tubes or lines. In each module, push the
tube (or line) into the appropriate guide.
Figure 8: Tubing chase with tubing guides (left: view from inside, right:
view from top)
No. Use for
1 Solvent tubing (up to three solvent lines)

2 Solvent tubing (up to three solvent lines)
3 Wash liquid tubing (seal wash, autosampler needle wash)
4 Detector waste line

Operating Manual
5 • Installation
Tubing Brackets
Tubing brackets are available for holding the tubing in place. Slip the
bracket side onto the drain pipe.
Figure 9: Tubing bracket (left), tubing bracket installed (right)
Dual System Arrangements

The number of tubes may exceed the capacity that the tubing guides can
hold. In this case, it is recommended to place the solvent lines in the
tubing guides and route any additional tubes freely in the tubing chase.
Guide Holes and Capillary Clips

Guide holes and capillary clips are provided at specific positions on the
system modules. Route flow connections from one module to the next
module in the Vanquish system through the appropriate guide hole or
capillary clip when instructed to do so in the manual.
5.6.3 Connecting Fittings, Capillaries, and Tubing

This section provides information about how to connect and handle
capillaries, fittings, and tubing.
5.6.3.1 General Guidelines

When connecting capillaries and tubing, follow these general
recommendations:
• Use only the capillaries and tubing (for example, solvent lines or
waste tubing) that are shipped with the product or additional or
spare capillaries and tubing as recommended by Thermo Fisher
Scientific.
• The connectors must be free from contaminants. Even minute

particles may cause damage to the system or lead to invalid test
results.

Operating Manual
5 • Installation
• Do not install capillaries or tubes that are stressed, nicked, kinked, or

otherwise damaged.
• Install capillaries and fittings only at the positions for which they are
intended.
• Follow the connecting instructions as required by the fitting

connection:
¨ For Viper connections, see Connecting Viper Capillaries
(} page 58).
¨ For capillaries with conventional fitting connections (non-Viper),
see Connecting Non-Viper Capillaries (} page 61).
5.6.3.2 Connecting Viper Capillaries

This section describes how to connect Viper™ capillaries. The following
Viper fittings are available:
• Viper fitting with torque toothing
• Viper fitting with knurl
Figure 10: Viper fittings (examples)
No. Description
1 Viper fitting, torque toothing

2 Viper fitting, knurl
When tightening or loosening a Viper capillary, observe the handling

instructions for the respective fitting.

Operating Manual
5 • Installation
Connecting Viper Fittings with Torque Toothing

To connect Viper fittings with torque toothing, follow these steps:
NOTICE
• Tighten or loosen Viper capillaries only with your fingers and the
special torque tool. Do not use tools others than those provided by
Thermo Fisher Scientific for this purpose. Use the tool only for the
connections for which it is intended.
• To avoid damage to the capillary or connection, tighten and loosen
the Viper capillaries only when the system pressure is down to zero.
• Mind the correct orientation of the tool when tightening or
loosening connections (see pictures).
Figure 11: Viper fitting with torque toothing
No. Description
1 Capillary
2 Torque toothing
1. Insert the Viper capillary into the connection port.
2. Tighten the connection with your fingers.
3. Use the installation tool to tighten the connection further.
Figure 12: Tool on torque toothing for tightening connections
4. Tighten the connection until the torque limitation has been reached,
which is indicated by a clicking sound.
5. Check whether the connection leaks. If leakage exists, follow the

steps further down.

Operating Manual
5 • Installation
Resolving Leakage with Viper Fittings with Torque Toothing
1. Remove the capillary.
2. Clean the capillary ends carefully by using a lint-free tissue wetted

with isopropanol.
3. Reinstall the capillary.
4. If the connection continues to leak, install a new Viper capillary.

To loosen a connection, use this side of the installation tool.
Figure 13: Tool on torque toothing for loosening connections
Connecting Viper Fittings with Knurls

To connect Viper capillaries with knurls, follow these steps:
NOTICE
• Tighten or loosen Viper capillaries only with your fingers. Do not use
tools other than the knurl that comes with the capillary.
• To avoid damage to the capillary or connection, tighten and loosen
the Viper capillaries only when the system pressure is down to zero.
Figure 14: Viper fitting with knurl
No. Description
1 Knurl
2 Capillary
3 Slot

Operating Manual
5 • Installation
1. Insert the Viper capillary into the connection port.

2. Tighten the connection by the knurl.
TIP Note the slot in the knurl. You can easily remove the knurl from the
capillaries through this slot if space is limited.

steps further down.
Resolving Leakage of Viper Fittings with Knurls
1. Tighten the connection a little more.
2. If leakage continues, remove the capillary.
3. Clean the capillary ends carefully by using a lint-free tissue wetted
with isopropanol.
5. If the connection continues to leak, install a new Viper capillary.
5.6.3.3 Connecting Non-Viper Capillaries

To connect capillaries with conventional fitting connections (using
ferrules) (non-Viper), follow these steps:
1. Insert the capillary into the connection port.
2. Tighten the connection with a wrench (wrench size: 1/4").
NOTICE
Overtightening may damage the connection (both, the ferrule and the
connection port). With a torque wrench, the torque should not exceed
3 Nm (for steel capillaries).

steps further down.
Resolving Leakage with Conventional Fitting Connections
1. Remove the capillary.
2. Clean the connection port with a cleaning swab.
4. If the connection continues to leak, install a new capillary.
NOTICE
To avoid increased dead volume, leakage, or damage to the system,
reuse fittings and ferrules only for the same capillary connection.

Operating Manual
5 • Installation
5.6.4 Guiding Liquids to Waste

The following liquids collect in the leak tray and flow off through the
drain port at the bottom right of the leak tray into the drain system of
the Vanquish system:
• Leaking liquid from the leak tray
• Waste liquid from the purge unit: When purging the pump, attach
silicone tubing to the purge outlet on the purge/sensor unit and
guide the free end of the tubing to the drain port outlet.
Figure 15: Drain port (view from top)
No. Description
1 Waste line from purge unit: routing path to drain port outlet (example)
2 Drain port
3 Drain port outlet (to Vanquish drain system)
4 Leak sensor
For information about how the liquid is discharged to waste through the
Vanquish drain system, refer to the Vanquish System Operating Manual.

Operating Manual
5 • Installation
5.6.5 Connecting the Solvent Lines

The pump is shipped from the manufacturing site with the solvent lines
installed between the components in the pump. To complete the setup,
install the solvent lines between the pump inlet ports and the solvent
reservoirs.
The flow path determines the pump inlet (component at which the
solvent enters the pump) and the solvent flow through the pump.
Pump Type Pump Inlet
Binary pump The pump inlets are the solvent selectors.

Isocratic pump The pump inlet is the pump head.
Quaternary pump, The pump inlet is the vacuum degasser.
dual pump
For the pump-specific operating principles that illustrate the solvent

flow through the pump, see Pump-Specific Information (} page 215).
Parts and tools required
• Solvent reservoir assemblies, including reservoir, reservoir cap, cap

plugs, and retaining guide for the solvent line
• Solvent lines
• Solvent line filters

Optional to shut off the solvent flow through the system at the solvent
reservoir
• Shut-off valve, kit containing one shut-off valve and fitting

connections
• Tubing cutter
Preparations
1. Assemble the solvent line filter.
2. Rinse the solvent reservoirs thoroughly. Use a high-purity solvent for

rinsing.
3. On the pump inlet, remove the plug that protects the inlet during
shipment, if applicable.
4. For easier access to the lower degas chambers, remove the seal
wash detector assembly (funnel and detector).

Operating Manual
5 • Installation
Assembling the Solvent Line Filter
Figure 16: Solvent line filter
No. Description
1 Solvent line filter, filter holder bottom part

2 Filter frit
3 Solvent line filter, filter holder top part
1. Assemble the solvent line filter, wearing appropriate clean gloves:

a) Place the frit in a level position in the filter holder (bottom part).
b) Screw the filter top to the filter bottom.
Removing the Seal Wash Detector Assembly
Grasp and pull the seal wash detector assembly (funnel and detector)
upward by the funnel. The detector including the tubing and cable can
remain connected to the funnel.
Figure 17: Removing the seal wash detector assembly
No. Description
1 Funnel, seal wash detector

2 Seal wash detector
3 Detector cable
4 Seal wash line

Operating Manual
5 • Installation
Connecting the Solvent Lines

Connecting the solvent lines comprises the following steps:
1. Routing the solvent lines to the solvent rack
2. Connecting the solvent lines to the solvent reservoirs
3. Optional: Installing shut-off valves in the solvent lines
TIP To avoid the formation of air bubbles in liquid lines, always place
reservoirs in the solvent rack on top of the system stack.
Routing the Solvent Lines to the Solvent Rack
1. Connect each solvent line to the pump inlet port for which it is
intended (see the labeling on the solvent lines and in the pump).
2. Route the solvent lines from the pump to the solvent rack, through
the tubing guides in the pump and all modules above the pump in
the system stack. Observe the routing guidelines in Guiding
Capillaries and Tubing Through the System (} page 56).
3. Route the solvent lines through the guide hole in the solvent rack
and fix them in the appropriate tubing guides.
Figure 18: Guide hole and tubing guides in the solvent rack
No. Description
A Guide hole (solvent rack)

1 Solvent lines (up to three solvent lines)
2 Solvent lines (up to three solvent lines)
3+4 Not to be used for solvent lines; reserved for other tubing

Operating Manual
5 • Installation
Connecting the Solvent Line to the Solvent Reservoir

Observe the guidelines and recommendations in Use of Solvents and
Additives (} page 90).
Figure 19: Preparing the solvent line and reservoir cap
No. Description
1 Solvent line
2 Retaining guide
3 Reservoir cap
4 Cap plugs
5 Solvent line filter
1. Feed each solvent line through a retaining guide.

2. Feed the solvent line through an open hole in a cap for a solvent
reservoir. The retaining guide keeps the solvent line in place in the
reservoir.
3. Close any open holes in the reservoir caps with the cap plugs.
4. Slide a solvent line filter holder onto each solvent line.
5. Fill the solvent reservoirs with solvent.
6. Tighten the reservoir cap hand-tight. Press the retaining guide into
the hole in the reservoir cap so that the tubing is kept in place in the
cap.
7. Place the solvent reservoirs in the solvent rack.
8. Position the solvent lines straight in the tubing guides.
9. Optional: Install shut-off valves in the solvent lines (see Installing
Solvent Shut-Off Valves (} page 67)).
10. Check the solvent lines across the entire flow path. Make sure that
the lines are not bent, pinched, or squeezed at any point in the flow
path.
11. Reinstall the seal wash detector assembly.

Operating Manual
5 • Installation
5.6.6 Installing Solvent Shut-Off Valves

These steps apply only when installing a shut-off valve during initial
setup of the pump. To install a shut-off valve after initial operation of
the pump, follow the steps in Installing Solvent Shut-Off Valves
(} page 107).
When
To shut off the solvent flow through the system at the solvent reservoir,
for example, to prevent solvent from flowing through the system when
you open a flow connection on the low-pressure side
Parts and additional items required

connections
• Tubing cutter
Preparations
Prepare the pump and follow the steps in Connecting the Solvent Lines
(} page 63).
Follow these steps
Figure 20: Installing a shut-off valve in the solvent line
No. Description
1 Solvent line
2 Fitting
3 Ferrule
4 Shut-off valve
1. Cut the solvent line about 10 cm from the reservoir cap with a
tubing cutter. Make sure that the cut is at a right angle to the length
of the line.
2. Onto the free end of each solvent line, slide a fitting and a ferrule.
Mind the correct orientation of the fitting and ferrule (see picture).

Operating Manual
5 • Installation
3. Tighten the solvent lines to the shut-off valve.
Figure 21: Solvent line with shut-off valve installed
No. Description
1 Shut-off valve
2 Retaining guide
path.

Operating Manual
5 • Installation
5.7 Seal Wash System

The flow path of the seal wash system passes through the metering
device head in the autosampler and the pump heads in the pump. The
seal wash system comprises the following parts:
• In the pump: Seal wash pump (peristaltic pump), seal wash lines,
and seal wash detector (drop detector)
• In the autosampler: Seal wash lines
• Reservoir for the seal wash liquid

Both, the autosampler and pump are shipped with the seal wash
components installed and the lines connected within each of the two
modules.
To complete the setup, interconnect the seal wash paths of the

modules, connect and fill the seal wash reservoir, and flush the seal
wash system (see Setting Up the Seal Wash System (} page 70)).
5.7.1 Choosing the Seal Wash Liquid

Use seal wash liquid that fulfills the following requirements:
• The seal wash liquid is miscible with the solvent that is used in the
pump.
• The seal wash liquid is compatible with the seal wash tubing.
• The seal wash liquid provides certain conductivity for reliable

performance of the seal wash detector.
¨ HPLC-grade water with 10% methanol is an appropriate choice.
¨ With a Vanquish Core system that has been modified for NP
applications, the appropriate liquid depends on the application:
NP application:
Use ammonium formate in isopropanol (2 mmol/L).
RP application:
Use HPLC-grade water with 10% methanol.

Operating Manual
5 • Installation
5.7.2 Setting Up the Seal Wash System

• Seal wash reservoir assembly, including reservoir, reservoir cap, cap
plugs, and retaining guide for the seal wash line
• Seal wash line (silicone tubing) for connection to the seal wash
pump; the line is pre-installed to the seal wash outlet of the
metering device head
• Seal wash line (silicone tubing) for connection to the seal wash
reservoir
TIP To avoid the formation of air bubbles in liquid lines, always place
reservoirs in the solvent rack on top of the system stack.
Figure 22: Seal wash system in the Vanquish system (examples with a single split sampler,
left: with quaternary pump, right: with binary pump, as example for two-head pump)

Operating Manual
5 • Installation
No. Description
1 Seal wash reservoir

2 Seal wash lines in the autosampler (thick tubing), with
2a Wash line from reservoir to inlet port
2b Seal wash inlet port (right tubing connector)
2c Wash line from inlet port to metering device head
2d Wash line to seal wash pump
3 Metering device head
4 Seal wash pump (peristaltic pump)
5 Seal wash lines in the pump (thin tubing), with:
5a Wash lines from seal wash pump to pump head (binary pump, dual
pump: to left pump head)
5b Isocratic pump, quaternary pump: Wash line from pump head to seal
wash detector
Binary pump, dual pump: Wash line from left pump head to right pump
head
5c Binary pump, dual pump: Wash line from right pump head to seal wash
detector
Preparations
Rinse the seal wash reservoir thoroughly. Use a high-purity solvent for
rinsing.
Follow these steps

Setting up the seal wash system comprises the following steps:
1. Engaging the peristaltic tubing
2. Connecting the seal wash line between autosampler and pump
3. Routing the seal wash line to the solvent rack
4. Connecting the seal wash line to the seal wash reservoir
5. Flushing the seal wash system

Follow the steps in the respective sections.

Operating Manual
5 • Installation
Engaging the Peristaltic Tubing

In the pump, engage the peristaltic tubing (PharMed™ tubing) in the seal
wash pump:
Figure 23: Seal wash pump
No. Description
1 Pump lever
2 Pump rotor
3 Tubing holder (peristaltic tubing)
4 Tubing connector
5 Seal wash line from autosampler (silicone tubing)
6 Peristaltic tubing
7 Seal wash tubing to pump head (silicone tubing)
1. Press down the lever on the seal wash pump and hold it in that
position with one hand.
2. With your other hand, insert the tubing between the lever and the
rotor and wind it around the rotor.
3. Release the lever.
4. Check that the peristaltic tubing is inserted properly in the tubing

holders. If it is not, push the tubing into the holders. Make sure that
the tubing is not pinched or squeezed in the holders.
5. Check that the right tubing connector rests on the tubing holder. If it
does not, push the tubing connector onto the holder.

Operating Manual
5 • Installation
Connecting the Seal Wash Line between Autosampler and Pump
1. In the autosampler, locate the seal wash line (clear silicone tubing)
to the pump:
¨ Single split sampler: The seal wash inlet port is located on the
top enclosure frame (right tubing connector). The seal wash line
to the pump is interconnected to the seal wash inlet port.
¨ Dual split sampler: The seal wash inlet port is located on the
right enclosure frame (top tubing connector). The seal wash line
to the pump interconnects seal wash inlet and outlet port.
2. Disconnect the seal wash line from the seal wash inlet port.
3. Route the seal wash line from the seal wash outlet in the
autosampler through the tubing guides to the peristaltic tubing in
the pump.
¨ Single split sampler: The seal wash outlet is located on the
bottom end of the metering device.
¨ Dual split sampler: The seal wash outlet is located on the right
enclosure frame (bottom tubing connector).
Figure 24: Seal wash connections
No. Description
A Single split sampler: Seal wash connections on the top enclosure frame
B Dual split sampler: Seal wash connections on the right enclosure frame
1 Seal wash inlet port
1a Seal wash line to reservoir

Operating Manual
5 • Installation
No. Description
2 Seal wash outlet

2a Seal wash line to pump
4. In the pump, connect the seal wash line to the tubing connector on
the free end of the peristaltic tubing.
Routing the Seal Wash Line to the Solvent Rack
1. Locate the seal wash line for connection from the autosampler to
the seal wash reservoir.
2. Connect the seal wash line on the autosampler:

¨ Single split sampler: Connect the line to the seal wash inlet port
on the top enclosure frame (right tubing connector).
¨ Dual split sampler: Connect the line to the seal wash inlet port
on the right enclosure frame (top tubing connector).
3. Route the seal wash line from the autosampler to the solvent rack
through the tubing guides in the autosampler and all modules above
the autosampler in the system stack.
4. Route the seal wash line through the guide hole in the solvent rack
and fix it in the appropriate tubing guide.
Figure 25: Guide hole and tubing guides in the solvent rack
No. Description
A Guide hole (solvent rack)

1+2 Not to be used for seal wash line; reserved for other tubing
3 Tubing guide for seal wash line
4 Not to be used for seal wash line; reserved for other tubing

Operating Manual
5 • Installation
Connecting the Seal Wash Line to the Seal Wash Reservoir

Mind the requirements outlined in Choosing the Seal Wash Liquid
(} page 69).
Figure 26: Wash line and reservoir cap
No. Description
1 Wash line
2 Retaining guide
3 Reservoir cap
4 Cap plugs
1. Feed the wash line through the retaining guide.
2. Feed the wash line through an open hole in the cap of the wash
reservoir. The retaining guide keeps the tubing in place in the
reservoir.
3. Close any open holes in the reservoir cap with cap plugs.
4. Fill the wash reservoir with wash liquid.
5. Tighten the reservoir cap hand-tight. Press the retaining guide into
the hole in the reservoir cap so that the tubing is kept in place in the
cap.
6. Place the wash reservoir in the solvent rack.
7. Position the wash lines straight in the tubing guides.
8. Check the wash lines over the entire flow path:

a) Make sure that no bending (kink), pinching or squeezing of the
wash lines is present at any point in the flow path.
b) If you have to cut tubing to length, use a tubing cutter. Make
sure that the cut is at right angle to the length of the line.
Flushing the Seal Wash System

To flush the seal wash system, follow the procedure in Flushing the Seal
Wash System (} page 76).

Operating Manual
5 • Installation
5.7.3 Flushing the Seal Wash System

To flush the seal wash system, select one of the following alternatives:
• Turn on the pump.

Whenever the pump is turned on, the pump starts operation with a
seal wash cycle.
• Flush the seal wash system from the Chromeleon software.
• Flush the seal wash system from hand.

Select this alternative to flush the seal wash system when the pump
is powered off.
Flushing the Seal Wash System from the Chromeleon software

To flush the seal wash system from the Chromeleon software, start a
seal wash cycle by setting the seal wash pump to Active mode
(SealWashPump = Active).
During the seal wash cycle, the seal wash system is automatically filled
with the seal wash liquid. It will take 5 minutes for the liquid to travel
through the entire flow path.
Flushing the Seal Wash System from Hand

To flush the seal wash system from hand, follow these steps:
1. Disconnect the tubing from the seal wash detector.
Figure 27: Seal wash detector
No. Description

2 Tubing connection port (port labeled in)

Operating Manual
5 • Installation
2. Insert a syringe into the open end of the tubing.
3. To allow the liquid to travel easily through the seal wash system,
press down the lever of the seal wash pump and hold it in that
4. Pull out the syringe plunger to draw seal wash liquid into the tubing.
5. Release the lever of the seal wash pump when the liquid reaches the
syringe.
6. Remove the syringe and reconnect the tubing to the connection port
on the seal wash detector.
Mind the port labeling. To ensure correct functioning of the seal
wash detector, the tubing needs to be connected to the port labeled
in.

Operating Manual
5 • Installation
5.8 Connecting the Pump and Autosampler

Parts required
Capillary to connect the pump to the autosampler, as required for the
flow path
Follow these steps
1. On the connecting capillary, remove the knurls.
2. Guide the connecting capillary through the guide holes in the

housings of both, the pump and autosampler.
Figure 28: Guide holes in the autosampler and pump (left: view from VF‑/
VH-autosampler (example); right: view from pump)
No. Description
1 Capillary connecting the pump and autosampler:

1a Capillary end connected to the autosampler injection valve
1b Capillary end to be connected to pump outlet
2 Guide holes in autosampler housing and pump housing:
2a Guide hole in autosampler housing (view from above)
2b Guide hole in pump housing (view from below)
3. Reattach the knurls to the connection capillary.
4. In the pump, connect the capillary to the pump outlet.
5. In the autosampler, connect the capillary to the injection valve.

Operating Manual
5 • Installation
5.9 Turning On the Device

TIP
Before turning on the power to a Vanquish system module for the first
time, verify that the chromatography software is installed on the data
system computer. When the power is turned on, the required USB
drivers are automatically found and the Windows™ operating system
can detect the device.
To turn on the power to the device, follow these steps:
1. Check that the power button on the front left of the Vanquish
system base (system power button) is pressed in. If the power
button stands out, press the power button to turn on the power on
the system base.
2. Turn on the device with its main power switch.

Turn off the device with the main power switch, when instructed to do
so, for example, during maintenance. Pressing the system power button
will not be sufficient to turn off the power to the device completely.
When Powering Up the Pump

Whenever the power to the pump is turned on, the following sequence
of events occurs:
• The pump performs a self-test.

If the self-test is not successful, the status indicators are red, and the
pump is not ready for analysis. Check the Instrument Audit Trail for
the related message and take appropriate remedial action.
• The pump starts operation with a seal wash cycle. Before turning on
the pump, check the liquid level in the seal wash reservoir. Consider
checking also the liquid level in the waste container.
See also
2 Power On/Off Control (} page 89)

Operating Manual
5 • Installation
5.10 Setting Up the Device in the Software

This manual assumes that the chromatography software is already
installed on the data system computer and a valid license is available.
For more information about setting up the Vanquish system in the

software, refer to the Vanquish System Operating Manual.
The Help for the software that you are using provides detailed
information about the settings on each property page.

Operating Manual
6 • Operation
6 Operation
This chapter describes the elements for device control, provides
information for routine operation and for shutdown.

Operating Manual
6 • Operation
6.1 Introduction to this Chapter

The information in this chapter assumes that the initial setup of the
device has already been completed. If this is not the case, see the
instructions in Installation (} page 45).
For a basic description of instrument control and automated sample

analysis with the Chromeleon software, refer to the Vanquish System
Operating Manual. Details on control and operation of the device are
available in the Chromeleon Help.
Software descriptions in this manual refer to Chromeleon 7.

Terminology may be different to that of other software versions.

Operating Manual
6 • Operation
6.2 Safety Guidelines for Operation

When operating the device, pay attention to the following safety
guidelines:

CAUTION—High Luminosity of LED

The high luminosity produced by the LED illuminating the inside of the
device can be harmful to the eyes.
• Do not look directly into the light produced by the LED.
• Do not use light-focusing instruments for viewing the light beam.
NOTICE
Pay attention also to the following guidelines:
• To prevent damage resulting from leakage or from running the
pump dry, always set the lower pressure limit for the pump.
• If there is evidence of leakage in the device, turn off the pump flow
and remedy the situation immediately.
• If the pump flow is interrupted, act appropriately to protect the
components in the detector. For details, refer to the Operating
Manual for the detector.
• Always verify that the autosampler is turned on before the pump
flow is on and pressure builds up. If the autosampler is turned off,
for example, after a power failure, stop the pump flow and wait until
the pressure is down to zero before turning on the autosampler or
other modules again.

Operating Manual
6 • Operation
6.3 Control Elements

The device is designed to be operated mainly from a computer running
with the chromatography software.
In addition, the following elements are available on the device:
• Keypad
The keypad buttons allow you to perform certain functions directly
from the device.
• Status indicators
The LEDs (Light Emitting Diodes) on the status indicator LED bar on
the front side of the device and the STATUS LED on the keypad
provide a quick visual check of the operational status of the device.
Pump Block Status LED

The status indicator LED is located inside the pump above the pump
head (pump block LED). The LED indicates the operational status of the
pump block.
6.3.1 Keypad
The keypad inside the device allows you to perform certain functions
directly from the device. When you press a button, a short beep
confirms that the function is performed.
When the device is connected in the Chromeleon software, some

functions may not be available from the keypad (see further down in this
section).
Figure 29: Keypad
STATUS
The STATUS LED provides a quick visual check of the operational status
of the device.
When the doors are closed, the LED bar on the front side indicates the
operational status.
For status details, see Status Indicators (} page 86).

Operating Manual
6 • Operation
MUTE ALARM
Beeping alerts you when the device detects a problem, for example,
leakage. To turn off the beep for the current alarm, press this button.
Eliminate the source for the alarm within 10 minutes. Otherwise,
beeping starts again. If the device detects a different problem, beeping
alerts you again immediately.
SELECT
Binary pump and dual pump
Pressing the button selects the pump head for you which you can
perform a DOCK or PURGE function from the keypad. The LEDs next to
the button indicate the selection:
LED Description
LED L = green Left pump head selected

LED R = green Right pump head selected
Before performing a DOCK or PURGE function from the keypad, select

the pump head for which you want to perform the action.
Isocratic pump and quaternary pump

The button is disabled.
DOCK
Pressing the button moves the pistons of the selected pump head to the
appropriate position for maintenance procedures, such as pump head or
piston replacement, and undocks the pistons.
When undocking is complete, the LED next to the FLOW button starts
flashing green for the selected pump head. The LED continues flashing
while no pistons are docked. Pressing the button again docks the
pistons. Docking is complete when the LED stops flashing green.
Note the following:
• To avoid damage to the pump, remove or install the pump heads

only while the pistons are undocked (LED is flashing).
• Before you press the button to undock the pistons, open the purge
valve by turning the valve knob counterclockwise.
• When docking is complete, close the purge valve.
PURGE
Pressing the button starts a purge cycle. Pressing the button while a
purge cycle is running stops the cycle. See Purging the Pump
(} page 100).

Operating Manual
6 • Operation
FLOW
Pressing the button starts or stops the flow, considering the selected
flow rate, solvent composition, and flow acceleration/deceleration.
The LEDs next to the button indicate the following:
LED Description
Off (dark) The pump flow is off or zero.

Green The pump head is delivering.
Green, flashing The pistons are undocked.
When the Device is Connected in the Chromeleon Software

The button functionality is as follows when the device is connected in
the Chromeleon software:
• No injection or sequence is running:

All functions are available from the keypad.
• An injection or sequence is running:

The MUTE ALARM function remains available from the keypad,
allowing you to turn off the beep for the current alarm.
6.3.2 Status Indicators

This section provides information about the status LED bar on the front
side of the device, the STATUS LED on the inside keypad, and the pump
block status LED.
The status LED bar on the front side of the device and the STATUS LED
on the inside keypad provide information about the device status.
LED Bar
The LED bar colors provide the following information:
TIP—Dual pump only: With a dual pump, the LED bar is a two-part bar,
with the lights on the left referring to the left pump and the lights on the
right referring to the right pump.
LED Bar Description
Off (dark) The power to the device is turned off.

Dimmed The doors of the device are open.
Yellow, flashing slowly The power to the device is turned on, but the device
is not connected in the chromatography data
system.

Operating Manual
6 • Operation
LED Bar Description
Yellow The device is connected in the Chromeleon

software, but the device is not equilibrated. The
pump flow is off.
Green, flashing A purge cycle is running.
Green The device is equilibrated, but no data acquisition is
running. The pump flow is on.
Blue An injection or sequence is running, including data
acquisition.
Red A problem or error has occurred. For the related
message, check the Instrument Audit Trail. For
remedial action, see Troubleshooting (} page 197).
STATUS LED
The STATUS LED on the keypad inside the device provides the following
information:
STATUS LED Description
Off (dark) The power to the device is turned off.

Green The device is functioning properly.
Red A problem or error has occurred. For the related message, check
the Instrument Audit Trail. For remedial action, see
Troubleshooting (} page 197).
For information about the LEDs that are present next to a button on the
keypad, see Keypad (} page 84).

pump block.
LED Operational Status
Off (dark) No flow

Green The pump head is delivering.
Green, flashing – during In addition, the message "Compression limit reached"
normal operation (code 4156) appears in the Instrument Audit Trail.
The compression value was 100% during each of the
past three strokes. If the compression value is lower
than 100% for several strokes afterward, the message
"Compression back to normal"(code 4157) will appear
in the Instrument Audit Trail.
For more information about the compression values,
see Checking the Compression Values (} page 211).
Green, flashing – during The pistons are in the appropriate position for piston
pump maintenance (seal) replacement.

Operating Manual
6 • Operation
LED Operational Status
Red, flashing The pistons are not in the appropriate position for
normal operation (for example, after piston (seal)
replacement) or an error occurred during internal
maintenance (see Internal Maintenance (} page 120)).
In both cases, an accompanying message appears in the
Instrument Audit Trail when you try to start the flow,
for example, "The pump drive is still in undock
position; Please execute a dock command" (code
4127). Follow the remedial actions for the
accompanying message in Messages (} page 200).

Operating Manual
6 • Operation
6.4 Power On/Off Control

The power switch on the device is the main switch for power on/off
control. The main power switch is turned on during initial installation of
the device.
For easier handling, you can use the power button on the front left of
the Vanquish system base (system power button) for power on/off.
• All modules in the Vanquish system that are connected to the

system base via system interlink cables are turned on or off
simultaneously when the system power button is pressed.
• When the power is on, the system power button is pressed in. When
the power is off, the system power button stands out.
• If the main power switch on a device is off, you cannot turn on the
device with the system power button.
• To turn off a device completely, you have to turn it off with the main
power switch on the device. Pressing the system power button will
not be sufficient to turn off the power to the device completely.
When Powering Up the Pump

Whenever the power to the pump is turned on, the following sequence
of events occurs:
• The pump performs a self-test.

If the self-test is not successful, the status indicators are red, and the
pump is not ready for analysis. Check the Instrument Audit Trail for
the related message and take appropriate remedial action.
• The pump starts operation with a seal wash cycle. Before turning on
the pump, check the liquid level in the seal wash reservoir. Consider
checking also the liquid level in the waste container.

Operating Manual
6 • Operation
6.5 Use of Solvents and Additives

Particles entering the chromatography system can block capillaries and
valves, increase wear, and damage the column or system. Especially with
aqueous solvents, algae and other microorganisms can grow and deposit
in the system and block the solvent line filters. Blocked capillaries or
filters can cause increased or unstable system pressure.
TIP In a Vanquish Core system, normal-phase (NP) compatible solvents

and additives may be used if the system modules have been modified
for NP applications. Refer to the Vanquish System Operating Manual.
For optimum performance of the chromatography system, observe the

following guidelines:
Solvent Quality and Filtration
• Use high-quality high-purity solvents (filtered) and additives as

required by the application, for example, UHPLC-grade or LC/MS-
grade. If a fluorescence detector is used in the system, consider
using fluorescence-grade solvents.
Filtered high-purity solvents are usually labeled accordingly by the
vendor.
• Use high-quality water for example, UHPLC-grade or LC/MS-grade

(0.2 µm filtered).
• When you use water from water purification systems, polymeric

contamination may occur if the purification system is not
maintained properly.
• When preparing salt solutions or buffers and preparation is

complete, use membrane filtration (0.2 µm) to remove any
particulate matter and to reduce microbial growth.
• Use fresh solvents at regular intervals. Avoid adding up (refreshing)

solvents. With premixed solvents, be especially sure that they are
properly prepared and fresh.
• Always use the appropriate solvent line filters as recommended by

Thermo Fisher Scientific. Check the filter frits for permeability at
regular intervals and replace them as necessary.
• For best seal performance, do not recycle or recirculate solvents.
• Note the special properties of the solvents, such as viscosity, boiling

point, or UV absorption.

Operating Manual
6 • Operation
Solvent Reservoirs
• Before filling a solvent reservoir, rinse the reservoir thoroughly with

a high-purity solvent.
• To reduce the growth of algae, consider using amber glassware or

using appropriate additives, for example, formic acid.
• Avoid using methanol from aluminum reservoirs.
Flushing after Operation
• Flush out buffers and solutions that form peroxides.
• Never leave buffers, salt solutions, or aggressive solvents in the

system for a longer period without flow.
• Before you change from a buffer or salt solution to organic solution,

flush the system thoroughly with de-ionized water.
• Before you change solvents, make sure that the new solvent is
miscible with the previous solvent. If the solvents are not miscible,
flocculation may occur.
Mix immiscible solvents with an intermediate solvent to replace
them step by step. For example, use isopropanol.

Operating Manual
6 • Operation
6.6 Preparing the Device for Operation

This section gives information on any additional steps that are required
to prepare the device for operation and sample analysis.
Before Operating the Device for the First Time

Prepare the device for the first-time operation, observing the following:
NOTICE
Flush the system flow path thoroughly before operating the device for
the first time:
• When you install devices or components to the system, always flush
them to waste before connecting them in the system flow path. To
flush the Vanquish modules, follow the instructions in the Vanquish
System Operating Manual.
• Some components of the device are filled with isopropanol when
the device is shipped from the manufacturing site. When operating
the device for the first time, use solvents that are miscible with
isopropanol. If they are not, use an appropriate intermediate
solvent.
• To remove the isopropanol from the device components:

¨ Verify that the flow cell and the column are not connected in the
flow path.
¨ Purge the pump and then have the pump deliver flow for a short
time.
• Verify that any air bubbles are completely flushed out of the system
flow path.
• Quaternary pump and dual pump: Synchronize the injection time of

the Vanquish autosampler with the strokes of the pump. See
Synchronizing the Injection Time with the Pump Strokes
(} page 224).
Before Starting Sample Analysis

Before starting an analysis:
• Check the liquid level in the solvent reservoirs. Verify that the
amount of solvent is sufficient for the analysis.

Operating Manual
6 • Operation
• Close the doors of all modules in the Vanquish system, if not already
done.
NOTICE
During pumping cycle keep the pump doors closed. Otherwise,
functionality may be adversely impacted.
• Make sure that the chromatography system is properly equilibrated

(see further down).
System Equilibration
System equilibration should include the following operations:
• Purging the pump (all channels, including those not used for the
application)
• Flushing the entire chromatography system with the starting solvent

to rinse out any solvent from a previous analysis run
• Warming up (or cooling down) all temperature-controlled devices in

the system to the starting temperature. Temperature-controlled
devices can be, for example
¨ Column compartment and post-column cooler
¨ Sample compartment thermostatting in the autosampler
¨ Flow cell in a fluorescence detector
¨ Evaporation tube in a charged aerosol detector
• Turning on the lamp (or lamps) in the UV/VIS detector
• Monitoring the pump pressure and pressure ripple and checking

that the pressure is stable and the ripple within reasonable limits for
the application
• Monitoring the detector signal and checking whether the detector

signal is stable so that the drift and signal noise are within
reasonable limits for the application
• Performing an autozero of the detector baseline
TIP The Chromeleon software supports procedures for automatically

starting a chromatography system in the software (Smart Startup). The
startup procedure includes the operations for system equilibration. For
details, refer to the Chromeleon Help.

Operating Manual
6 • Operation
6.7 Important Operating Parameters

The parameters described in this section should be considered for
routine operation of the device. You can usually access these
parameters from the Chromeleon user interface.
If a parameter listed below is not available in the Chromeleon software,

consider updating the firmware and Chromeleon version.
For more information, refer to Chromeleon Help and documents.
Flow Parameters
Parameter Description
Flow The allowed flow range is indicated in the dialog box

for the pump in the Instrument Configuration
Manager. You can change the upper and lower limit
for the flow rate within the allowed range.
Flow ramps Set the flow acceleration and flow deceleration.
Recommendation: Set the parameters to a value
between 1/3 and factor 3 of the (column) flow rate.
Flow acceleration The flow acceleration (Maximum Flow Ramp Up)
determines how fast the pump starts delivering with
the selected flow rate. If the value is too low, it will
take correspondingly long for the pump to build up
the necessary pressure and start delivering the
required flow. If the value is too high, this may impair
the column lifetime.
Flow deceleration The flow deceleration (Maximum Flow Ramp Down)
determines how fast the pump reduces the flow. If
the value is too low, it will take correspondingly long
for the pump to reduce the flow and thus the
pressure. If the value is too high, this may impair the
column lifetime.

Operating Manual
6 • Operation
Pressure Parameters
Pressure limits The allowed pressure range is indicated in the dialog

box for the pump in the Instrument Configuration
Manager. You can adapt the upper and lower
pressure limits within the allowed range.
• The lower pressure limit helps to prevent the pump
(and column) from running dry. A typical setting is
1 MPa.
• The upper pressure limit helps to protect the column
from too high pressure. The column and the
application determine the appropriate setting.
When the pump pressure is outside the specified
limits, the Chromeleon software stops the pump flow
and aborts a running Queue.
Pump pressure In the dialog box for the pump in the Instrument
Configuration Manager, the Pump_Pressure check
box is selected as a standard when the pump is set up
in the Chromeleon software. The Chromeleon
software uses this setting to generate the channel for
recording the pump pressure (which corresponds to
the column pressure). With the dual pump, the check
boxes are labeled PumpLeft_Pressure for the left
pump and PumpRight_Pressure for the right pump.
Always record the pump pressure. If a problem
occurs, the information from the pump pressure
channel can provide helpful information to identify
and eliminate the source for the problem.

Operating Manual
6 • Operation
Solvent and Waste Liquid Parameters
Solvent composition In the dialog box for the pump in the Instrument
Configuration Manager, set the number of the
solvents to be used with the pump. You can change
the standard solvent names as required. The solvent
names appear in the Chromeleon user interface.
In the Chromeleon Client, set the solvent composition.
For more information, see the related section in
Pump-Specific Information (} page 215).
Solvent consumption You can monitor the liquid level in the solvent
reservoir (solvent consumption) when you have
entered the required information for the related
solvent. Based on this information, the Chromeleon
software calculates the liquid level. To monitor the
liquid level in real time, based on real physical
measurement, install the Vanquish Solvent Monitor.
The solvent monitor is available as an option (see
Optional Accessories (} page 267)).
For monitoring from the Chromeleon software, enter
the following information:
• Volume of solvent in the reservoir (at the beginning
of a sequence)
• Lower limit for the solvent in the reservoir, which is
the minimum volume of liquid that must be
available in the reservoir
The Remain Time property for the solvent reports
the time left until the liquid level is expected to
reach the lower limit. The Chromeleon software
calculates the time from the current flow rate and
volume entered.
• Warning limit when you want to be informed about
the liquid level in the reservoir
When the liquid in the reservoir reaches the lower
limit, the Chromeleon software stops the pump as
specified in the Emergency Instrument Method if
available or aborts the Queue and stops the pump
flow.
Relevant for dual pump only
You can monitor the solvent consumption of the dual
pump as a whole if the two pumps share the same set
of solvent reservoirs. If the pumps are connected to
different sets of solvent reservoirs, you can monitor
the solvent consumption separately each pump (see
Monitoring the Solvent Consumption (} page 226)).

Operating Manual
6 • Operation
Waste level You can monitor the liquid level in the waste
container when you have entered the required
information. Based on this information, the
Chromeleon software calculates the liquid level. To
monitor the liquid level in real time, based on real
physical measurement, install the Vanquish Solvent
Monitor. The solvent monitor is available as an option
(see Optional Accessories (} page 267)).
For monitoring from the Chromeleon software, enter
the following information:
• Volume of liquid in the waste container at the
beginning of a sequence
• Upper limit for the liquid level in the waste container
The Remain Time property for the waste reports the
time left until the liquid level is expected to reach
the upper limit. The Chromeleon software calculates
the time from the current flow rate and calculated
current liquid level.
• Warning limit when you want to be informed about
the liquid level in the waste container
Relevant for dual pump only
You can monitor the liquid level in the waste
container for the dual pump as a whole if the two
pumps share the same container. If the waste liquid is
guided to different waste containers, you can monitor
the liquid level for each pump. For details, see
Monitoring the Liquid Level in the Waste Container
(} page 227).

Operating Manual
6 • Operation
Other Parameters
Compression The compression values of the pump head can

provide valuable information for troubleshooting. For
details, see Checking the Compression Values
(} page 211).
Curve You can specify linear or non-linear (curved) gradient
profiles.
• Curve 5 (default setting) is linear. Changes in the
composition of the delivered solvent over time are
constant.
• Curves 1 through 4 are convex upward. Convex
curves cause rapid changes in solvent composition
at the beginning of the gradient and slower changes
at the end. Slope changes over time become
extreme as curves go from 4 (least convex) to 1
(most convex).
• Curves 6 through 9 are concave upward. Concave
curves cause slower changes in solvent composition
at the beginning of the gradient and rapid changes
at the end. Slope changes over time become
extreme as curves go from 6 (least concave) to 9
(most concave).
In addition, you can define step gradients directly in
the gradient table (for example, step A and step B).
Thus, more than 11 different options are available to
change the gradient.
Degasser The degasser is enabled as a standard when the pump
is shipped (Degasser = On). This setting is the
preferred setting.
Leak detection Leak detection is enabled as a standard when the
device is shipped (Leak Sensor Mode = Enabled). This
is the preferred setting.
Purge Purge the pump in the following situations:
• To remove air bubbles that might be trapped in the
system
• When changing to a different type of solvent
See Purging the Pump (} page 100).

Operating Manual
6 • Operation
Seal washing The seal wash system is enabled and cannot be

disabled. As a standard, the pump performs a seal
wash in the following situations:
• Once per hour
• Each time the pump is turned on
If required, you can start an additional seal wash cycle
or stop a running cycle:
• If the seal wash pump is in Idle mode, select Active
to start a wash cycle.
• If the seal wash pump is in Active mode, select Idle
to stop a running wash cycle.
You can disable the drop counter functionality by
setting Rear Seal Wash Monitoring to Disabled. Note
that disabling drop detection will not disable the seal
wash system. However, messages relating to the seal
wash system (for example, when the system has run
out of wash liquid) or piston seal leakage will no
longer alert you in the user interface.
Synchronization of the Relevant for quaternary pump and dual pump only
injection time with the Synchronizing the injection time with the pump
pump strokes strokes enhances the retention time precision. For
details, see Synchronizing the Injection Time with the
Pump Strokes (} page 224).

Operating Manual
6 • Operation
6.8 Purging the Pump

Purging the pump means rinsing the pump for a short time at a higher
flow rate, using the selected solvents.
Settings
The following settings are considered for the purge cycle:
Setting Description
Purge flow The standard setting is 5 mL/min.

You can adapt the setting in the Chromeleon software if
required. The setting is considered also when purging the pump
from the keypad.
Purge time The standard purge time is 5 minutes.
You can adapt the setting in the Chromeleon software if
required. The setting is considered also when purging the pump
from the keypad.
Channel to be The purge cycle is performed with the most recently selected
purged and channel and eluent composition.
solvent to be used You can adapt the settings in the Chromeleon software if
required. The settings are considered also when purging the
pump from the keypad.
To Purge the Pump

The following alternatives are available:
Procedure Description
Automatic purging Automatic purging runs without further user interaction.

Automatic purging is possible only when certain prerequisites
are fulfilled. When the prerequisites are fulfilled, automatic
purging is performed by default when you press the PURGE
button on the keypad.
See Automatic Purging (} page 101).
Manual purging With manual purging, user interaction is required at the
beginning and at the end of the purge cycle.
See Manual Purging (} page 102).
TIP With a dual pump, purge each pump separately.

Operating Manual
6 • Operation
6.8.1 Automatic Purging

Automatic purging means that the solvent is automatically directed to
waste, through the wash port of the Vanquish autosampler, without
further user interaction.
Prerequisites
Automatic purging is possible only when the pump is fluidically
connected to the Vanquish autosampler and when both modules have
an appropriate firmware installed.
When these prerequisites are fulfilled, automatic purging runs by default

when you press the PURGE button on the keypad.
Dual pump: If the second pump is not connected fluidically to a Vanquish

autosampler, purge the pump manually (see Manual Purging
(} page 102)).
When
• The pump is operated for the first time

To flush out the isopropanol that is present in some components of
the pump when the pump is shipped from the manufacturing site
• One or more solvent lines have been empty
• To remove air bubbles that might be trapped in the system (pump

head, solvent lines) because air bubbles in the system may lead to
the following problems:
¨ Pressure pulsation
¨ High noise level or pulsation during pump operation
¨ Non-reproducible analysis
• When changing to a different type of solvent, for example, when

changing to a different analytical method
Items required
Solvents suitable for purging
To flush out the isopropanol when operating the pump for the first time,
use solvents that are miscible with isopropanol. If they are not, use an
appropriate intermediate solvent.

Operating Manual
6 • Operation
Follow these steps
1. In the Chromeleon software, set the channel that you want to purge
to 100%.
2. Optional: In the Chromeleon software, adapt the settings for the

purge flow or purge time if required.
3. Start the purge cycle. You can start the purge cycle from the
Chromeleon software or by pressing the PURGE button on the
keypad.
The purge cycle ends automatically when the specified purge time
ends. If you want to stop purging before the purge time ends, turn
the purge off from the Chromeleon software or by pressing the
PURGE button on the keypad.
4. Repeat the above steps for all channels, including those that are not
used for the application.
6.8.2 Manual Purging

Manual purging requires user interaction. The user must open and close
the purge valve by hand to direct the solvent to waste, through the
purge outlet on the purge/sensor unit.
The procedure depends on the reason for purging:
• When the pump is operated for the first time or when solvent lines
are empty, follow the steps in Purging with First Time Operation or
Empty Solvent Lines (} page 102).
• To remove air bubbles, or to change to a different type of solvent, or

when using a fresh reservoir of solvent after a longer period without
flow, follow the steps in Purging for Removing Air Bubbles or
Changing to Different Solvent Type (} page 105).
6.8.2.1 Purging with First Time Operation or Empty Solvent Lines

When
• The pump is operated for the first time

To flush out the isopropanol that is present in some components of
the pump when the pump is shipped from the manufacturing site
• One or more solvent lines have been empty
TIP To remove air bubbles or to change to a different type of solvent,

follow the steps in Purging for Removing Air Bubbles or Changing to
Different Solvent Type (} page 105).

Operating Manual
6 • Operation
Items required
• Solvents suitable for purging

To flush out the isopropanol when operating the pump for the first
time, use solvents that are miscible with isopropanol. If they are not,
use an appropriate intermediate solvent.
• Silicone tubing
• Tissue
• Syringe
TIP For first time-operation: Silicone tubing and a syringe are available in
the ship kit.
Preparations
1. To be able to generate negative pressure, connect an autosampler

or another type of flow restriction to the pump outlet. If necessary,
close the pump outlet with a fitting plug.
2. On the purge/sensor unit, attach silicone tubing to the purge outlet

(if it is not yet connected).
3. Insert the syringe tip into the open end of the tubing.
4. Open the purge valve by turning the valve knob counterclockwise.
Follow these steps
to 100%.

3. Binary pump and dual pump: For purging from the keypad, verify
that you have selected the pump head (pump) for which you want to
perform the procedure.
keypad.
5. Use the syringe to draw enough solvent for filling the solvent line to
the purge outlet.
6. When the liquid enters the silicone tubing, examine the solvent line.
If the solvent line is completely filled with liquid and no air bubbles
are visible, stop the purge cycle (from the Chromeleon software or
by pressing the PURGE button).

Operating Manual
6 • Operation
7. Remove the syringe from the silicone tubing, absorbing any liquid
that leaves the tubing with a tissue.
8. Route the free end of the tubing to the drain port outlet (see
Guiding Liquids to Waste (} page 62)).
9. Perform the above steps for all channels, including those that are
not used for the application.
If necessary, empty the syringe before starting the procedure for the
next channel.
10. When purging is complete, close the purge valve by turning the
valve knob clockwise.
NOTICE
Turn the valve knob only with your fingers. If the knob leaks, tighten a
little more. Be careful; overtightening may damage the purge valve
seals.
11. Empty the silicone tubing.
12. Dual pump only: If applicable, perform the purge procedure also for
the other pump.
Emptying the Silicone Tubing
NOTICE
Always empty the silicone tubing when purging is complete. When the
purge valve is closed, purge liquid remains in the tubing connected to
the purge outlet. Leaving the liquid in the tubing for a longer period
limits the tubing lifetime.
1. To absorb any liquid that might be leaving the purge outlet when the
tubing is removed, place the tissue under the outlet.
2. On the purge/sensor unit, remove the silicone tubing from the purge
outlet. The other end of the tubing remains in the purge drain port
outlet.
3. Hold the tubing so that any liquid that is present in the tubing flows
off through the drain port outlet.
4. On the purge/sensor unit, consider reconnecting the silicone tubing.

Operating Manual
6 • Operation
6.8.2.2 Purging for Removing Air Bubbles or Changing to Different Solvent Type
• To remove air bubbles that might be trapped in the system (pump
head, solvent lines) because air bubbles in the system may lead to
the following problems:
¨ Pressure pulsation
¨ High noise level or pulsation during pump operation
¨ Non-reproducible analysis
• When changing to a different type of solvent, for example, when

changing to a different analytical method
TIP When the pump is operated for the first time or when solvent lines
are empty, follow the steps in Purging with First Time Operation or
Empty Solvent Lines (} page 102).
Items required
• Solvents suitable for purging
• Silicone tubing
• Tissue
Preparations
1. To be able to generate negative pressure, connect an autosampler

or another type of flow restriction to the pump outlet. If necessary,
close the pump outlet with a fitting plug.

Follow these steps
to 100%.

3. Binary pump and dual pump: For purging from the keypad, verify
that you have selected the pump head (pump) for which you want to

Operating Manual
6 • Operation
keypad.
5. Perform the above steps for all channels, including those that are
not used for the application.
6. When purging is complete, close the purge valve by turning the

valve knob clockwise.
NOTICE
Turn the valve knob only with your fingers. If the knob leaks, tighten a
little more. Be careful; overtightening may damage the purge valve
seals.
7. Empty the silicone tubing.
8. Dual pump only: If applicable, perform the purge procedure also for
the other pump.
NOTICE
outlet.
Troubleshooting with Persistent Air Bubbles

If you are unable to remove air bubbles with purging, purge the pump
against backpressure. Follow the procedure for running in new piston
seals in Recommendations for New Piston Seals (} page 149).

Operating Manual
6 • Operation
6.9 Optimizing the Performance of the Device

This section provides information for best performance of the device
and gives hints on what you can do to optimize the performance further.
6.9.1 General Guidelines

To optimize the performance of the device, consider the following
general guidelines:
• Monitor the usage of specific device components that are subject to

wear and stress and schedule appropriate maintenance intervals
(see Predictive Performance (} page 125)).
• Observe the general guidelines and recommendations on the use of

solvents and additives in the chromatography system (see Use of
Solvents and Additives (} page 90)).
• Pumps with built-in vacuum degasser: Always use the built-in

vacuum degasser.
• Purge the pump when changing to a different type of solvent or

when restarting the pump after periods of inactivity.
TIP Shut-off valves for solvent lines are available as an option (see
Installing Solvent Shut-Off Valves (} page 107)). These valves allow you
to shut off the solvent flow through the system at the solvent reservoir,
the pump flow is zero for a longer period.
6.9.2 Installing Solvent Shut-Off Valves

When
To shut off the solvent flow through the system at the solvent reservoir,
you open a flow connection on the low-pressure side
The steps in this section apply only when installing a shut-off valve after
initial operation of the pump. To install a shut-off valve during initial
setup of the flow connections, follow the steps in Connecting the
Solvent Lines (} page 63).

Operating Manual
6 • Operation

connections
• Tubing cutter
• Solvent suitable for purging the pump
Preparations
1. Turn off the pump flow and wait until the system pressure is down
to zero.
2. Prepare the pump for purging (see Purging the Pump (} page 100)).
Follow these steps

Follow the steps for each solvent line in which you want to install a shut-
off valve.
Figure 30: Installing a shut-off valve in the solvent line
No. Description
1 Solvent line
2 Fitting
3 Ferrule
4 Shut-off valve
1. Unscrew the cap of the solvent reservoir and remove the cap
together with the solvent line from the reservoir.
2. Start a purge cycle as appropriate.
3. Stop purging as soon as the solvent line is empty.
4. Retighten the reservoir cap hand-tight. The retaining guide must

remain in the hole in the reservoir cap. If it does not, press the
retaining guide into the hole so that the tubing is kept in place in the
cap.

Operating Manual
6 • Operation
5. Cut the solvent line about 10 cm from the reservoir cap with a
tubing cutter. Make sure that the cut is at a right angle to the length
of the line.
6. Onto the free end of each solvent line, slide a fitting and a ferrule.
Mind the correct orientation of the fitting and ferrule (see picture).
7. Tighten the solvent lines to the shut-off valve.
path.
9. To remove any air from the solvent lines, purge the pump using the
solvent of your application.
Figure 31: Solvent line with shut-off valve installed
No. Description
1 Shut-off valve
2 Retaining guide

Operating Manual
6 • Operation
6.10 Shutting Down the Device

If the device will not be operated for some time, follow the instructions
in this section to shut down the device.
TIP The Chromeleon software provides procedures for automatically

preparing the chromatography system for shutdown. The procedures
include, for example, operations for reducing the flow rate, reducing the
temperature in temperature-controlled devices, and turning off the
detector lamps. For information about Smart Shutdown and Smart
Standby, refer to the Chromeleon Help.
6.10.1 Short-Term Shutdown (Interruption of Operation)

To interrupt operation of the device for a short period (short-term
shutdown), for example, overnight, observe these guidelines for the
Vanquish system modules, as required by your system arrangement:
• For your Vanquish detector, note the following:
Detector Type Description
Charged aerosol Check that sufficient gas is available to continue gas flowing
detector through the detector. This is to prevent any build-up of
residue from solvents or analytes. Gas must be flowing when
pump flow is delivered to the detector.
UV/VIS detectors The lamp(s) in the detector can remain turned on.
Variable wavelength detector and VH-D10 diode array
detector only: The shutter can be moved to a closed position
for protection of the flow cell.
Fluorescence Turn off temperature control for the flow cell.
detector
• Apply a flow of 0.05 mL/min and have the pump deliver an

appropriate solvent.
Check the lower pressure limit for the pump and adapt the value if
necessary. If the pressure falls below the lower limit, the pump stops
the flow.
• Set the injection valve in the autosampler to the Inject position.
• Make sure that the temperature of the column does not exceed
40 °C.
• When resuming operation, let the flow equilibrate and verify that
the operating parameters for the other system modules are set as
required before proceeding.

Operating Manual
6 • Operation
6.10.2 Long-Term Shutdown

To interrupt operation for a longer period, follow the instructions in this
section.
TIP Shutting down the device affects the operation of the system. When
shutting down the device, also observe the shutting down instructions
for the other Vanquish system modules and take appropriate action
(refer to the Operating Manuals for the modules).
1. Remove the column.
2. Flush the system with an appropriate solvent (minimum HPLC-

grade). Observe the following:
TIP With a Vanquish Core system that has been modified for using
normal-phase compatible solvents and additives, refer to the
information about the flushing liquid in the Considerations with Normal-
Phase Compatible Solvents and Additives section in the Vanquish System
Operating Manual.
Situation after Shutdown If no additive is used If an additive is used
Device remains in the Flush the system, for Flush the system with
laboratory after shutdown example with methanol. several volumes of
100% acetonitrile should methanol and water
not be used. (50:50) (for example,
1.0 mL/min for
10 minutes with the
standard system) to
prevent salt buildup in the
fluidics. If the solvents in
the device are not
miscible with water, use
an appropriate
intermediate solvent.
Device shall be Flush the system with Flush the system first with
transported or shipped isopropanol. several volumes of
after shutdown methanol and water
(50:50) (for example,
1.0 mL/min for
10 minutes with the
standard system) to
prevent salt buildup in the
fluidics. If the solvents in
the device are not
miscible with water, use
an appropriate
intermediate solvent.
Afterward, flush the
system with isopropanol.

Operating Manual
6 • Operation
to zero.
4. Disconnect the solvent lines. See Disconnecting the Solvent Lines

(} page 112).
TIP Removing the solvent lines from the tubing guides is usually not
required (not even for replacing the slide-in module). However, when
you remove the solvent lines from the tubing guides in the pump and all
modules above the pump in the system stack, be careful not to pull on
other tubing in the guides.
5. Empty the seal wash system. See Emptying the Seal Wash System
(} page 113).
6. The step depends as follows:
Situation Steps
Device and all other system modules Turn off the system with the system
remain in the system stack and are to be power button on the system base.
turned off
Device shall be transported or shipped If one of the modules shall be removed
after shutdown from the system stack, turn off all
system modules with their main power
switch. Pressing the system power
button will not be sufficient to turn off
the power to the devices completely.
Follow the instructions in Transporting or
Shipping the Device (} page 187).
Disconnecting the Solvent Lines
1. Unscrew the caps of the solvent reservoirs.
2. Together with the caps, remove the solvent lines from the
reservoirs.
3. Protect the solvent line filters from contamination as appropriate.
4. Empty the solvent lines. See Emptying the Solvent Lines

(} page 169).
5. Disconnect the solvent lines on the pump inlets.
6. Close the pump inlets with appropriate plugs.

Operating Manual
6 • Operation
Emptying the Seal Wash System
1. Unscrew the cap of the seal wash reservoir.
2. Together with the cap, remove the seal wash line from the seal wash
reservoir.
3. Remove the peristaltic tubing from the seal wash pump. When the
tubing is removed, any liquid that may be present in the seal wash
line, flows off to waste.
6.10.3 Restart after Long-Term Shutdown

To restart the device after a long-term shutdown, follow these steps:
1. Engage the peristaltic tubing in the seal wash pump.
2. Reconnect the seal wash line and the solvent lines to the
appropriate reservoirs.

cap.
4. Turn on the device. Observe the following:
Situation Action
If the device remained in the system Turn on the system with the system
stack and all system modules were power button on the system base.
turned off.
If the device is restarted after transport. Turn on the device with the main power
switch.
5. Prepare and restart the other modules in the Vanquish system,

following the instructions in the Operating Manuals for the modules.
Pay special attention to the Preparing the Module for Operation
section.
6. Purge the pump and then have the pump deliver for a short time.
7. Before starting an analysis, let the device equilibrate and be sure

that it is ready for operation. See Preparing the Device for Operation
(} page 92).

Operating Manual
6 • Operation

Operating Manual
7 • Maintenance and Service
7 Maintenance and
Service
This chapter describes the routine maintenance and the service
procedures that the user may perform.

Operating Manual
7.1 Introduction to Maintenance and Service

This chapter describes the routine maintenance and service and repair
procedures that the user may perform.
Additional maintenance or service procedures must be performed only

by service personnel certified by Thermo Fisher Scientific (for brevity,
referred to as Thermo Fisher Scientific service personnel).
The device is designed for easy maintenance and service. The user-
serviceable parts of the device can be accessed from the front. If not
stated otherwise, the maintenance procedures do not require that you
remove the device from the system.
The maintenance procedures do not require that you remove the doors.
However, it is possible to remove a door if this should ever be required
for a specific reason or procedure. If you need to remove a door, follow
the related steps in Replacing the Doors (} page 185).

Operating Manual
7.2 Safety Guidelines for Maintenance and Service

When performing maintenance or service procedures, pay attention to
the following safety guidelines:

WARNING—High Voltage
shock.
Do not open the housing or remove protective panels unless specifically
instructed to do so in this manual.
WARNING—Escape of Hazardous Substances from Flow Connections

Flow and capillary connections can be filled with substances that can
pose health risks. Solvent can spray when capillaries burst, slip out of
their fittings, or are not properly tightened or when capillary
connections are otherwise open.
• Wear appropriate protective equipment and follow good laboratory
practice.
• Before starting maintenance or repair procedures, flush out harmful
substances with an appropriate solvent.
WARNING—Tilting Liquid Reservoirs

Liquids in the reservoirs on the solvent rack might contain harmful
substances. Spilling of these substances can pose health and safety risks.
To prevent the reservoirs from tilting, be careful not to pull on the liquid
lines when performing maintenance.
CAUTION—Spraying Solvent
Solvents can spray when under high pressure.
• Stop the pump flow prior to opening the flow path.
• Wait until the system pressure is down to zero.
• When opening the flow path, wear appropriate protective
equipment.

Operating Manual
CAUTION—Hydrostatic Pressure
Solvent may spill when you open the flow path. This is due to hydrostatic
pressure in the system when the solvent reservoirs are located above
the pump outlet. Before you loosen a connection in the flow path:
• Turn off the pump flow and wait until the system pressure is down
to zero.
• Unscrew the caps of the solvent reservoirs and remove the solvent
lines together with the caps from the reservoirs.
• Empty the solvent lines. See Emptying the Solvent Lines
(} page 169).
• Retighten the reservoir caps.

After the power to the device is turned off, the device is still energized
as long as the power cord is connected. Repair work on the device while
the device is connected to power could lead to personal injury.
• Always unplug the power cord before starting repair work inside the
device.
• If you were instructed to remove any housing covers or panels, do
not connect the power cord to the device while the cover or panels
are removed.

Operating Manual
7.3 General Rules for Maintenance and Service

For successful maintenance and service procedures, follow the rules and
recommendations below.
General Rules
• Before starting maintenance or service procedures, shut down the

device when instructed to do so.
• Use only the replacement parts specifically authorized and qualified

for the device by Thermo Fisher Scientific.
• Follow all instructions step by step and use the tools recommended
for the procedure.
Opening Flow Path Connections
• Before opening the flow path to replace capillaries in the system,

turn off the pump flow and wait until the system pressure is down to
zero.
• Dirty components can contaminate the chromatography system.

Contamination leads to poor performance of the modules and entire
system or can even cause damage to the modules and system.
Therefore:
¨ Always wear appropriate gloves.
¨ Place the components only on a clean, lint-free surface.
¨ Keep your tools clean.
¨ Use only lint-free cloth for cleaning.
• After you have performed maintenance or service on the flow

connections in the pump, test the pump for leakage before you
resume operation.
Depot Repair
• If you need to return the device for depot repair, follow the
instructions in Transporting or Shipping the Device (} page 187).

Operating Manual
7.4 Routine and Preventive Maintenance

Optimum device performance, maximum uptime of the device, and
accurate results can be obtained only if the device is in good condition
and properly maintained.
7.4.1 Internal Maintenance

Every six weeks, the pump automatically performs an internal
maintenance procedure when you initiate a purge cycle. The purge cycle
starts automatically when internal maintenance is complete. This may
take some seconds. While internal maintenance is running, the purge
valve must remain open.
If no purge cycle is initiated after another 6 weeks, a message appears in

the Instrument Audit Trail, reminding you to start a purge cycle.
7.4.2 Maintenance Plan

Perform the maintenance procedures in the table on a regular basis. The
frequency given in the table is a suggestion. The optimum frequency for
maintenance depends on several factors, such as the types and amounts
of samples and solvents used with the device.
Frequency What you should do...
Daily • Inspect the flow connections for signs of leakage or

blockage.
• Inspect the flow connections for indications of salt
deposits.
• Inspect the flow connections for indications of air
bubbles. Degas the solvents and purge the pump if
necessary.
• If the solvent is pure water or an aqueous buffer, replace
the solvent in the reservoir daily.
• Check the liquid level in the seal wash reservoir. Fill the
seal wash reservoir with fresh seal wash liquid if
required.
• When you use buffers or salt solutions, flush the device
thoroughly after use with an appropriate solvent that
does not contain buffers or salts.

Operating Manual
Frequency What you should do...
Regularly • Check the liquid level in the solvent reservoirs to prevent

the pump from running dry.
Especially with phosphate buffer applications: The solvent
reservoirs must not run empty while the pump is running.
If they do, problems with check valves and/or
proportioning valves might occur. When the system is not
operated for more than 1 day, flush the system and
solvent lines, including those that are not used for the
application, with buffer-free solvent.
• Replace the wash liquid in the seal wash reservoir with
fresh liquid. Rinse the reservoir thoroughly before filling
it. Use a high-purity solvent for rinsing.
• Test the seal wash system for leakage (see Testing the
Seal Wash System for Leakage (} page 128)).
• Replace the peristaltic tubing in the seal wash pump
every 6 months (see Replacing the Seal Wash Lines
(} page 129)).
• Inspect the flow connections for damage, such as cracks,
nicks, cuts, or blockage.
• When you use additives, inspect the pump for leakage
once a month.
• Test the permeability of the static mixer (see Testing the
Static Mixer for Permeability (} page 166)).
• To avoid contamination of the degasser, prepare fresh
solvents, clean the solvent lines, and flush the degasser.
• Check that all warning labels are still present on the
device and clearly legible. If they are not, contact Thermo
Fisher Scientific for replacement.
Annually • Clean the check valves in an ultrasonic bath (see Cleaning
the Check Valves (} page 164)).
• Replace the seal wash seals (see Replacing the Seal Wash
Seals (} page 151)).
• Replace the seal wash lines (see Replacing the Seal Wash
Lines (} page 129)).
• Inspect the pistons for particle deposits or indications of
damage, for example, scratches or scores (see Cleaning
the Piston (} page 144)).
• Have Thermo Fisher Scientific service personnel perform
preventive maintenance once a year.
A maintenance kit is available for the pump, which includes all parts that
are required for routine maintenance (see Consumables and
Replacement Parts (} page 270)).
TIP The Chromeleon software supports functions for estimating the

lifetime of consumables (see Predictive Performance (} page 125)).

Operating Manual
7.4.3 Flushing the Pump to Avoid Contamination

Items required
Fresh solvent
Observe the following guidelines

The following guidelines refer to conventional use of the Vanquish
system as recommended in this manual, such as using fresh high-quality
solvents (minimum UHPLC-grade or LC/MS-grade) that are replaced
frequently:
• Regularly flushing the pump with fresh solvent is usually sufficient.
• If you use water, acetonitrile, or methanol for your chromatography,

flushing the pump once a week is an appropriate interval.
• Mobile phases containing salts, buffering agents and/or other

additives are inherently prone to organic contamination and/or
biodegradation. When using non-volatile buffers, observe the
following:
¨ Mobile phases must be filtered before use.
¨ For continuous trouble-free operation, the system must be
flushed with, for example, > 60 % isopropanol or ethanol as a
weekly procedure.
• Adapt the interval to the solvents in use.
TIP With persistent contamination, for example, if ghost peaks appear

reproducibly in your blank chromatogram without injecting a sample,
see Flushing the Pump with Persistent Contamination Only (} page 123).

Operating Manual
7.4.4 Flushing the Pump with Persistent Contamination Only

When
TIP With conventional use of the Vanquish system as recommended in

this manual, regularly flushing the pump is usually sufficient (see
Flushing the Pump to Avoid Contamination (} page 122)).
For example, if ghost peaks appear reproducibly in your blank

chromatogram without injecting a sample, consider a harsher cleaning
procedure. Follow the instructions below.
• Backpressure capillary (from Diagnostics tool kit)
• 6 molar (6 M) nitric acid (HPLC-grade)
• Waste container (for collecting the nitric acid)
• Fresh water (HPLC-grade)
• Fresh acetonitrile (HPLC-grade)
• New solvent reservoirs with fresh solvent
• New frits for solvent line filters
Follow these steps
to zero.
2. Install the backpressure capillary on the pump outlet. Guide the free
end of the capillary to the waste container.
3. Replace the frits in the solvent line filters with new frits.
4. Replace the installed waste container with the new waste container
to prevent any chemical reaction between the nitric acid and the
solvent in the waste container.
5. For 1 hour, apply the flow rate of your application and flush the
pump with 6 M nitric acid.
6. Flush the pump with fresh HPLC-grade water until the pH value is
neutral.
7. Remove the waste container with the nitric acid and re-install the
waste container that was installed previously.
8. For 2 hours, apply the flow rate of your application and flush the
pump with fresh acetonitrile.

Operating Manual
9. Connect the new solvent reservoirs, which contain fresh solvent.
to zero.
11. Uninstall the backpressure capillary and reconnect the system as

required by your application.
12. Purge the pump.
13. Equilibrate the system.
7.4.5 Cleaning or Decontaminating the Device

Cleaning and decontamination must be performed by qualified
personnel wearing suitable personal protective equipment. Always
observe national and local regulations.
NOTICE
Wipe up all liquids spilled onto the system immediately. If surfaces are
exposed for longer periods, these liquids can cause damage.
Decontamination
Decontamination is required, for example, when leakage or spillage has
occurred, or before service or transport of the device. Use a suitable
cleaning detergent or disinfectant to ensure that the treatment renders
the device safe to handle.
Parts required
• Suitable cleaning detergent (or disinfectant)
• Purified water
• Lint-free cloths or wipes
CAUTION—Explosive Gas Mixtures from Alcoholic Cleaning Detergents

Alcohol-containing cleaning detergents may form flammable and
explosive gas mixtures when exposed to air.
• Use such cleaning detergents only when required and only in
adequately ventilated rooms.
• Avoid open flames or exposure to excessive heat during the cleaning
process.
• Wipe the cleaned components thoroughly dry after cleaning. Do not
operate the device before it is completely dry.

Operating Manual
NOTICE
• Only use cleaning detergents that will not damage the surfaces of
the system.
• Never use sharp tools or brushes for cleaning any surfaces.
• Do not use sprays for cleaning.
• Prevent cleaning detergent from entering the flow path.
• Do not use excessively wetted cloth or wipes for cleaning. Prevent
any liquids from entering the functional components of the device.
Liquids can cause a short circuit when getting in contact with the
electronic components.
Preparations
1. Turn off the power to the device and disconnect the power cord
from the power source.
Follow these steps
1. Wipe the surfaces clean with a clean, dry, soft, lint-free cloth or
wipe. If necessary, slightly dampen the cloth or wipe with a solution
of lukewarm water and a suitable cleaning detergent.
2. Allow the cleaning detergent to react as recommended by the

manufacturer.
3. Wipe the cleaned surfaces with purified water to ensure that all
cleaning detergent residues have been removed.
4. Wipe the surfaces dry using a soft, lint-free cloth or wipe.
7.4.6 Predictive Performance

General Overview
The Chromeleon software supports functions for estimating the lifetime
of consumables and for monitoring and recording service and
qualification information about the device. These functions are called
Predictive Performance. They allow you to schedule maintenance
procedures based on the actual operating and usage conditions of the
device.
On special wellness, service, and qualification panels, you can define

intervals for replacing components that are subject to wear or stress and
for service procedures or qualification procedures. In addition, you can
set limits to alert you before and when the replacement, service, or
qualification is due.

Operating Manual
Color-coded bars on special panels provide visual feedback, allowing you

to easily check and monitor the status. If a warning limit was set, a
message in the Chromeleon Audit Trail alerts you when the action is
due.
Some counters can be reset to zero after the required action was
performed. To keep the Predictive Performance information up-to-date,
consider resetting the counter when a maintenance, service, or
qualification procedure has been performed.
For more information, refer to the Chromeleon Help.
Available Parameters for the Pump

The list shows the most important Predictive Performance counters for
the pump. Consider resetting these parameters after performing the
related maintenance procedure:
Predictive Performance To perform…

Command
CheckValvesServiceDone After replacement of the check valves.

For each pump head, a common counter is
available for all check valves (inlet check valves
and outlet check valves).
PistonsChanged After replacement of the pistons or pump head.
available for both pistons.
SealsChanged After replacement of the piston seals or pump
head.
available for all piston seals in the pump head.
MixerChanged After replacement of the static mixer.
QualificationDone After qualification procedures, for example,
Instrument Qualification or Performance
Qualification.
ServiceDone After annual maintenance by service personnel.

Operating Manual
7.5 Seal Wash System

Follow the sequence of steps for the maintenance procedure that you
want to perform:
• To test the seal wash system for leakage, follow the steps in Testing
the Seal Wash System for Leakage (} page 128).
• To replace the seal wash lines, follow the steps in Replacing the Seal
Wash Lines (} page 129).
• To replace the seal wash detector (drop detector), follow the steps
in Replacing the Seal Wash Detector (} page 132).
TIP To replace the seal wash seals, which are part of the pump head, see
Replacing the Seal Wash Seals (} page 151).

Operating Manual
7.5.1 Testing the Seal Wash System for Leakage

When
• At regular intervals
• When you installed the pump head during maintenance procedures
Items required
• Syringe (12 mL)
• Seal wash liquid
Follow these steps
No. Description

5. When about 10 mL of liquid are present in the syringe, release the
lever of the seal wash pump.
6. Press the lever firmly onto the tubing and press the liquid from the
syringe into the seal wash system.

Operating Manual
7. Check whether liquid escapes from the connections of the seal wash
system or under the pump heads.
Observation Remedial Action
Leakage is present Tighten or replace leaky connections. Repeat

the inspection.
No leakage is present Remove the syringe and reconnect the tubing
to the seal wash detector (port labeled in).
7.5.2 Replacing the Seal Wash Lines

When
• Damage or blockage of the seal wash lines
• Peristaltic tubing: Every 6 months as preventive maintenance for the

seal wash pump
• Other seal wash lines: Once a year
• Seal wash lines as required:

¨ Seal wash lines that connect the seal wash reservoir to the
peristaltic tubing in the pump
For more information, refer to the Operating Manual for the
Vanquish autosampler.
¨ Seal wash lines that connect the components in the pump
¨ Peristaltic tubing (PharMed tubing)
• Fresh seal wash liquid

For an overview of the seal wash system, see the picture in Setting Up
the Seal Wash System (} page 70).
Tools required
Tubing cutter (optional)
Preparations
1. Unscrew the cap of the seal wash reservoir and remove the seal
wash line together with the cap from the reservoir.
2. To empty the seal wash line, press down the lever of the seal wash
pump. Release the lever when the line is empty.

Operating Manual
Follow these steps
NOTICE
When you must remove a seal wash line from the tubing guides, be
careful not to pull on other tubing in the guides.
Follow the sequence of steps for the seal wash line that you want to
replace:
• For the seal wash lines that connect the seal wash reservoir to the
peristaltic tubing in the pump, follow the steps in the Operating
Manual for the Vanquish autosampler.
• For the peristaltic tubing, see Replacing the Peristaltic Tubing

(} page 130).
• For the seal wash lines from peristaltic tubing to the pump heads
and on to the seal wash detector, see Replacing the Seal Wash Lines
between the Peristaltic Tubing and the Seal Wash Detector
(} page 131).
Replacing the Peristaltic Tubing
Figure 33: Seal wash pump
No. Description
1 Pump lever
2 Pump rotor
3 Tubing holder (peristaltic tubing)
4 Tubing connector
5 Seal wash line from autosampler (silicone tubing)
6 Peristaltic tubing
7 Seal wash tubing to pump head (silicone tubing)

Operating Manual
1. Disconnect the peristaltic tubing from the tubing connectors that

connect it to the silicone tubing.
2. Press down the lever on the seal wash pump and remove the
peristaltic tubing from the pump and from the tubing holders.
3. Connect the new peristaltic tubing to the silicone tubing using the
tubing connectors. Cut tubing to required length, if applicable.
4. Insert the peristaltic tubing into the right tubing holder. Make sure
that the tubing connector rests on the tubing holder. Push the
tubing connector vertically down onto the holder if required.
5. Press down the lever on the seal wash pump and hold it in that
6. With your other hand, insert the tubing between the lever and the
rotor and wind it around the rotor.
7. Release the lever.
8. Insert the peristaltic tubing into the left tubing holder.
9. Check that the peristaltic tubing is inserted properly in the tubing

holders. If it is not, push the tubing into the holders. Make sure that
the tubing is not pinched or squeezed in the holders.
Restarting the Seal Wash System

cap.

3. Flush the seal wash system, using fresh seal wash liquid (see
Flushing the Seal Wash System (} page 76)).
Replacing the Seal Wash Lines between the Peristaltic Tubing and the Seal Wash Detector
1. Disconnect the seal wash tubing from the tubing connectors. Do not
remove the tubing connectors.
2. Connect the new seal wash lines.

Operating Manual

cap.

7.5.3 Replacing the Seal Wash Detector

When
• Contamination of detector electrodes
• Impaired functionality of the seal wash system
Parts required
Seal wash detector assembly, consisting of the detector and funnel
Preparations
To prepare the new seal wash detector assembly push the seal wash
detector into the funnel. Mind the orientation of the funnel.
1b
1a
Figure 34: Assembling the seal wash detector parts
No. Description
1a Funnel (bottom side)

1b Funnel (top side)

Operating Manual
Follow these steps
No. Description

3 Detector cable
4 Seal wash line
1. Disconnect the seal wash line from the seal wash detector (port
labeled in).
2. Unplug the detector cable from the DROP DET port.
3. Grasp and pull the seal wash detector assembly upward by the
funnel.
4. Push the new seal wash detector assembly into the pump.
Figure 36: Installing the seal wash detector assembly
5. Reconnect the seal wash line to the seal wash detector (port labeled
in).
6. Connect the detector cable to the DROP DET port.

Operating Manual
7.6 Pump Head

want to perform:
NOTICE
All pumps except VC-P21 and VC-P33: Whenever you remove the pump
head, you must replace the seal wash seals.
• To replace a pump head, see Replacing the Pump Head (} page 136).
• To replace a piston, see Replacing the Pistons (} page 142).
• To clean a piston, see Cleaning the Piston (} page 144).
• To replace the piston seals or support ring, see Replacing the Piston
Seals or Support Ring (} page 145).
• To replace the seal wash seals, see Replacing the Seal Wash Seals
(} page 151).
• To replace the pump head seals, see Replacing the Pump Head Seals
(} page 154).
• To test the pump for piston seal leakage, see Testing the Piston Seals
for Leakage (} page 156).
For an overview of the pump head parts, see Overview of Pump Head
Parts (} page 135).

Operating Manual
7.6.1 Overview of Pump Head Parts

The picture shows the main pump head parts.
Figure 37: Overview of pump head parts
No. Description
1 Inlet check valve, including:

1a Valve nut
1b Valve cartridge
2 Pump head
3 Pump head seals (2 PTFE O-ring seals)
4 Piston seals
5 Support rings
6 Seal wash bodies (pump head bushing)
7 Seal wash seals
8 Seal wash plate
9 Pistons
10 Outlet check valve, including:
10a Valve nut
10b Valve cartridge
11 Connectors for seal wash tubing (pluggable)
12 U-tube (capillary from working cylinder to equilibration cylinder)

Operating Manual
7.6.2 Replacing the Pump Head

When
Damage of pump head
Parts required
• Pump head
• Spacing tool (pump head tool)
Tools and additional items required
• Hexagon wrench, size 6
• Depending on the capillary that connects the pump head to the

purge/sensor unit:
¨ Viper capillary: Installation tool for Viper capillaries with torque
toothing
¨ Conventional capillary (non-Viper): Open-end wrench, size 1/4"
• Solvent suitable for purging to flush out harmful substances
• Solvent suitable for your application
Preparations
1. To flush out harmful substances, purge the pump with an

to zero.
Follow these steps
1. Remove the pump head. See Removing the Pump Head

(} page 137).
2. Install the pump head. See Installing the Pump Head (} page 138).

Operating Manual
7.6.2.1 Removing the Pump Head

Preparations
Prepare the pump for removing the pump head. See Replacing the Pump
Head (} page 136).
Follow these steps
Figure 38: Pump head
No. Description
1 Pump head inlet

2 Pump head screw
3 Pump head outlet
4 Seal wash tubing
2. As required by the pump type:
Pump Type Action
Binary pump Select the pump head for which you want to
Dual pump Select the pump for which you want to perform
the procedure.
Isocratic pump, quaternary pump Continue with the next step.
3. Undock the pistons either from the keypad or from the Chromeleon
software. Wait until undocking is complete before proceeding with
the next step.
4. Remove the capillary that connects the pump head to the purge/
sensor unit. Disconnect the capillary on both the pump head outlet
and the purge/sensor unit.

Operating Manual
5. On the pump head, disconnect the following tubing and capillaries:

¨ On the pump head inlet, disconnect the tubing.
¨ Remove the seal wash lines from the tubing connectors on the
pump head. Do not remove the tubing connectors.
6. Binary pump: Unplug the cable of the pressure sensor from the P-
WORK connector.
7. Loosen the pump head screw with the hexagon wrench.
8. Hold the pump head with one hand, remove the pump head screw,
and then remove the pump head by pulling it toward you.
9. It may happen that the seal wash plate remains in the pump when
you remove the pump head. Follow these steps:
a) Insert the spacing tool between the pump head and pump block.
b) Carefully pull the seal wash plate away from the pump block.
Figure 39: Removing the seal wash plate
7.6.2.2 Installing the Pump Head

Preparations
1. Remove the pump head. See Removing the Pump Head

(} page 137).
2. Before you begin, note the information for reinstalling pump heads
and installing new pump heads (replacement pump heads).
Reinstallation of pump heads (binary pump or dual pump only): Be sure
not to interchange the pump heads.
• Binary pump: To identify the correct installation position, note the

labeling on the pressure sensor cable (A for the left pump head or B
for the right pump head).

Operating Manual
• Dual pump: To identify the correct installation position, note the

labeling on the U-tube (capillary from working cylinder to
equilibration cylinder) (A for the pump head of the left pump or B
for the pump head of the right pump).
Installation of new pump heads (replacement pump heads)
• With binary pump and dual pump: New pump heads can be installed
in either position when installed for the first time. They have no
label on the pressure sensor cable or U-tube. For easier
identification during future maintenance, consider labeling them
according to the installation position (A for the left pump head or B
for the right pump head).
• To protect the pistons during shipment, the spacing tool is installed

between the seal wash plate and the pistons. Remove the spacing
tool. Be careful not to pull out the pistons any further.
Figure 40: Removing the spacing tool
No. Description
1 Seal wash plate

2 Spacing tool
3 Pistons
Follow these steps
1. Insert the pump head into the pump and tighten the pump head
screw (recommended torque: 10 Nm).
2. On the pump head, reconnect the following tubing and capillaries:

¨ On the pump head inlet, reconnect the tubing. Avoid cross-
threading.
¨ Connect the seal wash lines to the tubing connectors on the
pump head.
3. Reconnect the capillary that connects the pump head to the purge/
sensor unit. Observe the following:
Install the capillary in the direction of solvent flow (indicated by the
arrow on the capillary).

Operating Manual
4. Binary pump: Connect the cable of the pressure sensor to the P-

WORK connector.
5. Dock the pistons either from the keypad or from the Chromeleon
software. Wait until docking is complete before proceeding with the
next step.
6. Flush the seal wash system with seal wash liquid (see Flushing the
Seal Wash System (} page 141)).
7. Purge the pump using the solvent of your application.
8. Inspect all flow connections on the pump head for indications of

leakage. Tighten leaky connections when the system pressure is
down to zero.
9. In the Chromeleon software, consider updating the Predictive

Performance information for the pump head components.
10. Test the seal wash system and pump for leakage (see Testing the
Seal Wash System for Leakage (} page 128) and Testing the Pump
for Leakage (General Test) (} page 177)).
11. Recommended: From the Chromeleon software, perform

performance qualification for the pump:
¨ Run the pump-specific Performance Qualification tests (PQ
tests) (= Flow Precision Test and Gradient Accuracy Test). For
details, refer to the Operational and Performance Qualifications
manual.
¨ When the tests are completed, execute the QualificationDone
command.

Operating Manual
7.6.2.3 Flushing the Seal Wash System

When
To flush the seal wash system during pump head installation, follow the
steps in this section.
To flush the seal wash system for any other reason, see Flushing the Seal
Wash System (} page 76).
Follow these steps
No. Description

5. When about 10 mL of liquid are present in the syringe, release the
lever of the seal wash pump.

Operating Manual
7.6.3 Replacing the Pistons

When
Damage of piston
• Pistons
• Syringe filled with isopropanol
• Seal wash seals (and seal-handling tool)
NOTICE
Preparations
Remove the pump head (see Replacing the Pump Head (} page 136)).
Follow these steps
1. Remove the pistons:

¨ If the seal wash plate was removed together with the pump
head: Hold down the seal wash plate onto the pump head and
pull out the pistons.
¨ If the seal wash plate was removed separately: Pull out the
pistons from the seal wash plate.
2. When reinstalling a piston that you removed

Clean the piston. Follow the steps in Cleaning the Piston
(} page 144).
3. Replace the seal wash seals (see Replacing the Seal Wash Seals
(} page 151)).
4. To facilitate piston installation, inject a few drops of isopropanol into

the piston cavity in which you want to install the piston.

Operating Manual
5. Place the spacing tool onto the pump head.
Figure 42: Installing the spacing tool and pistons
No. Description
1 Pistons (in the picture, the piston bases are marked)

2 Spacing tool
6. Grasping the pistons by the piston base, push in the pistons until
they contact the tool.
7. Remove the spacing tool. Be careful not to pull out the pistons any
further.
8. Install the pump head (see Installing the Pump Head (} page 138)).
9. Flush the seal wash system with seal wash liquid (see Flushing the
Seal Wash System (} page 141)).
10. Purge the pump using the solvent of your application.
down to zero.

Performance information for the pistons.

manual.
command.

Operating Manual
7.6.4 Cleaning the Piston

When
Before reinstalling a piston that you removed
Items required
• Dry, lint-free tissue
• Light source
• Isopropanol
Follow these steps
1. Inspect the piston for signs auf damage.
TIP Hold the rear side of the piston into the light. The refraction of the
light makes dirt particles appear larger.
2. Even if the piston seems to be clean: Hold the piston and carefully
move your fingernail over the piston surface. You should not feel
inconsistent or rough areas.
3. Depends on the situation:
Situation Action
No damage visible, no inconsistent or 1. Carefully rinse the piston, using

rough areas isopropanol.
2. With a dry, lint-free tissue, rub the
piston several times.
3. Reinstall the piston.
Piston is scratched or scored Install a new piston.

Operating Manual
7.6.5 Replacing the Piston Seals or Support Ring

When
• Damage to piston seals, leaky seals
• Unstable flow rates or baseline noise
Parts required
• Piston seals
• Support ring
Note that the support ring is not a wear part. You need not replace
the support ring when you replace a piston seal. Replace the support
ring only when applicable.
NOTICE
• Cleaning swab
• Lint-free tissue
• Seal-handling tool
Figure 43: Seal-handling tool
No. Description
1 Seal removal pin

2 Seal insertion pin

Operating Manual
Preparations
1. Remove the pump head (see Replacing the Pump Head

(} page 136)).
2. Remove the pistons (see Replacing the Pistons (} page 142)).
Follow these steps
1. Remove the seal wash plate from the pump head if applicable.
Figure 44: Pump head, seal wash plate removed
No. Description
1 Pistons
2 Seal wash plate
3 Seal wash bodies
4 Support ring
2. Remove the seal wash bodies from the pump head.
3. Remove the support ring.

Gently tap the pump head on a clean work surface to make the
support ring drop out.
If the support ring does not drop out, use the seal-handling tool.
With the insertion pin, push the seal-handling tool at a slight angle
into the pump head and remove the tool. The support ring is
removed together with the tool.
NOTICE
Do not use the seal removal pin to remove the support ring. The support
ring can be removed from the tool only with difficulties.

Operating Manual
4. Remove the piston seal.

With the removal pin, push the seal-handling tool into the pump
head as far as it goes in and remove the tool. The piston seal is
removed together with the tool. Once the seal has been removed, it
cannot be reused.
5. Required if you reinstall the support ring

Clean the support ring from the inside and outside, using
isopropanol, a cleaning swab, and a lint-free tissue.
6. Pipette a few drops of isopropanol into cavity in the pump head, on

the edge on which the piston seal will rest.
Figure 45: Pump head (left: no piston seal installed, right: piston seal
installed)
No. Description
1 Edge on which the piston seal will rest

2 Piston seal installed
7. Slide the support ring onto the insertion pin of the seal-handling
tool.
8. Slide the piston seal onto the insertion pin, with the open side of the
seal facing away from the tool.
Figure 46: Support ring and piston seal on insertion pin
No. Description
1 Support ring
2 Piston seal (open side facing away from the tool)

Operating Manual
9. With the insertion pin, push the seal-handling tool into the pump
head as far as it goes in.
10. Remove the tool from the pump head. The piston seal and support
ring remain in the pump head.
Figure 47: Pump head, piston seals, and support rings installed
11. Insert the seal wash bodies into the pump head. Mind the correct
orientation. The even side faces the pump head.
Figure 48: Orientation of the seal wash body
No. Description
1 Side facing the seal wash plate

2 Side facing the pump head (even side)
12. Replace the seal wash seals. Follow the appropriate steps in
Replacing the Seal Wash Seals (} page 151).
13. Install the pistons. Follow the related steps in Replacing the Pistons
(} page 142).
15. Observe the recommendations for new piston seals (see

Recommendations for New Piston Seals (} page 149)).
down to zero.

Performance information for the piston seals.

Operating Manual

manual.
command.
7.6.6 Recommendations for New Piston Seals

When
When new piston seals have been installed
TIP The actions recommended in this section directly influence pump

performance and the piston seal life cycle.
Items required
• Backpressure capillary (length: 15 m) and Viper union (from the

Diagnostics tool kit)
• nanoViper™ capillary (length: 750 mm, inner diameter: 75 µm)
• Silicone tubing
• Isopropanol
Recommendations
• Allow new piston seals to run in.

• Never run the pump dry.
Running the pump dry can damage the pistons or piston seals.
Allowing New Piston Seals to Run In

4. Install the backpressure capillary on the pump outlet.

Operating Manual
5. With the Viper union, connect the nanoViper capillary to the

backpressure capillary. Guide the free end of the capillary to the
waste container.
6. Operate the pump. For 15 minutes, apply a flow of 1.3 mL/min using
isopropanol.
7. Close the purge valve by turning the valve knob clockwise.
8. Generate the necessary backpressure. For 30 minutes, apply the
flow indicated in the table using isopropanol.
Pump Type Flow Backpressure
VC-pumps 1 mL/min (approximately) 45 MPa (approximately)

VF-pumps 2 mL/min (approximately) 80 MPa (approximately)
to zero.
10. Remove the capillary from the pump outlet and reconnect the pump
to the system.
11. Purge the pump using the solvent for your application.
12. When purging is complete, empty the silicon tubing.
13. If an increased leakage rate is observed with new piston seals after
several hours of operation, operate the pump for at least 2 hours at
35 MPa.
TIP If the piston seals are not sufficiently tight yet, have the pump build
up high pressure and hold the pressure for some minutes.
NOTICE
outlet.

Operating Manual
7.6.7 Replacing the Seal Wash Seals

When
• Damage to the seal wash seal, leaky seal
• Whenever you removed the pump head
• Once a year
Parts required
Seal wash seals
Figure 49: Seal-handling tool
No. Description
1 Seal removal pin

2 Seal insertion pin
Preparations

(} page 136)).

Operating Manual
Follow these steps
Figure 50: Pump head, seal wash plate, and pistons removed
No. Description
1 Pump head
2 Seal wash plate, channel side
3 Seal wash seals
4 Pistons
2. Remove the seal wash seal.

On the seal wash plate (channel side), set the insertion pin of the
seal-handling tool at a slight angle to the seal. Push the seal out of
the plate and remove the tool.
Figure 51: Removing the seal wash seal
3. Slide the new seal onto the insertion pin of the seal-handling tool.
4. To facilitate seal installation, inject a few drops of isopropanol into

the seal cavities on the seal wash plate (no-channel side).
5. On the seal wash plate (no-channel side), set the insertion pin of the
seal-handling tool at a 90° angle to the plate and push the insertion
pin vertically into the plate as far as it goes in.

Operating Manual
6. Remove the tool from the seal wash plate. The seal remains in the
plate.
Figure 52: Seal wash plate (no-channel side)
No. Description
1 Seal wash plate (no-channel side)

2 Seal wash seals
7. Place the seal wash plate onto the pump head, with the seals facing
the pump head.
Figure 53: Pump head with seal wash plate installed
(} page 142).
down to zero.
12. If you also replaced the piston seals, proceed with the specific steps
further down.

Operating Manual
Specific Steps After Piston Seal Replacement

If you replaced the piston seals together with the seal wash seals,
proceed with these steps:
1. Observe the recommendations for new piston seals (see

Recommendations for New Piston Seals (} page 149)).

Performance information for the piston seals.

manual.
command.
7.6.8 Replacing the Pump Head Seals

When
Damage to pump head seals, leaky seals
• Pump head seals
NOTICE
Preparations

(} page 136)).
Follow these steps
2. Remove the seal wash bodies from the pump head if applicable.

Operating Manual
3. Remove the pump head seals.
Figure 54: Pump head seals
No. Description
1 Seal wash bodies

2 Pump head seal, O-ring 32x1.5
3 Pump head seal, O-ring 9x1.5
4. Install the new seals.

Place the seal onto the receiving groove. With your finger on the
seal, follow the groove shape until the seal rests exactly in the
groove.
5. Insert the seal wash bodies into the pump head. Mind the correct
orientation. The even side faces the pump head.
Figure 55: Orientation of the seal wash body
No. Description
1 Side facing the seal wash plate

2 Side facing the pump head (even side)
6. Replace the seal wash seals (see Replacing the Seal Wash Seals
(} page 151)).
(} page 142).

Operating Manual

down to zero.
7.6.9 Testing the Piston Seals for Leakage

When
• Pressure pulsation, shift in retention times, and/or poor
reproducibility can indicate possible piston seal leakage.
• If messages regarding piston seal leakage appear in the
chromatography software, for example, "The piston seal leakage
has exceeded the recommended limit (code 4121)".
• Backpressure capillary (from Diagnostics tool kit) (optional)
• Isopropanol
Follow these steps
1. From the Chromeleon software, start a seal wash cycle.
2. When the seal wash cycle is complete, disconnect the tubing from
the seal wash detector (port labeled in).
No. Description


Operating Manual
3. Remove some liquid from the tubing, for example, by shaking the
tubing.
4. Set up the system in such a way that the backpressure indicated in

the table is produced.
For example, install an appropriate backpressure capillary on the
pump outlet (outlet of the static mixer).
Pump Type Backpressure
VC-pumps 60 MPa (approximately)

VF-pumps 80 MPa (approximately)
5. Apply a flow rate of 2 mL/min using isopropanol.
6. To evaluate possible leakage, observe the liquid level in the tubing.

Finish the observation before a new seal wash cycle starts (after one
hour).
7. Depends on your observation:
Liquid level in the tubing remains The piston seals seal tightly. Reconnect the
unchanged seal wash tubing to the seal wash detector
(port labeled in). This completes the test.
Liquid level in the tubing is The seal wash seals are leaky:
decreasing 1. Replace the seal wash seals.
2. Reconnect the seal wash tubing to the seal
wash detector (port labeled in).
3. Repeat the test starting with step 1.
Liquid level in the tubing is One or more piston seals are leaky.
increasing Isocratic pump and quaternary pump:
1. Replace the piston seals in the pump head.
Binary pump and dual pump:
Continue with the next steps.
8. On the right pump head, remove the seal wash tubing that connects
the left pump head to the right pump head.
9. Depends on the pump type:
Pump Type Action
Binary pump Apply a flow rate of 2 mL/min for 100%

solvent A using isopropanol.
Dual pump Apply a flow rate of 2 mL/min for the left
pump using isopropanol.

Operating Manual
10. For about 5 minutes, observe the liquid level in the tubing. Finish the
observation before a new seal wash cycle starts.
11. Depends on your observation:
Liquid level in the tubing is 1. Replace the piston seals in the left pump
increasing again head.
2. Reconnect the seal wash tubing to the right
pump head.
Liquid level in the tubing does not 1. Replace the piston seals in the right pump
increase again head.
2. Reconnect the seal wash tubing to the right
pump head.
TIP If you observe leakage from a pump head, verify that the seal wash
tubing is properly connected to the pump head. If the tubing is not
properly connected or if the tubing is crimped or kinked, seal wash liquid
may leak into the pump.

Operating Manual
7.7 Check Valves

want to perform:
• To replace the inlet check valves, see the next section.
• To replace the outlet check valves, see Replacing the Outlet Check
Valves (} page 161).
• To clean the check valves, see Cleaning the Check Valves

(} page 164).
7.7.1 Replacing the Inlet Check Valves

The picture shows the parts that must be removed.
Figure 57: Replacing the inlet check valve
No. Description
1 Tubing on inlet check valve

2 Inlet check valve, including:
2a Valve nut
2b Valve cartridge
3 Pump head

Operating Manual
When
• Issue with the check valve that could not be solved by cleaning (for
example, persistent leakage)
• Damage of inlet check valve
Parts required
• Valve cartridge
• Valve nut, required only when leakage is present at the fitting

connection to the valve
• Open-end wrench, size 13 mm
• Tweezers, flat tips or curved tips
Preparations

to zero.
Follow these steps
1. On the valve nut, disconnect the tubing.
2. Use the open-end wrench to loosen and remove the valve nut from
the pump head.
3. Remove the valve cartridge:
Valve Cartridge Action
Valve cartridge removed together with Hold the nut over your hand and turn it
valve nut upside down to allow the cartridge to drop
into your hand.
Valve cartridge remained in pump Pull out the cartridge using the tweezers.
4. Insert the new cartridge into the valve nut. Insert the cartridge in
the direction of flow (indicated by the arrow on the cartridge).

Operating Manual
5. Screw the valve nut into the pump head and tighten with the open-
end wrench.
NOTICE
Overtightening may damage the valve cartridge. The torque should not
exceed 10 Nm.
6. On the valve nut, reconnect the tubing.
7. Rinse the pump thoroughly:

¨ Use the solvent for your application.
¨ Open the purge valve to prevent the rinsing liquid from entering
the Vanquish system.
8. Inspect the inlet check valve and fitting connection for indications of
down to zero.
9. Optional: Test the pump for leakage (see Testing the Pump for
Leakage (General Test) (} page 177)).
7.7.2 Replacing the Outlet Check Valves

The picture shows the parts that must be removed.
Figure 58: Replacing an outlet check valve (example, here VF-pump)
No. Description
1 U-tube
2 Outlet check valve, including
2a Valve nut
2b Valve cartridge
3 Pump head

Operating Manual
When
• Issue with the check valve that could not be solved by cleaning (for
example, persistent leakage)
• Damage of outlet check valve
Parts required
• Valve cartridge
• Valve nut, required only when leakage is present at the fitting

connection to the valve
• Open-end wrench, size 13 mm
• Tweezers, flat tips or curved tips
• Depending on the capillary connections:

¨ Viper capillary: Installation tool for Viper capillaries with torque
toothing
Preparations

to zero.
Follow these steps
1. Remove the capillary that connects the pump head to the purge/
sensor unit. Disconnect the capillary on both the pump head outlet
and purge/sensor unit.
2. Remove the U-tube.
3. Use the open-end wrench to loosen and remove the valve nut from
the pump head.

Operating Manual
4. Remove the valve cartridge:
Valve Cartridge Action
Valve cartridge removed together with Hold the nut over your hand and turn it
valve nut upside down to allow the cartridge to drop
into your hand.
Valve cartridge remained in pump Pull out the cartridge using the tweezers.
5. Insert the new cartridge into the valve nut. Insert the cartridge in
the direction of flow (indicated by the arrow on the cartridge).
6. Screw the valve nut into the pump head and tighten with the open-
end wrench.
NOTICE
Overtightening may damage the valve cartridge. The torque should not
exceed 10 Nm.
7. Reinstall the U-tube.
8. Reconnect the capillary that connects the pump head to the purge/
sensor unit. Observe the following:
Install the capillary in the direction of solvent flow. Note that one
end of the capillary is longer than the other end. Connect the longer
end to the pump head.
9. Rinse the pump thoroughly:

¨ Use the solvent for your application.
¨ Open the purge valve to prevent the rinsing liquid from entering
the Vanquish system.
down to zero.
11. Optional: Test the pump for leakage (see Testing the Pump for
Leakage (General Test) (} page 177)).

Operating Manual
7.7.3 Cleaning the Check Valves

The cleaning procedure includes the following:
• Ultrasonic cleaning with pure isopropanol
• Running-in the check valves in the pump at high backpressure
When
• Dirty or malfunctioning check valves
• Once a year
• Syringe (12 mL), filled with isopropanol
• Small beaker filled with isopropanol
• Ultrasonic bath
• Solvents suitable for your application (for purging)
• Solvents suitable for the run-in procedure

In most cases, you can use the solvents of your application. To avoid
electrostatic discharge in the backpressure capillary, at least 20%
water should be present in the 50/50 mixture of solvents A and B. If
you are using water-free solvents like normal-phase solvents, use
80% isopropanol in water on both, channel A and channel B.
• Backpressure capillary
You can use any Viper capillary that can generate the backpressure
indicated in the table with a flow rate between 1 mL/min and
4 mL/min. For example, you can connect the two Viper capillaries
(length: 15 m each) from the Diagnostics tool kit with the connection
union to obtain a 30 m capillary with 180 µm inner diameter.
Pump Requested Backpressure Approximate Flow Rate*
VC-pump Approximately 62 MPa Approximately 1.2 mL/min

VF-pump Approximately 92 MPa Approximately 1.8 mL/min
* Approximate flow rate with 80% isopropanol in water and 30 m capillary with
180 µm inner diameter
Preparations
Remove the check valves that you want to clean.
Recommended: Clean the inlet check valves and outlet check valves of all
pump heads at the same time. To remove the check valves, follow the
steps in Replacing the Inlet Check Valves (} page 159) and Replacing the
Outlet Check Valves (} page 161).

Operating Manual
Follow these steps
1. In the direction of flow, fill the check valves with isopropanol, using
the syringe.
2. Place the check valves in the beaker. Clean them in the ultrasonic
bath for 10 minutes.
3. In the direction of flow, flush the check valves with isopropanol,

using the syringe.
4. Reinstall the check valves. Follow the steps in Replacing the Inlet
Check Valves (} page 159) and Replacing the Outlet Check Valves
(} page 161).
5. Install the backpressure capillary on the pump outlet. Guide the free
end of the capillary to the waste container.
6. Have the pump deliver the solvents suitable for the run-in
procedure: Start with 50% B and a flow rate of 1 mL/min. Increase
the flow rate until the system pressure is well above 60 MPa
(VC-pump) or 90 MPa (VF-pump) and run the pump for 20 minutes.
7. Inspect the pump heads and check valves for indications for leakage.
Tighten leaky connections only when the system pressure is down to
zero.
8. Uninstall the backpressure capillary and reconnect the pump as

required by your application.
9. Purge the pump, using the solvents of your application.
10. Test the pump for leakage (see Testing the Pump for Leakage
(General Test) (} page 177)).

Performance information for the check valves.

Operating Manual
7.8 Mixing System

TIP The information and references to the static mixer in this section
apply equally to the inline filter if installed.
want to perform:
• To test the static mixer for permeability, see Testing the Static Mixer
for Permeability (} page 166).
• To replace the static mixer or capillary mixer, see Replacing the

Static Mixer or Capillary Mixer (} page 167).
7.8.1 Testing the Static Mixer for Permeability
TIP With the dual pump, test each static mixer separately.
When
If you observe pressure pulsation, inconstant pressure, or high
backpressure at the column and pump
Additional items required
• Water as solvent
• Tissue
Follow these steps
NOTICE
Turning the static mixer in the mounting bracket when loosening or
tightening capillaries can damage the mounting bracket.
To prevent the mixer from turning in the bracket, hold the mixer with an
open-end wrench when you loosen or tighten capillaries on the mixer.
1. Disconnect the capillary on the outlet of the static mixer.
2. To absorb liquid leaving the static mixer, place the tissue on the
mixer outlet.
3. Apply a flow of 2 mL/min using water.
4. Observe the pump pressure.

Operating Manual
5. Depends on the pressure reading:
Pressure Reading Action
Pressure is less than 0.8 MPa Continue with the next step.

Pressure is 0.8 MPa or higher Replace the static mixer.
6. Reconnect the capillary to the outlet of the static mixer.
7. Test the pump for leakage. See Testing the Pump for Leakage
(General Test) (} page 177).
7.8.2 Replacing the Static Mixer or Capillary Mixer

When
• Impaired permeability of the static mixer
• Damage of static mixer
• Leaky capillary mixer
Parts, tools and additional items required
• As applicable
¨ Static mixer
¨ Capillary mixer
• Depending on the capillary connection:

¨ Viper capillary: Viper knurl (usually present on the capillary)
• Solvent suitable for purging
Preparations

2. To remove harmful substances from the components in the flow

path after the purge unit, have the pump deliver for a short time
with the solvent that was used for purging.
to zero.

Operating Manual
Follow these steps
NOTICE
1. On the static mixer outlet, disconnect the capillary that connects the
static mixer to the autosampler injection valve.
2. Disconnect the capillary mixer on the purge/sensor unit.
3. Pull the static mixer out of the mounting bracket.
4. Remove the assembly of static mixer and capillary mixer from the
pump.
5. Disconnect the capillary mixer from the static mixer.
6. Connect the capillary mixer to the static mixer.

Mind the direction of flow through the static mixer and capillary
mixer (indicated by the arrow on the mixer).
7. Insert the assembly of static mixer and capillary mixer into the
pump.
8. Insert the static mixer into the mounting bracket.
9. Connect the capillary mixer on the purge/sensor unit.
10. On the static mixer outlet, connect the capillary to the autosampler
injection valve.
11. Apply the flow rate of your application and have the pump deliver
for a short time.
12. Inspect the flow connections on the mixer for indications of leakage
before resuming operation.
13. When the static mixer has been replaced: In the Chromeleon
software, consider updating the Predictive Performance information
for the static mixer (MixerChanged command).

Operating Manual
7.9 Solvent Lines and Solvent Line Filters

want to perform:
• To empty the solvent lines, see Emptying the Solvent Lines

(} page 169).
• To replace solvent lines, see Replacing Solvent Lines (} page 170).
• To replace the solvent line filter, see Replacing the Solvent Line Filter
(} page 173).
7.9.1 Emptying the Solvent Lines

When
To empty the solvent lines, for example, for maintenance or service
procedures
Parts required
• Silicone tubing
• Syringe
Preparations
to zero.
2. Prepare the pump for purging (see Purging the Pump (} page 100)).
Follow these steps
2. Start a purge cycle as appropriate.
3. Stop purging as soon as the solvent line is empty.

Operating Manual
7.9.2 Replacing Solvent Lines

To replace solvent lines, follow the sequence of steps for the solvent line
that you want to replace.
The flow path determines the pump inlet (component at which the
solvent enters the pump) and the solvent flow through the pump.
Pump Type Pump Inlet
Binary pump The pump inlets are the solvent selectors.

Isocratic pump The pump inlet is the pump head.
Quaternary pump, The pump inlet is the vacuum degasser.
dual pump
For the pump-specific operating principles that illustrate the solvent

flow through the pump, see Pump-Specific Information (} page 215).
• Solvent line from the solvent reservoir to the pump inlet: Follow the
steps in Solvent Lines From Reservoir To Pump Inlet (} page 171).
• Depending on the pump type

Solvent line from the pump inlet to the proportioning valve or
degasser: Follow the steps in Solvent Lines From Pump Inlet to
Proportioning Valve or Degasser (} page 171).
• Depending on the pump type

Solvent line from the proportioning valve or degasser to the pump
head: Follow the steps in Solvent Line From Proportioning Valve or
Degasser To Pump Head (} page 172).

Operating Manual
7.9.2.1 Solvent Lines From Reservoir To Pump Inlet

When
Damage or blockage of the solvent line

• Solvent line between solvent reservoir and pump inlet
Preparations

2. Empty the solvent lines (see Emptying the Solvent Lines

(} page 169)).
Follow these steps
1. Remove the solvent line from the reservoir cap:

a) Remove the filter from the solvent line.
b) Remove the retaining guide.
c) Pull the solvent line out of the reservoir cap.
2. Disconnect the solvent line on the pump inlet.
3. Remove the solvent line from the pump and all modules above the
pump in the system stack. When removing the solvent line from the
tubing guides, do not pull on other tubing in the guides.
4. To install the new solvent line, follow the related steps in Connecting
the Solvent Lines (} page 63).
7.9.2.2 Solvent Lines From Pump Inlet to Proportioning Valve or Degasser

This section applies to all pumps except the isocratic pump.
When
• Solvent line between pump inlet and proportioning valve or

degasser inlet, as applicable for the pump

Operating Manual
Preparations
• Empty the solvent lines (see Emptying the Solvent Lines

(} page 169)).
Follow these steps

cap.
2. Remove the solvent line on the pump inlet and on the degasser.
3. Install the new solvent line.
7.9.2.3 Solvent Line From Proportioning Valve or Degasser To Pump Head

This section applies to all pumps except the isocratic pump.
When
• Solvent line between proportioning valve or degasser and pump

head inlet, as applicable for the pump
Preparations
• To flush out harmful substances, purge the pump with an

Follow these steps
1. Remove the solvent line on the proportioning valve or degasser and

on the pump head inlet.
2. Install the new solvent line.

Operating Manual
7.9.3 Replacing the Solvent Line Filter

When
• Damage of solvent line filter
• Impaired permeability of filter frit
Figure 59: Solvent line filter
No. Description
1 Solvent line filter, filter holder bottom part

2 Filter frit
3 Solvent line filter, filter holder top part
• As applicable:
¨ Filter holder
¨ Filter frit
Preparations
to zero.
Follow these steps
2. Remove the filter holder from the solvent line.
3. As applicable: Open the filter holder and remove the filter frit.

Operating Manual
4. Assemble the solvent line filter, wearing appropriate clean gloves:

a) Place the frit in a level position in the filter holder (bottom part).
b) Screw the filter top to the filter bottom.
5. Slide the filter holder onto the solvent line.

cap.

Operating Manual
7.10 Replacing the Purge Valve Knob

When
• Leakage is observed around the valve knob when the valve is open.
• Leakage is observed on the purge outlet when the valve is closed.
Parts required
Purge valve knob (with integrated seals)
Figure 60: Purge valve knob with integrated seals
No. Description
1 Purge valve knob

2 Ring seal
3 Cap seal
NOTICE
Avoid holding the new valve knob by the seal end. Scratches on the seals
will prevent a proper seal and cause leakage.
• Cleaning swab
Preparations

to zero.

Operating Manual
Follow these steps
1. To remove the purge valve knob from the purge/sensor unit, turn
the valve knob counterclockwise all the way and pull it straight off
the purge/sensor unit.
2. Before installing the new purge valve knob, clean the opening in the
purge/sensor unit with a cleaning swab.
3. Insert the new purge valve knob into the purge/sensor unit.
4. To tighten, turn the valve knob clockwise with your fingers until it is
finger-tight.
NOTICE
Turn the valve knob only with your fingers. Overtightening may damage
the purge valve seals.
5. Resume operation.
6. Inspect the purge outlet. If liquid leaves the outlet, the valve knob
may not be tightened enough. Tighten a little more.

Operating Manual
7.11 Testing the Pump for Leakage (General Test)

When
Following maintenance on the fluidic system of the pump, such as the
flow connections, pump heads, or check valves
To Test the Pump

The following tests are available:
Test Description
Automatic testing See Automatic Testing (} page 177).

Prerequisite: The chromatography data
system supports tightness testing for the
Vanquish system configuration.
Manual testing See Manual Testing (} page 178).
7.11.1 Automatic Testing

Automatic testing means that the test runs automatically without
further user interaction. The test checks the tightness of the pump and
autosampler.
Prerequisite
A compatible chromatography data system that supports basic tightness
testing for the configuration of your Vanquish system
Follow these steps
1. In the chromatography data system, run the Basic Tightness Test

from the Diagnostic Tests menu.
2. If the test fails, check the Instrument Audit Trail for a message.
3. Take remedial action as suggested for the message in the

Troubleshooting section of Operating Manual for the module for
which the test failed.

Operating Manual
7.11.2 Manual Testing

If the Basic Tightness Test is not available in the chromatography data
system for your Vanquish system configuration, test the pump manually.
Manual testing requires user interaction.
TIP With the dual pump, test each pump separately.
• Fitting plug, Viper
Follow these steps
1. Disconnect the capillary on the pump outlet.
2. Close the pump outlet with the fitting plug.
3. In the chromatography data system, set the upper pressure limit to

the appropriate value:
Pump Upper Pressure Limit
VC‑pump 60 MPa
VF‑pump 80 MPa
4. Apply a flow of 50 µL/min and use the solvent for the application.
5. Observe the pressure. When the pressure reading is as indicated in

the table, change the flow rate to a lower value.
Pump Pressure
VC‑pump Between 30 MPa and 40 MPa

VF‑pump Between 60 MPa and 70 MPa
6. Have the pump deliver until the following pressure has built up:
Pump Pressure
VC‑pump 55 MPa
VF‑pump 75 MPa

Operating Manual
7. When the pressure has built up, apply the following flow:
Pump Flow
Standard pump
VC‑P10, VC‑P20, VC‑P32, VC‑P40 1 µL/min
VC‑P21, VC‑P33 4 µL/min
VF‑pump 1 µL/min
Pump modified for NP applications
VC-P20, VC-P21, 4 µL/min
VC-P32, VC-P32, VC‑P40
VC-P10 6 µL/min
8. Observe the pressure.

The pressure should increase or remain constant for a minimum of
1 minute. A drop in pressure indicates possible leakage.
9. Find and eliminate the cause for the leak.

Take remedial action only when the system pressure is down to
zero.
Possible Source Remedial Action
Capillary connections Inspect the capillary connections for signs of leakage.

Tighten or replace leaky connections when the system
pressure is down to zero.
Piston seals • Test the piston seals for leakage. Replace leaky piston
seals.
• If leakage is observed with new piston seals, run in the
seals. Using the solvent of your application or water,
operate the pump for 2 hours or longer at 35 MPa.
Check valves • If leakage is observed on the connection port, turn off
the pump flow. When the system pressure is down to
zero, tighten the check valve a little more.
• Remove the valve cartridge. Clean the cartridge in an
ultrasonic bath. If cleaning is not sufficient, replace the
cartridge.
Purge valve knob Inspect the purge valve knob and purge outlet for
indications of leakage.
10. After taking a remedial action, test the pump.

Testing the Pump
1. Pressure up the pump.

This is the best way to identify whether a connection is leaky.
2. Allow 5 minutes for the pressure to stabilize.

This is important. The pressure drops faster during the first 5
minutes until the seals and other components have adjusted to the
pressure.

Operating Manual
3. After the stabilization time, monitor the pressure drop.
4. Tighten the connection that you want to test a little more. The
pressure will suddenly increase a little.
5. Monitor if the pressure drops at the same rate as before. If the

pressure drops significantly slower, the connection was leaky.
6. When testing the pump for leakage is complete, reset the upper
pressure limit to the value used before the leakage test.

Operating Manual
7.12 Replacing the Main Power Fuses

When
Blown fuses
Parts required
Fuses (2 fuses, 3.15 AT, 250 V AC, slow-blow, 5 x 20 mm) from Fuses Kit
Tools required
Slotted screwdriver, any size between 3.3 mm and 5.5 mm is
appropriate
Preparations
WARNING—Electric Shock
shock or damage to the device.
• Turn off the device with its main power switch. Disconnect the
power cord from both the power source and the device.
• Use only the fuses of the type and current rating specified for the
device by Thermo Fisher Scientific.
• Do not use repaired fuses and do not short-circuit the fuse holders.
Follow these steps

The fuse holder is located next to the main power switch.
Figure 61: Fuse holder
No. Description
1 Main power switch (on/off control)

2 Fuse holder
3 Power-inlet connector

Operating Manual
1. Use the screwdriver to remove the fuse holder.
2. Replace the two fuses with new fuses of the specified type and
current rating. Always replace both fuses.
3. Reinstall the fuse holder.
4. Reconnect the power cord to the power source and to the device.
5. Turn on the device with the main power switch.

Operating Manual
7.13 Updating the Device Firmware

The description in this section refers to the Chromeleon 7
Chromatography Data System.
When
Updating the device firmware might be required, for example, when a
new firmware version is released that adds functionality or solves
problems of a previous version.
Items required
Firmware version/Chromeleon version as appropriate
TIP When a new firmware version is released, the new version will be
included in the next available Chromeleon version. The new firmware
will not be transferred automatically to the device when you install the
Chromeleon version.
Preparations
1. Read the release notes provided with the firmware and/or
Chromeleon version.
2. Connect the device in the Chromeleon software.
3. Stop all operations on the Instrument that includes the device.
4. Wait until the Instrument is idle.
to zero.
Follow these steps
1. Start the Instrument Configuration Manager program.

2. Perform a firmware update from the General tab page in the
configuration dialog box for the device. For details, refer to the
Chromeleon Help.
The firmware update may take several minutes.
NOTICE
A firmware downgrade or incomplete firmware update may result in loss
of functionality or malfunctioning of the device.
• Do not interrupt communication between the Chromeleon software
and the device at any time during the procedure.
• At the beginning of the update process, a message appears showing
the firmware version currently installed in the device and the
version that will be transferred from the Chromeleon software. If
the firmware installed in the device is a later version than the
version in the Chromeleon software, cancel the download.

Operating Manual
3. Monitor the Audit Trail of the Instrument Configuration Manager

program to see whether the firmware update was successful or
failed.
4. Depends on the situation:
Situation Action
Firmware update successful Requalification of the device may be

required. Refer to the release notes.
Firmware update failed Turn the device off and on again. Repeat
the firmware update.
Firmware update fails repeatedly Contact Thermo Fisher Scientific
Technical Support.

Operating Manual
7.14 Replacing the Doors

When
Damage of door
TIP The maintenance procedures do not require that you remove the
doors. If this should ever be required for a specific reason or procedure,
follow the steps in this section.
Parts required
Replacement door
Preparations
If the door to be replaced is located directly below the solvent rack,
remove all reservoirs from the solvent rack.
If the display is installed next to the door to be replaced, consider
loosening the fastening block of the display to push the display toward
the system rear.
Follow these steps
NOTICE
To avoid damage to the door hinges, be careful when performing the
following sequence of steps and do not apply force.
1. If the door is located directly below the solvent rack, lift the solvent
rack slightly on the front edge.
2. To remove a door, push the door upward while opening.
Open the door to a position in which the two hinges on the housing
are aligned in the grooves on the door. You can remove the door
only when the hinges are in the grooves.
Figure 62: Unhinging a door
No. Description
1 Hinge on the housing

2 Reception groove on the door

Operating Manual
3. Slightly tilt the door to the outside, away from the housing, and
remove the door.
4. To install the door, align the door with the hinges on the housing. Do
not clamp tubing or capillaries between the door and the enclosure.
5. Insert the hinges in the groove, by pushing up and slightly turning

the door.
6. Push the door downward to lock it in place.

You can close the door only when it is properly installed.

Operating Manual
7.15 Transporting or Shipping the Device

If you want to transport the device to a new location or if you need to
ship the device, first prepare the device for transport, and then move or
ship the device as required. Follow the instructions in this section.
Observe the following safety guidelines:

guidelines:
Follow these steps
1. Prepare the device for transport. See Preparing the Device for
Transport (} page 187).
2. The step depends as follows:

¨ To transport the device to a new location, follow the instructions
in Transporting the Device to a New Location (} page 188).
¨ To ship the device, follow the instructions in Shipping the Device
(} page 189).
7.15.1 Preparing the Device for Transport

To prepare the device for transport, follow these steps:
1. Perform a long-term shut down of the device (see Long-Term

Shutdown (} page 111)).
2. Turn off the device with its main power switch and disconnect the
power cord.
3. Remove all cables and flow connections to other devices.
4. Close open flow connections with appropriate plugs, for example,

the plugs you removed when setting up the pump.

Operating Manual
5. Check the leak tray and drain port. If liquid is present, absorb the
liquid with a tissue.
6. Remove the device or slide-in module from the system stack as

required:
Install the carrying handles and remove the device from the
Vanquish system. Follow the instructions on dismounting the system
stack in the Transporting or Shipping the System section of the
Vanquish System Operating Manual.
‑or‑
Remove the slide-in module from the device enclosure in the system
stack (see Removing the Slide-In Module (} page 190)).
7.15.2 Transporting the Device to a New Location

Preparations
Prepare the device for transport. See Preparing the Device for Transport
(} page 187).
Follow these steps
1. Observe the notes for handling and lifting the device safely.
2. Transport the device to the new location.
3. Install and set up the device in the system stack. Follow the
instructions on mounting the system stack in the Vanquish System
Operating Manual.
4. Set up the device:

a) Connect the device and set up flow connections (see Installation
(} page 45)).
b) Prepare the device for operation (see Preparing the Device for
Operation (} page 92)).
5. Before starting an analysis, let the device equilibrate and be sure

that it is ready for operation.

Operating Manual
7.15.3 Shipping the Device

Preparations
Prepare the device for transport. See Preparing the Device for Transport
(} page 187).
CAUTION—Possible Contamination
Hazardous substances may have contaminated the device during
operation and may cause personal injury to service personnel.
• Decontaminate all parts of the device that you want to return for
repair.
• Fill in and sign the Health and Safety Form. Thermo Fisher Scientific
refuses to accept devices for repair if the Health and Safety Form is
missing, incompletely filled in, or unsigned.
Follow these steps
1. Follow the unpacking instructions in this manual in the reverse

order.
Use only the original packing material and shipping container. If the
original shipping container is not available, appropriate containers
and packing material can be ordered from the Thermo Fisher
Scientific sales organization.
2. If you need to return the device to Thermo Fisher Scientific for depot
repair, contact your local Thermo Fisher Scientific support
organization for the appropriate procedure.
Restarting the Device after Shipping

To install the device after shipping, follow the instructions on mounting
the system stack in the Vanquish System Operating Manual.

Operating Manual
7.16 Replacing the Slide-In Module

You can remove the slide-in module from the enclosure of a module for
transporting or shipping purposes. The enclosure remains in the system
stack. To return a defective module to the factory, install the slide-in
module in the enclosure of the replacement module.
7.16.1 Removing the Slide-In Module

guidelines:
Tools required
Screwdriver, Torx T20
Preparations
1. Prepare the device for transport. See Transporting or Shipping the

Device (} page 187).
Follow these steps
1. Loosen the four captive screws on the front left and front right of
the device.
Figure 63: Captive screws on the slide-in module

Operating Manual
2. Push all tubing and capillaries, which are present in the tubing chase
of the Vanquish system modules, into the tubing chase. Otherwise,
you will not be able to remove the slide-in module properly from the
enclosure in the next step.
3. Grasp the slide-in module by the leak tray and pull the module out
of the enclosure by approximately 10 cm.
Figure 64: Pulling out the slide-in module
NOTICE
The slide-in module can fall down when pulling it out of the enclosure
too far.
Pull out the slide-in module just far enough so that you can grasp it on
both sides from below.
4. Remove the slide-in module from the enclosure. The following steps
require a team effort:
a) Take the slide-in module on both sides from below.
b) Pull the slide-in module from the rails towards the front.
c) Place the slide-in module on a clean and stable surface.

Operating Manual
7.16.2 Returning the Slide-In Module
CAUTION—Possible Contamination
Hazardous substances may have contaminated the device during
operation and may cause personal injury to service personnel.
• Decontaminate all parts of the device that you want to return for
repair.
• Fill in and sign the Health and Safety Form. Thermo Fisher Scientific
refuses to accept devices for repair if the Health and Safety Form is
missing, incompletely filled in, or unsigned.
Preparations
Remove the slide-in module from the enclosure. See Removing the Slide-
In Module (} page 190).
Follow these steps
1. Install the slide-in module to the enclosure of the replacement

device. Follow the steps for inserting the slide-in module in the
enclosure and tightening the captive screws in Installing the Slide-In
Module (} page 192).
2. Follow the instructions in Shipping the Device (} page 189).
NOTICE
Shipping the slide-in module improperly leads to damage to the device.
Always ship the slide-in module as described in this operating manual.
7.16.3 Installing the Slide-In Module

guidelines:
Tools required
Screwdriver, Torx T20

Operating Manual
Preparations
1. Unpack the replacement device. Remove the slide-in module from

its enclosure as described in Removing the Slide-In Module
(} page 190).
2. Verify that the device enclosure into which the slide-in module shall
be installed is clean. If required, clean the inner and outer surfaces
of the enclosure. See Cleaning or Decontaminating the Device
(} page 124).
3. When installing the slide-in module to an enclosure in the system

stack, check that the enclosure is placed correctly in the stack.
Follow these steps
1. Push all tubing and capillaries, which are present in the tubing chase
of the Vanquish system modules, into the tubing chase. Otherwise,
you will not be able to insert the slide-in module properly into the
enclosure in the next step.
2. On the slide-in module, check that you can move the captive screws
back and forth with your fingers. If you cannot, screw them in until
you can.
3. Insert the slide-in module in the enclosure. The following steps

require a team effort:
a) Take the slide-in module on both sides from below.
b) Lift the slide-in module to the height of the enclosure.
c) Place the slide-in module in the enclosure so that the module
sits in the enclosure by approximately 25 cm.
d) Push the slide-in module onto the rails and into the enclosure
until the slide-in module sits completely in the enclosure.
Figure 65: Inserting the slide-in module

Operating Manual
4. To facilitate tightening the slide-in module in the enclosure, pull out

the module a few millimeters (approximately 2 to 5 mm).
5. With the screwdriver, move each captive screw back and forth while
pressing inward until the screw slips into the thread.
6. Push the slide-in module back into the enclosure as far as it goes in.
7. Gradually and evenly, tighten the four captive screws on the slide-in
module hand-tight.
NOTICE
• Verify that the screws are tightened. Pull the slide-in module by the
leak tray towards the front and check whether the screws move. If
they do not move, the slide-in module is installed properly.
• If the screws move, tighten the screws further. With a torque
wrench, the recommended torque is 1.2 Nm.
8. Set up and restart the module.
7.16.4 Setting Up the Slide-In Module

After you have installed the slide-in module in the enclosure, set up and
restart the device.
Follow these steps
1. Set up the slide-in module:

a) Connect the slide-in module and set up flow connections (see
Installation (} page 45)).
b) Prepare the slide-in module for first-time operation (see
Preparing the Device for Operation (} page 92)).
c) If you installed a replacement slide-in module, update the
instrument configuration in the chromatography data system
accordingly.
2. Prepare all other modules of the Vanquish system for operation and
restart them. Refer to the Operating Manuals for the modules.
3. Before starting an analysis, let the chromatography system

equilibrate and be sure that it is ready for operation.

Operating Manual
4. From the Chromeleon software, perform performance qualification

for the pump:
manual.
command.

Operating Manual

Operating Manual
8 • Troubleshooting
8 Troubleshooting
This chapter is a guide to troubleshooting issues that may arise during
operation of the device.

Operating Manual
8.1 General Information about Troubleshooting

The following features help you to identify and eliminate the source for
problems that may arise during operation of the device.
NOTICE
When the Vanquish system includes a Vanquish charged aerosol
detector, the detector may affect the operation and/or performance of
the pump. For example, errors in the detector may affect the pump by
automatically stopping the pump flow. For more information, refer to
the Operating Manual for the detector.
TIP For information about operating issues that might occur during the
operation of a Vanquish system, refer to the Vanquish System Operating
Manual.
If you are unable to resolve a problem following the instructions given

here or if you experience problems that are not covered in this section,
contact Thermo Fisher Scientific Technical Support for assistance. See
the contact information at the beginning of this manual.
To facilitate device identification, have the serial number and technical

name available when communicating with Thermo Fisher Scientific.
Status Indicators
The status indicator LED bar on the front side of the device and the
STATUS LED on the keypad inside provide quick visual feedback on the
operational status of the device. If the device firmware detects a
problem, the status indicators are red.

pump block.
Alarms
Leaks are a potential safety issue. Therefore, if a leak sensor detects
leakage, beeping starts to alert you in addition to the message in the
Instrument Audit Trail and the status indicators changing to red. Follow
the instructions in this manual to find and eliminate the source for the
leakage.

Operating Manual
Instrument Audit Trail Messages

If the device firmware detects a problem, the problem is reported to the
chromatography data system.
The data system logs information about all events related to instrument
operation for the current day in an Instrument Audit Trail. The
Instrument Audit Trail is named with the current date, using the format
yyyymmdd. For example, the Instrument Audit Trail for May 15, 2019, is
named 20190515.
The Instrument Audit Trails can be found on the ePanel Set (Audit
ePanel). In addition, Audit Trails for each instrument are available in the
Chromeleon 7 Console Data view, in the folder of the Instrument.
Messages in the Instrument Audit Trail are preceded by an icon. The icon
identifies the seriousness of the problem. For possible causes and
remedial actions, see Messages (} page 200).
Firmware Failure
If a firmware failure occurred during operation of the module, an
exception log has been created about the processes during the firmware
failure. The firmware sends the exception log to the Instrument Audit
Trail when the module is connected in the chromatography data system.
In this case, observe the following:
• Send the Instrument Audit Trail as .cmbx file to the Technical

Support before you clear the log.
• To clear the exception log and continue operation of the module,

perform the command ExceptionLogClear.
For more information, refer to the Chromeleon Help.

Operating Manual
8.2 Messages
This section provides information about the messages that may appear
in the Instrument Audit Trail during operation of the pump. For easier
identification of the source for a problem, note the Device information
that may appear in front of the message:
Device Information Description
[Main Device Name] With messages relating to the entire pump, for example, to
the leak detection, main board or with a communication
error
[Pump Device Name] With messages relating to the entire flow unit, for example,
to the system pressure
[Pump Device With messages relating to the right pump block or
Name]_ components in the right pump head, for example, the
Wellness_RightBlock pistons or check valves.
[Pump Device With messages relating to the left pump block or
Name]_ components in the left pump head, for example, the pistons
Wellness_LeftBlock or check valves.
The Device Names are specified in the dialog box for the pump in the
Instrument Configuration Manager. The default names are:
Pump Device Name Default Name
Binary pump, [Main Device Name] PumpModule

Isocratic pump,
[Pump Device Name] Pump
Quaternary pump
Dual Pump Main [Device Name] PumpModule
Left [Pump Device Name] PumpLeft
Right [Pump Device Name] PumpRight
The table lists the most frequently observed messages for the device
and provides troubleshooting assistance.
Each message consists of a code number and a text. The code number is
the unique identifier for the problem while the wording may change.
Note the following:
• To facilitate finding a message, the table lists the messages sorted by

code.
• If you cannot find the code you are looking for, check the message
text. The two messages "Unexpected module behavior" and
"Module malfunction detected" can be assigned to different codes.
See the beginning of the table for more information.

Operating Manual
TIP If you are unable to resolve the problem following the instructions in
this manual, or if you encounter a message not listed in the table, write
down the code and wording of the message and contact us. For details,
see the Contacting Us section at the beginning of this manual.
Message and Code Description and Remedial Action
Unexpected module behavior. Code xx xx = Two-digit to four-digit code number.

When the message appears, write down the message code and
turn off the module. Wait for 5 seconds and turn on the module
again.
TIP If the message appears with codes 74 or 103, the firmware
may be defective or incomplete. Update the firmware, see
Updating the Device Firmware (} page 183). If the message
appears again, contact Technical Support.
Module malfunction detected. Code xx xx = two-digit to four-digit code number
When the message appears, write down the message code. Turn
off the module and contact Technical Support.
Code 33 Leak detected – eliminate within Find and eliminate the source for the leakage (see Resolving
approx. 180 seconds. Liquid Leaks (} page 210)). The pump flow stops if leakage is not
resolved within 3 minutes.
Code 34 Leak detected. The pump stopped because of leakage. The message appears
because the leakage reported earlier with code 33 was not
resolved within 3 minutes. Find and eliminate the source for the
leakage (see Resolving Liquid Leaks (} page 210)).
Code 36 Download failed. The firmware download has not been successful. Repeat the
download.
Code 37 Download firmware mismatch. You tried to download a firmware file that is invalid for the pump.
Repeat the download with a firmware file that is valid for the
pump.
Code 52 Module software incomplete. The firmware is incomplete, for example, because the
Download firmware (again). communication between the chromatography data system and
the module was interrupted during the firmware download.
Repeat the download.
Code 89 Liquid leak sensor missing or Contact Thermo Fisher Scientific Technical Support for assistance.
defective. To operate the device nevertheless, you can disable the leak
sensor functionality in the chromatography data system by setting
Leak Sensor Mode to Disabled.
Code 90 Download firmware mismatch – You tried to download an incompatible firmware with an earlier
invalid version. version number than the firmware that is currently installed in the
module. Downgrading the firmware may result in loss of
functionality or malfunctioning of the module. If required, repeat
the download with a firmware version later than the version
currently installed in the module.
Code 91 Data changed during read. • This may be a temporary error. Turn off the module. Wait for 5
seconds and turn on the module again.
• The firmware may be defective. Update the firmware.

Operating Manual
Code 92 Data verification failed. • This may be a temporary error. Turn off the module. Wait for 5
• The firmware may be defective. Update the firmware.
Code 118 USB Buffer Overflow. This is a software problem. The module produces data faster than
the computer on which the chromatography data system is
running reads the data.
1. In the chromatography data system, disconnect and reconnect
the module.
2. If this does not solve the problem, update the firmware or the
chromatography data system version.
3. If the problem persists: Also, third-party software on the
computer, for example, virus scanners or poor computer
performance can cause the problem. Contact the onsite IT
department.
Code 120 System interlink request timed Communication with the module failed. The module did not
out. respond in time.
For the module for which the message appears:
1. Turn on the module if it is not yet turned on.
2. Check the system interlink connections to the module. Verify
that all system interlink cables are connected at both ends.
3. If the message persists, replace the system interlink cables.
Code 126 Device lost system interlink A system interlink cable may be disconnected from the module or
connection. defective.
Code 128 System interlink data errors. A system interlink cable may be disconnected from the module or
defective.
Code 129 Device X not found on system X = serial number
interlink. The module with the given serial number may be disconnected,
turned off or a firmware update is running.
1. Check the system interlink connections to the module.
2. If the message persists, check the module operational status.
Code 131 System interlink bus not A system interlink cable may be disconnected from the module or
operable. defective.
Code 136 Lock request rejected – already X = lock holder ID, with USB address referring to the
locked by X. chromatography data system or system interlink address referring
to the system controller or a module
The module is already locked by another software (system
controller or chromatography data system).
Wait until the module is released from the locked state.

Operating Manual
Code 137 Lock by X expired. X = lock holder ID, with USB address referring to the
chromatography data system or system interlink address referring
Inform Thermo Fisher Scientific about the occurrence. No further
action required.
Code 145 Lock holder X lost. X = lock holder ID, with USB address referring to the
chromatography data system or system interlink address referring
The lock was released automatically since its holder disappeared
from system interlink.
Check the system interlink connections to the module.
Code 152 Assignment or command Module is not ready to accept command or property assignment
rejected – device locked. since locked by another software (system controller or
chromatography data system).
Wait until module is released by the current software (system
controller or chromatography data system).
Code 4098 Upper pressure limit Check the flow path for blockage.
exceeded If the flow path is blocked:
• The column may be contaminated. Rinse or replace the column.
If the problem occurs due to column ageing, it may be sufficient
to increase the setting for the upper pressure limit.
• The autosampler may be blocked. Check the autosampler
components and eliminate the source for the blockage.
If the flow path is not blocked:
Test the static mixer for permeability (see Testing the Static Mixer
for Permeability (} page 166)).
Code 4099 Pressure fallen below lower Check the following causes:
limit. • One or more solvent reservoirs are empty. Fill the reservoirs and
purge the pump. If you are monitoring the solvent consumption
from the Chromeleon software, the message "Code 4158 Out of
eluent X" alerts you when a reservoir is empty.
• Air bubbles may be trapped in the solvent lines. Check the
solvent line filters. Purge the pump.
• Leakage may be present in the system. Resolve the leakage. For
the pump, see Resolving Liquid Leaks (} page 210). For the other
system modules, refer to the Operating Manuals for the
modules.
• A check valve may be contaminated or defective. Clean or
replace the check valves as appropriate (see Check Valves
(} page 159)).
• With the applied flow, the pump cannot build up enough
pressure to reach the lower pressure limit. Adapt the lower
pressure limit or increase the flow.

Operating Manual
Code 4100 Purge pressure limit exceeded A pressure of more than 5 MPa built up after a purge cycle has
started.
Perform the following sequence of steps:
1. Open the purge valve if it is not yet open.
2. Check the flow path for indications of blockage. See also
Code 4098 Upper pressure limit exceeded.
3. Take appropriate remedial action as necessary.
4. Mute the alarm by pressing the MUTE ALARM button on the
pump keypad.
5. Start a new purge cycle.
Code 4101 Not ready. Please run self- The pump is not ready because the self-test was not successful.
test. Perform the following sequence of steps:
1. Open the purge valve.
2. Repeat the self-test.
3. Close the purge valve.
Code 4112 Self-test failed because of Changes in pressure have occurred during the self-test. Perform
fluctuating pressure. the following sequence of steps:
Code 4113 Self-test failed because The pressure has not been down to zero during the self-test.
pressure is out of range. Verify that the pressure sensor cables are properly connected.
If the message appears again, the system pressure sensor may be
defective. Contact Technical Support.
Code 4114 The device is busy. Please The pump is not ready because, for example, a self-test is running.
retry after 1 minute. Retry after 1 minute. If the message appears again, perform the
following sequence of steps:
Code 4115 Working piston pressure zero The message may appear for the pressure sensor in a pump head
out of range. or for the system pressure sensor:
• If the message appears for only the right pump block or the left
pump block, the cable for the pressure sensor in the pump head
may not seat properly in the P-WORK connector.
• If the message appears for both pump blocks at the system time,
the cable for the system pressure sensor may not seat properly
in the P-SYS connector.
Verify that the pressure sensor cable is properly plugged into the
connection port and retry. If the problem persists, contact
Technical Support.

Operating Manual
Code 4116 The pressure signals are not The pressure calibration factor for the working piston is out of
consistent. There may be air in the range. Perform these steps:
working cylinder. 1. Verify that the degasser is working.
2. Purge the pump.
Code 4119 Can’t start pump while alarm An alarm is present, for example, because leakage has been
is on. detected. You can restart the pump flow only when the alarm is
no longer present. Mute the alarm by pressing the MUTE ALARM
button on the pump keypad. Find and eliminate the source for the
alarm as suggested for the accompanying message.
Code 4120 The rear seal wash system has This message alerts you only when the drop counter functionality
run out of wash solution. of the seal wash detector is enabled (standard setting).
• Verify that wash liquid is present in the seal wash reservoir.
• Inspect the seal wash lines across the entire flow path for
indications of blockage or leakage. Verify that all seal wash lines
are properly connected and routed. Replace the seal wash lines
as necessary (see Replacing the Seal Wash Lines (} page 129)).
• Inspect the peristaltic tubing for indications of blockage or
damage. Replace the tubing as necessary (see Replacing the Seal
Wash Lines (} page 129)).
• Verify that the peristaltic tubing is properly inserted in the seal
wash pump and that the lever of the pump is not blocked.
• Inspect the electrodes of the seal wash detector for
contamination or damage. Replace the seal wash detector as
necessary (see Replacing the Seal Wash Detector (} page 132)).
• Make sure that the seal wash liquid is sufficiently conductive
(see Choosing the Seal Wash Liquid (} page 69)).
• Start an additional seal wash cycle from the Chromeleon
software. While the wash cycle is running, inspect the pump
heads. If droplets leave the pump head at the rear, the seal
wash seal is defective. Replace the seal wash seals (see
Replacing the Seal Wash Seals (} page 151)).
Code 4121 Piston seal leakage has This message alerts you only when the drop counter functionality
exceeded the recommended limit. of the seal wash detector is enabled (standard setting).
Test the pump for piston seal leakage and take the recommended
action (see Testing the Piston Seals for Leakage (} page 156)).
Code 4122 The rear seal leak sensor This message alerts you only when the drop counter functionality
detects drops constantly. of the seal wash detector is enabled (standard setting).
Inspect the electrodes of the seal wash detector for
contamination or damage. Replace the seal wash detector as
necessary (see Replacing the Seal Wash Detector (} page 132)).
The message appears also when the percentage of water in the
seal wash liquid is too high. Observe the information about the
composition of the seal wash liquid in Choosing the Seal Wash
Liquid (} page 69).

Operating Manual
Code 4125 Degasser malfunction The vacuum level monitoring function detected insufficient
degasser vacuum.
Turn the pump off and on again. In the chromatography data
system, check the degasser vacuum. After about 1 minute, the
setting should change from NotOk to Ok. If the degasser vacuum
is still insufficient, the degasser may be leaky. Locate the
DegasserPressure property in the Command window, write down
the pressure reading, which can provide helpful information to
identify the source for the problem, and contact Technical
Support.
Code 4127 The pump drive is still in The message alerts you during pump maintenance:
undock position. Please execute a dock This message alerts you during pump maintenance (for example,
command. when replacing the piston seals or pistons) when you try to start
the pump while the pistons are not yet in the correct position for
normal operation. To return the pistons into the correct position,
perform the following sequence of steps:
2. Dock the pistons.
The message alerts you during internal pump maintenance:
If the message appears during the internal maintenance
procedure, perform an additional purge cycle.
Code 4130 Pressure buildup during A pressure of more than 0.5 MPa built up during piston
maintenance operation. maintenance or piston seal maintenance. To reduce the pressure,
perform the following sequence of steps:
2. Dock or undock the pistons, depending on when the message
appeared.
If the message appears during the internal maintenance
procedure, perform an additional purge cycle.
Code 4148 Can’t perform this command You tried to run a self-test while the flow rate was not yet down
while the flow is on. to zero. Turn off the flow and repeat the command.
Code 4152 Pressure sensor malfunction. Verify that the cable for the pressure sensor is properly plugged
Check the cable connection and retry. into the connection port and retry. If the message appears again,
follow these steps:
2. Perform a self-test.
4. Restart the flow.
5. If this message appears again or if another message relating to
the pressure or a pressure sensor appears, contact Technical
Support.

Operating Manual
Code 4156 Compression limit reached. The compression value was 100% during the last stroke. If the
compression value is lower than 100% for several strokes
afterward, the message "Compression back to normal" (code
4157) appears. If this message does not appear, inspect the flow
connections for indications of air bubbles. Purge the pump if
necessary.
If the message "Compression limit reached" persists, see
Checking the Compression Values (} page 211).
Code 4158 Out of eluent X This message alerts you only if you are monitoring the solvent
consumption from the Chromeleon software. The message
indicates for which solvent the reservoir is empty.
Code 4159 The waste bottle is full. This message alerts you only if you are monitoring the liquid level
in the waste container. Empty the waste container when needed.
Code 4161 Pressure recalibration The pump pressure was not down to zero during the self-test.
deviates by xx bar. Verify that the pressure sensor cable is properly connected to the
P-SYS connector. Wait until the pressure is down and repeat the
test.
To speed up the pressure drop, open the purge valve and then,
start the self-test.
Code 4176 The pump pressure exceeded Follow these steps:
the absolute limit. Check pressure sensor 1. Verify that the pressure sensor cables are properly connected.
cables for proper connection and flow Reconnect the cables if necessary.
path for clogging. Then, perform a self-
2. Check the flow path for clogging and remedy the situation if
test.
necessary.
If the self-test is not successful, contact Technical Support.
Code 4234 The flow was stopped due to The pump flow was stopped because of a problem with another
a request from another module. module. Check the messages from other modules.
Code 4237 Out of solvent. The solvent reservoir is empty.
Refill the solvent reservoir and purge the pump.
Code 4238 Mainboard initialization Main board initialization has not been successful.
failed. 1. This may be a temporary error. Turn off the module. Wait for 5
2. If the message appears again, update the firmware.
3. If the message persists, the main board may be defective.
Contact Technical Support.
Code 4239 Could not build up enough • Air bubbles may be trapped in the system. Purge the pump.
pressure. • Leakage may be present. As leakage usually occurs at a
connection, visually inspect all components and connections in
the flow path. For tests that can help you to identify the source
for the leakage, see Testing the Pump for Leakage (} page 209).
Code 4240 Column temperature is too The procedure that you want to perform will stop the pump flow.
high. This may damage the column if the column temperature is too
high. Reduce the column oven temperature. Repeat the
procedure.

Operating Manual
Code 4241 An autosampler is required. To perform the procedure, an autosampler is required that is

unambiguously defined.
In the Chromeleon software, select the correct configuration for
your system and connect all devices.
Code 4242 The autosampler is offline. The autosampler is not accessible via a System Interlink
connection.
Check that the autosampler is properly connected via System
Interlink and that the autosampler is powered on.
Code 4243 Unsupported autosampler. The autosampler in the system configuration does not support
this procedure.
Code 4244 The column compartment is The column compartment in the system configuration is not
offline. accessible via the System Interlink connection.
Check that the column compartment is properly connected via
System Interlink and that the column compartment is powered
on.

Operating Manual
8.3 Testing the Pump for Leakage

When
If you suspect leakage in the pump
When the leak sensor reports leakage, see Resolving Liquid Leaks
(} page 210).
Tests
The following tests assist you in finding out whether leakage is present
in the pump and they help you to locate the source of a leak:
• Pump leak test (general test)

See Testing the Pump for Leakage (General Test) (} page 177)
• Piston seal leak test

See Testing the Piston Seals for Leakage (} page 156)
• Seal wash system leak test

See Testing the Seal Wash System for Leakage (} page 128)

Operating Manual
8.4 Resolving Liquid Leaks

TIP If leakage is observed around the purge valve knob (when the purge
valve is open) or on the purge outlet (when the purge valve is closed),
the purge valve knob may be defective (see Replacing the Purge Valve
Knob (} page 175)).
When
The leak sensor is wet. The leak sensor reports leakage.
If leakage is not resolved after 3 minutes, the pump stops the flow.
• Replacement part as required
• Cloth or tissue
Preparations
When resolving leakage, observe the safety guidelines and general rules
for maintenance and service as presented in Maintenance and Service
(} page 115).
Follow these steps
1. Locate the source of the leak.

As leakage usually occurs at a connection, visually inspect all
components and connections in the flow path.
The following tests can help you to identify the source:
¨ Leakage test for the seal wash system
See Testing the Seal Wash System for Leakage (} page 128).
¨ Leakage test for the piston seals
See Testing the Piston Seals for Leakage (} page 156).
¨ Leakage test for the entire pump
See Testing the Pump for Leakage (General Test) (} page 177).
After taking remedial action as required, proceed with the next
steps.
2. With a cloth or tissue, thoroughly absorb all liquid that has collected
in the leak tray and under the leak sensor. Be careful not to bend the
sensor.
3. Allow the sensor to adjust to the ambient temperature for a few

minutes.
4. If leakage is no longer reported, you can resume operation.

Operating Manual
8.5 Pressure Issues or Shifts in Retention Time

When you observe pressure issues or shifts in retention time, the
following sections help you to identify and eliminate the source for the
problem:
• The pressure is not down to zero when the purge valve is open
See Pressure Not Zero with Open Purge Valve (} page 211).
• Pressure pulsation
See Checking the Compression Values (} page 211) and Testing the
Static Mixer for Permeability (} page 166).
• Shift in retention time

See Checking the Compression Values (} page 211).
• Inconstant pressure or high backpressure at the column and pump

See Testing the Static Mixer for Permeability (} page 166).
8.5.1 Pressure Not Zero with Open Purge Valve

When
The pressure is not down to zero when the purge valve is open.
Follow these steps
1. For the pressure sensor for which the pressure is not down to zero,
check the pressure sensor cable and connector for proper contact.
a) Unplug the pressure sensor cable.
b) Reconnect the cable. To ensure proper contact push the cable
firmly into the connector.
3. If the self-test produces a message, follow the remedial actions

recommended for the message.
8.5.2 Checking the Compression Values

The compression values of the pump heads can provide valuable
information for troubleshooting.
When
You observe pressure pulsation or shifts in retention time.

Operating Manual
Follow these steps
1. In the Chromeleon software, check the Compression value for the

pump heads (= CompressionDrv1).
The values indicate the compression of the last stroke in percent.
The compression value should be less than 100%.
¨ With isocratic conditions, the compression value should remain
stable.
¨ When running a gradient, the compression value changes
roughly proportional to the pressure curve.
If the value is close to 100%, the required precompression may not
be reached and pulsation may occur.
The table shows guide values for some solvents (pure solvent,
degassed, delivered at 40 MPa) with the pump being purged and the
pressure being stable for some time. In a range between 30 MPa
and 60 MPa the values can be considered as linear to the pressure.
Solvent Compression in %
Water 25 % ± 10 %
Methanol 50 % ± 10 %
Acetonitrile 45 % ± 10 %
2. Take remedial action if required.
Compression Remedial Action
Lower than indicated in the table The outlet check valve may be defective.
Replace the valve cartridge. See Replacing the
Outlet Check Valves (} page 161).
Higher than indicated in the table • The piston seal may be defective. Replace
the piston seal. See Replacing the Piston
Seals or Support Ring (} page 145).
• The inlet check valve may be defective.
Replace the valve cartridge. See Replacing
the Inlet Check Valves (} page 159).
Very high (message "Compression • Air bubbles may be present in the pump.
limit reached" and low pressure) Make sure that no air bubbles are present in
the solvent lines and purge the pump.
• If solvent shut-off valves are installed: Verify
that the valves are open.
• Excessive leakage may be present on the
inlet check valve. Remove the solvent line
from the solvent reservoir and the solvent
line filter from the solvent line. While the
pump is running, observe the liquid in the
solvent line. If the liquid moves also against
the direction of flow during the stroke, the
inlet check valve may be defective. Replace
the valve cartridge. See Replacing the Inlet
Check Valves (} page 159).

Operating Manual
8.5.3 Testing the Static Mixer for Permeability
TIP The information and references to the static mixer in this section
apply equally to the inline filter if installed.
When
If you observe pressure pulsation, inconstant pressure, or high
backpressure at the column and pump
• Water as solvent
• Tissue
Follow these steps

Test the static mixer by following the steps in Testing the Static Mixer for
Permeability (} page 166).

Operating Manual
8.6 Removing Persistent Air Bubbles

If you are unable to remove air bubbles with purging, purge the pump
against backpressure. Follow the procedure for running in new piston
seals in Recommendations for New Piston Seals (} page 149).

Operating Manual
9 • Pump-Specific Information
9 Pump-Specific
Information
This chapter provides specific information about the pump, for example,
the interior components and operating principle.

Operating Manual
9.1 Introduction to this Chapter

This chapter provides information that is specific to the pumps, for
example the interior components and the operating principle:
• Quaternary Pump and Dual Pump (} page 217)
• Binary Pump (} page 228)
• Isocratic Pump (} page 233)

Operating Manual
9.2 Quaternary Pump and Dual Pump

This section provides specific information on the quaternary pump and
the dual pump.
TIP The dual pump combines two ternary pumps in a single enclosure.
The two pumps are referred to as left pump and right pump. If not
otherwise stated, the information in this section applies equally to the
quaternary pump and the two pumps of the dual pump.
Quaternary Pump and Dual Pump – See
• Interior Components (Quaternary Pump) (} page 218)
• Interior Components (Dual Pump) (} page 219)
• Operating Principle (} page 221)
• Dwell Volume of the Pump (} page 222)
• Setting the Solvent Composition (} page 223)
• Synchronizing the Injection Time with the Pump Strokes (} page 224)
Dual Pump Only - See
• Dual Pump Specifics (} page 225)
• Sharing the Dual Pump (} page 225)
• Monitoring the Solvent Consumption (} page 226)
• Monitoring the Liquid Level in the Waste Container (} page 227)

Operating Manual
9.2.1 Interior Components (Quaternary Pump)

the front doors:
Figure 66: Interior view
No. Description
1 Keypad with buttons for pump control

2 Proportioning valve (4 channels)
3 Tubing clips for routing solvent lines to the proportioning valve
4 Pump head
5 Purge/sensor unit including purge valve and system pressure sensor
6 Leak sensor
7 Type label, indicating the module name, serial number, part number, and
revision number (if any)
8 Drain port for guiding leaking liquid to waste
10 Vacuum degasser
11 Seal wash pump
12 Tubing chase with tubing guides
13 Pump block LED
14a Capillary mixer (as part of mixing system)
14b Static mixer (as part of mixing system)
15 Pump outlet (outlet of the static mixer)

Operating Manual
9.2.2 Interior Components (Dual Pump)

the front doors:
No. Description
1 Proportioning valve (3 channels) (left pump)

2 Tubing clips for routing solvent lines to the proportioning valve
4 Pump head (left pump)
5 Purge/sensor unit including purge valve and system pressure sensor (left
pump)
6 Proportioning valve (3 channels) (right pump)
7 Pump head (right pump)
8 Purge/sensor unit including purge valve and system pressure sensor (right
pump)
9 Leak sensor
13a Vacuum degasser: Degas chambers for left pump, upper chambers (solvents
AL BL CL)
13b Vacuum degasser: Degas chambers for right pump, bottom chambers
(solvents AR BR CR)
14 Seal wash pump
16a Capillary mixer (as part of mixing system, right pump)

Operating Manual
No. Description
16b Static mixer (as part of mixing system, right pump)

17 Pump block LED (right pump)
18 Pump outlet (outlet of the static mixer) (right pump)
19a Capillary mixer (as part of mixing system, left pump)
19b Static mixer (as part of mixing system, left pump)
20 Pump block LED (left pump)
21 Pump outlet (outlet of the static mixer) (left pump)

Operating Manual
9.2.3 Operating Principle

The picture illustrates how the pump operates:
Figure 68: Operating principle
No. Description
A-D Solvent options:

• 4 solvents available with the quaternary pump (solvents A-D)
• 3 solvents available with the dual pump (solvents A-C), with each of the
two pumps
1 Solvent degasser (vacuum degasser) (pump inlet)
2 Proportioning valve
3 Pump head, with
3a Working cylinder (pump head)
3b Equilibration cylinder (pump head)
4 Purge/sensor unit, with
4a Purge valve knob
4b Purge outlet
4c System pressure sensor
5 Mixing system, with
5a Capillary mixer
5b Static mixer
For additional information, see Operating Principle (} page 33).

Operating Manual
9.2.4 Dwell Volume of the Pump

The gradient delay volume of an HPLC system is defined as the volume
of the entire flow path between the point where the gradient is formed
and the point where the mobile phase enters the column (see Gradient
Delay Volume, Dwell Volume and Ripple (} page 236)).
The pump contributes to the system gradient delay volume by the dwell
volume, which is the calculated volume between the point where the
gradient is formed and the pump outlet.
Figure 69: Dwell volume of the pump
No. Description
A-D Solvent options:

• 4 solvents available with the quaternary pump (solvents A-D)
• 3 solvents available with the dual pump (solvents A-C), with each of the
two pumps
1 Solvent degasser (vacuum degasser)
2 Proportioning valve
3 Pump head
4 Purge/sensor unit
5 Mixing system with capillary mixer and static mixer
6 Pump outlet
7 Dwell volume of the pump
For the dwell volume of the pump, see Performance Specifications

(} page 252).

Operating Manual
9.2.5 Setting the Solvent Composition

This section describes how you set the solvent composition for the
quaternary pump (solvents A to D). The steps and examples apply
equally to the ternary pumps of the dual pump (solvents AR to CR and
AL to CL).
Follow these steps
1. In the Instrument Configuration Manager, in the dialog box for the

pump, check and the change the following if required:
¨ Number of the solvents to be used with the pump
¨ Standard solvent names
These solvent names appear in the Chromeleon user interface.
2. In the Chromeleon Client, determine the percentage of solvent that

you want to deliver.
Set the percentage for solvents B, C, and D (%B, %C, %D). Solvent A
(%A) automatically delivers the remaining volume.
Examples
• To deliver 100% of solvent %A:

Set %B, %C, and %D to 0%.
• To deliver 100% of solvent %B (or %C or %D):

Set %B (or %C or %D) to 100%. The remaining solvents are
automatically set to 0%.
• To deliver 20% of solvent %A, 40% of solvent %B, 30% of solvent %C,
and 10% of solvent %D:
Set %B to 40%, set %C to 30%, and set %D to 10%. %A is
automatically set to 20%.

Operating Manual
9.2.6 Synchronizing the Injection Time with the Pump Strokes

To enhance the retention time precision with gradient applications, you
can synchronize the injection time of the Vanquish autosampler with the
strokes of the Vanquish pump. The synchronization ensures that all
injections are performed at the same phase of the pump cycle.
Synchronization is possible only when configured in the Chromeleon

software (refer to the Chromeleon Help).
Then, the following properties are available in the Chromeleon software:
• SyncWithPump
To enable synchronization, set the property to On. To disable
synchronization, for example, for a specific application, set
SyncWithPump to Off.
• Pump
Shows the name of the pump to which the autosampler is linked.

Operating Manual
9.2.7 Dual Pump Specifics

Note the following:
• The dual pump combines two ternary pumps in a single enclosure.
• The two pumps are referred to as left pump and right pump.
¨ On the keypad, L refers to the left pump and R refers to the right
pump.
¨ In the Chromeleon user interface, Left refers to the left pump
and Right refers to the right pump, for example, as in
PumpLeft_Pressure and PumpRight_Pressure.
• The dual pump can be shared by two different instruments (see

Sharing the Dual Pump (} page 225)).
• You can monitor the solvent consumption of the dual pump as a

whole or separately for each pump (see Monitoring the Solvent
Consumption (} page 226)).
• You can monitor the liquid level in the waste container of the dual
pump as a whole or separately for each pump (see Monitoring the
Liquid Level in the Waste Container (} page 227)).
9.2.7.1 Sharing the Dual Pump

In the Chromeleon software, you can share the dual pump between two
instruments.
The default assignment for the two pumps is the instrument in which
the dual pump is installed.
To share the dual pump, follow these steps:
1. In the Instrument Configuration Manager, open the dialog box for

the dual pump.
2. On the Devices tab page, assign each pump to the instrument on

which you want to use the pump. Select the instrument from the list
of available instruments.
TIP Notice that the pumps now appear in the instruments to which they
have been assigned.

Operating Manual
9.2.7.2 Monitoring the Solvent Consumption
TIP When monitoring the liquid level in the solvent reservoirs (solvent
consumption) as described in this section, the Chromeleon software
calculates the liquid level. To monitor the liquid level in real time, based
on real physical measurement, install the Vanquish Solvent Monitor. The
solvent monitor is available as an option (see Optional Accessories
(} page 267)).
For monitoring the solvent consumption, note the following:
• The two pumps can share the same set of solvent reservoirs or they
can be connected to different sets of reservoirs.
• Depending on the setup, you can monitor the solvent consumption

for the dual pump as a whole or separately for each pump.
Monitoring the Solvent Consumption for the Dual Pump as a Whole
TIP It is possible to share solvent reservoirs even if the two pumps are
assigned to different instruments.

the dual pump.
2. On the Bottles tab page, select the Share Eluent Bottles check box.
3. In the Chromeleon user interface, enter the information that is

required for monitoring (see Important Operating Parameters
(} page 94)). Enter the information for both pumps.
Notice that the monitoring properties show the same values for both
pumps, for example, the RemainTime property.
Monitoring the Solvent Consumption for Each Pump Separately

the dual pump.
2. On the Bottles tab page, clear the Share Eluent Bottles check box.


Operating Manual
9.2.7.3 Monitoring the Liquid Level in the Waste Container
TIP When monitoring the liquid level in the waste container as described
in this section, the Chromeleon software calculates the liquid level. To
monitor the liquid level in real time, based on real physical
measurement, install the Vanquish Solvent Monitor. The solvent
monitor is available as an option (see Optional Accessories (} page 267)).
For monitoring the liquid level in the waste container, note the
following:
• The waste liquids from the two pumps can be guided into the same
waste container or into different waste containers.
• Depending on the setup, you can monitor the liquid level in the
waste container for the dual pump as a whole or separately for each
pump.
Monitoring the Liquid Level for the Pump as a Whole
TIP It is possible to share the waste container even if the two pumps are
assigned to different instruments.

the dual pump.
2. On the Bottles tab page, select the Share Waste Bottles check box.

Notice that the monitoring properties show the same values for both
pumps, for example, the RemainTime property.
Monitoring the Liquid Level for Each Pump Separately

the dual pump.
2. On the Bottles tab page, clear the Share Waste Bottles check box.


Operating Manual
9.3 Binary Pump

This section provides specific information on the binary pump. See
• Interior Components (overview) (} page 228)
• Dwell Volume of the Pump (} page 231)
• Setting the Solvent Composition (} page 232)
9.3.1 Interior Components

the front doors:
No. Description

2a Pump head (left)
2b Pump head (right)
3 Tubing clips for routing the solvent lines from the degasser outlets to the
pump heads
5 Leak sensor
6 Drain port
9a Vacuum degasser (solvent B)

Operating Manual
No. Description
9b Vacuum degasser (solvent A)

10a Solvent selector (solvent B)
10b Solvent selector (solvent A)
11 Seal wash pump
13 Pump block LEDs
14a Capillary mixer (as part of mixing system)
14b Static mixer (as part of mixing system)

Operating Manual

No. Description
1 Solvent selector (pump inlet)

2 Solvent degasser (vacuum degasser)
3 Pump head, left, with
3a Working cylinder (left pump head)
3b Equilibration cylinder (left pump head)
4 Pump head right, with
4a Working cylinder (right pump head)
4b Equilibration cylinder (right pump head)
5a Purge valve knob
5b Purge outlet
6 Mixing system, with
6a Capillary mixer
6b Static mixer

Operating Manual
9.3.3 Dwell Volume of the Pump

and the point where the mobile phase enters the column (see Gradient
Delay Volume, Dwell Volume and Ripple (} page 236)).
volume, which is the calculated volume between the point where the
gradient is formed and the pump outlet.
Figure 72: Dwell volume of the pump
No. Description
1 Solvent selectors
2 Solvent degasser
3+4 Pump heads
5 Purge/sensor unit
6 Mixing system with capillary mixer and static mixer
7 Pump outlet
8 Dwell volume of the pump
For the dwell volume of the pump, see Performance Specifications

(} page 252).

Operating Manual
9.3.4 Setting the Solvent Composition

For increased flexibility, the pump is shipped with two 3-port solvent
selectors. They allow forming binary gradients from three solvents per
channel. The solvent to be used for each channel is selected in the user
interface.
Follow these steps
1. In the Instrument Configuration Manager, in the dialog box for the

pump, check and the change the following if required:
¨ Number of the solvents to be used with the pump
¨ Standard solvent names
These solvent names appear in the Chromeleon user interface.
2. In the Chromeleon Client, set the solvent composition. For each of

the two channels, select the solvent and set the percentage of
solvent that you want to deliver.
Selecting the Solvent
1. For channel A, set %A_Selector to %A1 or %A2 or %A3.
2. For channel B, set %B_Selector to %B1 or %B2 or %B3.
Determining the Percentage of Solvent to Deliver

Set the percentage for solvent B (%B). Solvent A automatically delivers
the remaining volume.
Examples
• To deliver 100% of solvent B2:

Set %B_Selector to %B2 and set %B to 100%.
• To deliver 100% of solvent A3:

Set %A_Selector to %A3 and set %B to 0%.
• To deliver 30% of solvent A1 and 70% of solvent B3:

Set %A_Selector to %A1, set %B_Selector to %B3, and set %B to
70%.

Operating Manual
9.4 Isocratic Pump

This section provides specific information on the isocratic pump. See
• Interior Components (overview) (} page 233)
9.4.1 Interior Components

the front doors:
No. Description

2 Pump head
4 Leak sensor
8 Seal wash pump
10 Pump block LED
11a Capillary mixer (as part of mixing system, which serves as inline filter)
11b Static mixer (as part of mixing system, which serves as inline filter)

Operating Manual

No. Description
A Solvent
1 Pump head, with
1a Working cylinder
1b Equilibration cylinder
2a Purge valve knob
2b Purge outlet
3 Mixing system, serving as inline filter, with
3a Capillary mixer
3b Static mixer

Operating Manual
10 • Modifying the Pump for Specific Applications
10 Modifying the Pump

for Specific
Applications
This chapter provides information about how you can modify the pump
for specific applications.

Operating Manual
10.1 Gradient Delay Volume, Dwell Volume and Ripple

This section applies to binary pumps, quaternary pumps, and dual
pumps.

and the point where the mobile phase enters the column. Thus, the
gradient delay volume of an HPLC system is the volume that the pump
must deliver until a change in solvent composition reaches the column
inlet.
Figure 75: Gradient delay volume of an HPLC system
No. Description
1 Pump with
1a Point where the gradient is formed:
Quaternary pump: The gradient is formed after the proportioning valve.
Dual pump: The gradient is formed after the proportioning valve (with each
of the two pumps).
Binary pump: The gradient is formed in the purge/sensor unit.
2 Autosampler
3 Column
4 Detector
5 Gradient delay volume of the system
Reducing the gradient delay volume allows changes in the solvent

composition to become effective on the column much earlier and thus,
having a faster effect on the elution of analytes.
volume (see Pump-Specific Information (} page 215)). For the dwell
volume of the pump, see Performance Specifications (} page 252).

Operating Manual
In the standard configuration, the pump has been optimized for the
dwell volume and ripple. You can adapt the dwell volume or ripple to
your requirements by replacing the mixing system with which the pump
is shipped with a mixing system with a different volume:
• Mixing system with lower volume

Operating the pump with a lower volume mixing system reduces the
dwell volume of the pump and thus, the gradient delay volume of
the system but increases the ripple.
Consider installing a mixing system with lower volume for gradient
separations at low flow rates (for example, less than 100 µL) or for
very steep gradients.
• Mixing system with higher volume

Operating the pump with a higher volume mixing system reduces
the ripple but increases the dwell volume of the pump and thus, the
gradient delay volume of the system.
For information about the available mixing systems, see Available Mixing
Systems (} page 237).
10.1.1 Available Mixing Systems

Each mixing system comprises a static mixer and a capillary mixer. The
volumes of both mixers determine the entire volume of the mixing
system.
The table lists the available mixing systems:
Description Remarks
Set inline filter, volume: 35 µL, comprising: Requires also a different

• Inline filter (static filter), volume: 10 µL capillary to connect the pump to
the autosampler.
• Capillary mixer, volume: 25 µL
Mixing system, volume: 100 µL, comprising: Requires also a different
• Static mixer, volume: 75 µL capillary to connect the pump to
the autosampler.
Mixing system, volume: 200 µL, comprising: Binary VF-pump, isocratic pump:
• Static mixer, volume: 150 µL Mixing system with which the
pump is shipped.
With the isocratic pump, the
mixing system serves as inline
filter.
Other pumps: See TIP at the end
of this table.

Operating Manual
Description Remarks
Mixing system, volume: 400 µL, comprising: Binary VC-pump, quaternary

• Static mixer, volume: 350 µL pump, dual pump: Mixing
system with which the pump is
shipped.
The dual pump has two mixing
systems.
Other pumps: See TIP at the end
of this table.
Mixing system, volume: 800 µL, comprising: See TIP at the end of this table.
Mixing system, volume: 1550 µL, comprising: See TIP at the end of this table.
TIP With this mixing system, only the static mixer is different from the static mixer
with which the pump is shipped. The capillary mixer remains the same. Thus, if you
want to change to this mixing system, you need to order only the static mixer.
For ordering information, see Optional Accessories (} page 267).
To change to a different mixing system, see Exchanging the Mixing

System (} page 239).

Operating Manual
10.1.2 Exchanging the Mixing System

When
Changing to a mixing system with different volume
Follow these steps
1. Remove the mixing system with which the pump is shipped (see the
next section).
2. Install the new mixing system. Follow the sequence of steps for the
mixing system that you want to install. See:
¨ Installing a Mixing System with a Volume higher than 100 µL
(} page 240)
¨ Installing the 100 µL Mixing System (} page 243)
¨ Installing the 35 µL Inline Filter Set (} page 245)
10.1.2.1 Removing the Mixing System
Preparations

2. To remove harmful substances from the components in the flow

path after the purge unit, have the pump deliver for a short time
with the solvent that was used for purging.
to zero.
Follow these steps
NOTICE
1. On the static mixer outlet, disconnect the capillary that connects the
static mixer to the autosampler injection valve.
2. If you want to install the 100 µL mixing system or 35 µL inline filter
set: Disconnect the other end of the capillary on the autosampler
injection valve and remove the capillary.
3. Disconnect the capillary mixer on the purge/sensor unit.

Operating Manual
4. Pull the static mixer out of the mounting bracket.
5. Remove the assembly of static mixer and capillary mixer from the
pump.
6. Disconnect the capillary mixer from the static mixer.
10.1.2.2 Installing a Mixing System with a Volume higher than 100 µL
Parts required
Static mixer as required for the mixing system (see Available Mixing
Systems (} page 237)).
• Depending on the fitting connection on the capillaries

• Screwdriver, Torx T10 (required only for static mixers with a volume
of 750 µL or 1500 µL)
Preparations
1. If not yet done: Remove the mixing system with which the pump is
shipped (see Removing the Mixing System (} page 239)).
2. Only required if you want to install a static mixer with a volume of

750 µL or 1500 µL
These mixers require a different mounting bracket. Install the new
mounting bracket. The mounting bracket is included in the mixer
shipment.
Installing the New Mounting Bracket

Required only for static mixers with a volume of 750 µL or 1500 µL
1. Remove the mounting bracket that is installed in the pump. Mind

the orientation of the bracket. The orientation is important for the
new bracket.
Binary pump: Keep the spacer sleeves. You will need them when
installing the new mounting bracket.

Operating Manual
Figure 76: Removing the mounting bracket
No. Description
1 Mounting holes for mounting bracket

2 With binary pump only: spacer sleeves
3 Mounting bracket
4 Mounting screws (Torx)
2. Using the screws shipped with the mounting bracket, attach the new
bracket inside the pump (same position and orientation as the one
you removed).
Binary pump: Reinsert the spacer sleeves.
Figure 77: Installing the mounting bracket
No. Description
1 Mounting holes for mounting bracket

2 With binary pump only: spacer sleeves
3 Mounting bracket
Follow these steps
NOTICE

Operating Manual
1. Connect the capillary mixer to the static mixer.

Mind the direction of flow through the static mixer and capillary
mixer (indicated by the arrow on the mixer).
2. Insert the assembly of static mixer and capillary mixer into the
pump.
3. Insert the static mixer into the mounting bracket.
4. Connect the capillary mixer on the purge/sensor unit.
5. On the static mixer outlet, connect the capillary to the autosampler

injection valve.
6. In the Chromeleon software, set the StaticMixer property to the

value indicated on the static mixer. If the property is not set to the
correct value, the leak tests may not provide reliable results.
for a short time.


Performance information for the static mixer (MixerChanged
command).
When operating the pump, observe the following
• Operating the pump with a mixing system with a volume lower than
the volume installed in the pump upon shipment reduces the
gradient delay volume but increases the ripple.
• Operating the pump with a mixing system with a volume higher than
the volume installed in the pump upon shipment reduces the ripple
but increases the gradient delay volume.
• The maintenance procedures are the same as for the mixing system
with which the pump was shipped (see Mixing System (} page 166)).

Operating Manual
10.1.2.3 Installing the 100 µL Mixing System
Parts required
• Mixing system, volume: 100 µL, comprising a static mixer (volume:

75 µL) and a capillary mixer (volume: 25 µL)
• Capillary to connect the pump to the autosampler

Preparations
2. For easier installation, remove the seal wash detector assembly

(funnel and detector). Grasp and pull the assembly upward by the
funnel. The detector including the tubing and cable can remain
connected to the funnel.
No. Description

3 Detector cable
4 Seal wash line

Operating Manual
Follow these steps
1. Connect the capillary mixer on the purge/sensor unit. Mind the

direction of flow through the capillary mixer (indicated by the arrow
on the mixer).
TIP To facilitate installation of the static mixer, loosely tighten the

capillary mixer on the purge/sensor unit so that you can easily access
the free end of the capillary.
2. Connect the static mixer to the capillary mixer. Mind the direction of
flow through the static mixer (indicated by the arrow on the mixer).
3. Turn and insert the assembly of static mixer and capillary mixer into
the pump so that the knurl of the capillary mixer rests on the edge
of the purge/sensor unit.
Figure 79: 100 µL mixing system installed
No. Description
1 Static mixer
2 Capillary mixer
3 Knurl resting on the purge/sensor unit
4. Tighten the capillary mixer on the purge/sensor unit.
5. Reinstall the seal wash detector assembly in the pump (see

Replacing the Seal Wash Detector (} page 132)).
6. Connect the static mixer outlet to the autosampler injection valve

(see Connecting the Pump and Autosampler (} page 78)).

value indicated on the static mixer. If the property is not set to the

Operating Manual
8. With Chromeleon 7.2.8 and later: In the Chromeleon software, set

the CapillaryMixer property to the value indicated on the capillary
mixer.
for a short time.

command).
• Operating the pump with a mixing system with a volume lower than
the volume installed in the pump upon shipment reduces the
gradient delay volume but increases the ripple.
• The maintenance procedures are the same as for the mixing system
with which the pump was shipped (see Mixing System (} page 166)).
10.1.2.4 Installing the 35 µL Inline Filter Set
Parts required
• Set inline filter, volume: 35 µL, comprising an inline filter (static

filter, volume: 10 µL) and a capillary mixer (volume: 25 µL)
• Capillary to connect the pump to the autosampler

• Screwdriver, Torx T10
Preparations
2. The inline filer requires a different mounting bracket. Install the new
mounting bracket. The mounting bracket is included in the inline
filter ship kit.

Operating Manual
Installing the New Mounting Bracket
1. Unplug the system pressure sensor cable from the P-SYS connector.
2. Remove the seal wash detector assembly (funnel and detector).
Grasp and pull the assembly upward by the funnel. The detector
including the tubing and cable can remain connected to the funnel.
No. Description

3 Detector cable
4 Seal wash line
3. To attach the new mounting bracket inside the pump (above the
purge/sensor unit):
a) Remove the push rivets that cover the mounting holes while no
mounting bracket is installed.
b) Using the screws shipped with the mounting bracket, attach the
new bracket inside the pump.
Figure 81: Installing the mounting bracket
No. Description
1 Mounting holes for mounting bracket (covered by push rivets while no

mounting bracket is installed in this position)
2 Mounting bracket

Operating Manual
Follow these steps
1. Connect the capillary mixer on the purge/sensor unit. Mind the

direction of flow through the capillary mixer (indicated by the arrow
on the mixer).
TIP To facilitate installation of the inline filter, loosely tighten the

capillary mixer on the purge/sensor unit so that you can easily access
the free end of the capillary.
2. Connect the inline filter to the capillary mixer. Mind the direction of
flow through the inline filter (indicated by the arrow on the filter).
3. Turn and insert the assembly of inline filter and capillary mixer into
the mounting bracket.
Figure 82: Inline filter with capillary mixer installed
No. Description
1 Inline filter
2 Capillary mixer
4. Tighten the capillary mixer on the purge/sensor unit.
5. Reinstall the seal wash detector assembly in the pump (see

Replacing the Seal Wash Detector (} page 132)).
6. Reconnect the system pressure sensor cable.
7. Connect the inline filter outlet to the autosampler injection valve

(see Connecting the Pump and Autosampler (} page 78)).

value indicated on the inline filter. If the property is not set to the

Operating Manual
9. With Chromeleon 7.2.8 and later: In the Chromeleon software, set

the CapillaryMixer property to the value indicated on the capillary
mixer.
for a short time.

command).
• Operating the pump with the inline filter reduces the gradient delay
volume but increases the ripple.
• The maintenance procedures for the static mixer apply equally to

the inline filter (see Mixing System (} page 166)).

Operating Manual
10.2 Normal-Phase Compatible Solvents and Additives

This section applies to Vanquish Core system modules.
In a Vanquish Core system, normal-phase (NP) compatible solvents and

additives may be used if the system modules have been modified for NP
applications. Refer to the Vanquish System Operating Manual.

Operating Manual

Operating Manual
11 • Specifications
11 Specifications
This chapter provides the physical and performance specifications,
including information about the materials used in the flow path of the
device.

Operating Manual
11.1 Performance Specifications

For details on the performance specifications for the pumps, see the
next sections.
11.1.1 Quaternary Pump and Dual Pump

The pump performance is specified as follows:
Type Specification*
Operating principle Serial dual-piston pump

Compressibility compensation Fully automated, independent of the composition of the mobile phase
Flow range (settable) VC-pumps: VF-pumps:
0.001 – 10 mL/min in 1 µL/min 0.001 – 8 mL/min in 1 µL/min
increments increments
Flow accuracy ± 0.1%
Flow precision < 0.05% RSD or < 0.01 min SD, whichever is greater
Pressure range VC-pumps: VF-pumps:
2-70 MPa (20-700 bar, 290 – 2 – 103 MPa (20 – 1034 bar, 290 –
10100 psi) 15000 psi)
With a flow rate of > 5 mL/min, With a flow rate of > 5 mL/min,
the maximum pressure decreases the pressure range decreases
linearly down to 30 MPa (300 bar, linearly down to 80 MPa (800 bar,
4350 psi). 11600 psi).
Pulsation < 1.0% or < 0.2 MPa, whichever is greater
Gradient formation Low-pressure gradient proportioning
Proportioning accuracy ± 0.5% (of full-scale)
Proportioning precision < 0.15% SD
Number of solvents VC-pumps: VF-pumps:
VC-P20, VC-P21: 4 VF-P20: 4
VC-P32, VC-P33: 2 x 3 VF-P32: 2 x 3
Maximum stroke volume 80 µL
Mixer volume Standard configuration: 400 µL mixing system, consisting of a capillary
mixer (volume: 50 µL) and a static mixer (volume: 350 µL)
Other mixing systems are available as an option.
Dwell volume 679 µL (in standard pump configuration)
(contribution of the pump to the (314 µL to 1829 µL with optionally available mixing systems)
system gradient delay volume)
Solvent degassing VC-pumps: VF-pumps:
VC-P20, VC-P21: VF-P20:
Built‑in, 4 channels Built-in, 4 channels
VC-P32, VC-P33: VF-P32:
Built‑in, 6 channels Built-in, 6 channels

Operating Manual
Type Specification*
Biocompatible VC-pumps: no VF-pumps: yes

Communication USB:
1 USB port (USB 2.0, "B" type connector)
1 USB hub with 3 ports (USB 2.0, "A" type connectors)
I/O Interface:
2 Dig I/O ports (mini-DIN), each providing one input, one relay output,
and one bidirectional input/output
System Interlink:
2 system interlink ports (RJ45-8 connectors)
Control Chromeleon 7
The pump can be operated also with other data systems. For details,
Keypad with 5 buttons for performing certain functions directly from
the pump
Materials in the analytical flow path VC-pumps: VF-pumps:
Stainless steel, titanium, ceramics, MP35N, titanium, ceramics,
sapphire, PEEK, UHMW PE, sapphire, PEEK, UHMW PE,
fluoropolymers fluoropolymers
For information about the chemical resistance of materials refer to the
technical literature.
Solvent and additive information See Solvent and Additive Information (} page 26).
Safety features Leak detection and safe leak handling, excess pressure monitoring
Good Laboratory Practice (GLP) Predictive Performance functions for scheduling maintenance
features procedures based on the actual operating and usage conditions of the
pump.
All system parameters logged in the Chromeleon Audit Trail.
* Typical operating conditions for measurable specifications:
Flow accuracy, flow precision, pulsation: 1 mL/min at 20 MPa or 2 mL/min at 40 MPa, water
Proportioning accuracy, proportioning precision: 1 mL/min at 20 MPa or 2 mL/min at 40 MPa, 0-100%, water/
spiked water

Operating Manual
11.1.2 Binary Pump

Type Specification*

Flow range (settable) VC-pump: VF-pump:
0.001 – 10 mL/min in 1 µL/min 0.001 – 8 mL/min in 1 µL/min
increments increments
Pressure range VC-pump: VF-pump:
2-70 MPa (20-700 bar, 290 – 2 – 103 MPa (20 – 1034 bar, 290 –
10100 psi) 15000 psi)
With a flow rate of > 5 mL/min, With a flow rate of > 5 mL/min,
the maximum pressure decreases the pressure range decreases
linearly down to 30 MPa (300 bar, linearly down to 80 MPa (800 bar,
4350 psi). 11600 psi).
Gradient formation High-pressure gradient proportioning
Proportioning accuracy ± 0.2% (of full-scale)
Proportioning precision < 0.15% SD
Number of solvents 2 out of 6
Mixer volume VC-pump: VF-pump:
Standard configuration: 400 µL Standard configuration: 200 µL
mixing system, consisting of a mixing system, consisting of a
capillary mixer (volume: 50 µL) capillary mixer (volume: 50 µL)
and a static mixer (volume: and a static mixer (volume:
350 µL) 150 µL)
Other mixing systems are Other mixing systems are
available as an option. available as an option.
Dwell volume 400 µL (in standard pump 200 µL (in standard pump
(contribution of the pump to the configuration) configuration)
system gradient delay volume) (35 µL to 1550 µL with optionally (35 µL to 1550 µL with optionally
available mixing systems) available mixing systems)
Solvent degassing Built-in, number of channels: 2 out of 6
Biocompatible VC-pumps: no VF-pumps: yes

Operating Manual
Type Specification*
Communication USB:
I/O Interface:
System Interlink:
the pump
Materials in the analytical flow path VC-pumps: VF-pumps:
Stainless steel, titanium, ceramics, MP35N, titanium, ceramics,
sapphire, PEEK, UHMW PE, sapphire, PEEK, UHMW PE,
fluoropolymers fluoropolymers
pump.
Proportioning accuracy, proportioning precision: 1 mL/min at 20 MPa or 2 mL/min at 40 MPa, 0-100%, water/
spiked water

Operating Manual
11.1.3 Isocratic Pump

Type Specification*

Flow range (settable) 0.001 – 10 mL/min in 1 µL/min increments
Pressure range 2-70 MPa (20-700 bar, 290 – 10100 psi)
With a flow rate of > 5 mL/min, the maximum pressure decreases
linearly down to 30 MPa (300 bar, 4350 psi).
Number of solvents 1
Mixer volume With the isocratic pump, the mixing system serves as inline filter.
Standard configuration: 200 µL mixing system, consisting of a capillary
mixer (volume: 50 µL) and a static mixer (volume: 150 µL)
Other mixing systems (inline filters) are available as an option.
Solvent degassing No (available as optional accessory)
Biocompatible No
Communication USB:
I/O Interface:
System Interlink:
the pump
Materials in the analytical flow path Stainless steel, titanium, ceramics, sapphire, PEEK, UHMW PE,
fluoropolymers

Operating Manual
Type Specification*
pump.

Operating Manual
11.2 Physical Specifications

The physical conditions of the device are specified as follows:
Type Specification
Range of use Indoor use only

Ambient operating 5 °C - 35 °C
temperature
Ambient storage temperature -20 °C - 45 °C
Ambient operating humidity 20% - 80% relative humidity (non-condensing)
Ambient storage humidity Maximum 60% relative humidity (non-condensing)
Operating altitude Maximum 2000 m above sea level
Pollution degree 2
Power requirements 100 – 240 VAC, ± 10 %; 50/60 Hz, max. 245 W / 255 VA
Overvoltage category II
Emission sound pressure level < 70 dB(A), typically < 40 dB(A)
Dimensions 19.2 x 42 x 62 cm
(height x width x depth)
Weight Binary pump/dual pump: 20 kg, isocratic pump/quaternary pump: 17 kg

Operating Manual
12 • Accessories, Consumables and Replacement Parts
12 Accessories,
Consumables and
Replacement Parts
This chapter describes the standard accessories that are shipped with
the device and the accessories that are available as an option. This
chapter also provides information for reordering consumables and
replacement parts.

Operating Manual
12.1 General Information

The device must be operated only with the replacement parts and
additional components, options, and peripherals specifically authorized
and qualified by Thermo Fisher Scientific.
Accessories, consumables, and replacement parts are always maintained

at the latest technical standard. Therefore, part numbers are subject to
change. If not otherwise stated, updated parts will be compatible with
the parts they replace.

Operating Manual
12.2 Ship Kit

The ship kit includes the items listed in the table. The kit content is
subject to change and may vary from the information in this manual.
Refer to the content list included in the kit for the most recent
information about the kit content at the time when the device is
shipped.
12.2.1 Binary Pump

For reordering information of the ship kit components, see Consumables
and Replacement Parts (} page 270).
VC-P10 ship kit
Item Quantity in
shipment
Silicone tubing, 3 m 1

Syringe, plastic, 12 mL 1
Tubing connector (90°-angled) 2
Solvent line filter, filter holder (no filter frit included) 6
Solvent line filter, filter frit, 10 µm (pack of 10) 1
Plugs and retaining guides for reservoir caps, kit including 7
• Cap plug to close open holes in the reservoir cap (pack of 5)
• Retaining guide to keep the liquid line in place in the reservoir
cap (pack of 2)
Fitting plug, Viper 1
Tool kit, including 1
• Open-end wrench, size 11 x 13 mm
• Double-ended ring wrench, size 11 x 13 mm
• Open-end wrench, size 1/4" x 5/16"
• Spacing tool, pump head and pistons
Reservoir, 0.25 L, with reservoir cap 1
Tubing bracket 1
Solvent lines (pack of 6), from solvent reservoirs to solvent 1
selectors
System interlink cable (RJ45), 0.5 m 1
USB cable, type A to type B, high-speed, USB 2.0, cable length: 5 m 1

Operating Manual
VF-P10 ship kit
Item Quantity in
shipment

Solvent line filter, filter frit, biocompatible, 10 µm 6
cap (pack of 2)
Installation tool for Viper capillaries with torque toothing 1
Tubing bracket 1
Solvent lines (pack of 6), from solvent reservoirs to solvent 1
selectors

Operating Manual
12.2.2 Dual Pump

VC-P32, VC-P33 ship kit
Item Quantity in
shipment

cap (pack of 2)
Tubing bracket 1
Solvent lines (pack of 6) from solvent reservoirs to pump degasser 1
VF-P32 ship kit
Item Quantity in
shipment


Operating Manual
Item Quantity in
shipment

cap (pack of 2)
Tubing bracket 1
Solvent lines (pack of 6) from solvent reservoirs to pump degasser 1
12.2.3 Isocratic Pump

VC-P40 ship kit
Item Quantity in
shipment

cap (pack of 2)

Operating Manual
Item Quantity in
shipment

Tubing bracket 1
Solvent lines (pack of 2), from solvent reservoirs to pump head 1
12.2.4 Quaternary Pump

VC-P20, VC-P21 ship kit
Item Quantity in
shipment

cap (pack of 2)

Operating Manual
Item Quantity in
shipment
Tubing bracket 1
Solvent lines (pack of 4), from solvent reservoirs to pump degasser 1
VF-P20 ship kit
Item Quantity in
shipment

cap (pack of 2)
Tubing bracket 1
Solvent lines (pack of 4), from solvent reservoirs to pump degasser 1

Operating Manual
12.3 Optional Accessories

For accessories that are available as an option, see
• Optional Accessories (Miscellaneous) (} page 267)
• Optional Mixing Systems and Inline Filters (} page 268)
12.3.1 Optional Accessories (Miscellaneous)

Solvent shut-off valve
Description Part No.
Solvent shut-off valve 6036.0010

To prevent the solvent from flowing through the system, for
example, when opening a flow connection on the low-pressure
side.
Solvent monitor
Vanquish Solvent Monitor

To actively monitor the liquid level in solvent reservoirs and waste containers in real
time. Monitoring is based on real physical measurement.
Solvent monitor, 4-channel version 6230.1320
Solvent monitor, 8-channel version 6230.1310
Buffer Performance kit
Buffer Performance kit for quaternary or dual pumps 6040.5320

To avoid pressure pulsation issues with buffer applications in
quaternary pumps or dual pumps. Depending on the application,
two kits may be required with the dual pump.
Due to bad solubility of salts in organic fluids, mixing of a buffer
solution with organic fluids in a quaternary or dual pump can lead
to precipitation of salt at the mixing point. The precipitated salt
can deposit in the check valves and prevent them from closing.
This leads to pressure pulsation in buffer applications. Modifying
the sequence of the fluidics with the kit components enhances the
mixing performance.

Operating Manual
Degasser kit (VC-P40)
Degasser kit VC-P40 6045.3731

To retrofit the isocratic pump with a vacuum degasser.
Thermo Fisher Scientific service personnel must retrofit the pump
with the degasser.
Mixing systems, inline filters
Mixing systems, set inline filter

See Optional Mixing Systems and Inline Filters (} page 268).
12.3.2 Optional Mixing Systems and Inline Filters

system.
TIP With mixing systems (volumes: 200 µL, 400 µL, 800 µL or 1550 µL),

only the static mixer is different from the static mixer with which the
pump is shipped. The capillary mixer remains the same. Thus, if you
want to change to this mixing system, you need to order only the static
mixer. If you want to replace the capillary mixer nevertheless, order the
appropriate part number as indicated in the table.
Static mixers
Static mixers for use with 50 µL capillary mixer:

Static mixer, volume: 150 µL 6044.5110
(for total volume of mixing system: 200 µL)
Binary VF-pump, isocratic pump: The pump is shipped with the
mixing system with a volume of 200 µL.
With the isocratic pump, the mixing system serves as inline filter.
Binary VC-pump, quaternary pump: The pump is shipped with the
mixing system with a volume of 400 µL.
Dual pump: The pump is shipped with two mixing systems, each
with a volume of 400 µL.
Static mixer, volume: 750 µL 6044.5750A
Static mixer, volume: 1500 µL 6044.5450A

Operating Manual
Capillary mixers
Capillary mixer (volume: 50 µL) for use with static mixers

(volumes: 150 µL, 350 µL, 750 µL, and 1500 µL) for:
VC-pumps 6044.3015
VF-pumps 6044.5026
Mixing systems, set inline filter

VC-pumps Description Part No.
Mixing system, volume: 100 µL, including: 6045.5100

Set inline filter, volume: 35 µL, including: 6045.3020
• Inline filter (static filter) volume: 10 µL
In addition, order the capillary to connect the pump to the
autosampler.
Capillary to connect the pump to the autosampler, for use with 6040.2325
100 µL mixing system and 35 µL inline filter set
For use with binary pump, isocratic pump, and quaternary pump
Dual pump: The capillaries to use depend on the application
workflow and are provided in the respective Workflow Solution
Kits. For details refer to the documentation that comes with the
kit.
VF-pumps Description Part No.
Mixing system, volume: 100 µL, including: 6044.5100

Set inline filter, volume: 35 µL, including: 6044.3870
• Inline filter (static filter) volume: 10 µL
In addition, order the capillary to connect the pump to the
autosampler.
Capillary to connect the pump to the autosampler, for use with 6042.2330
the 100 µL mixing system and 35 µL inline filter set
For use with binary pump, isocratic pump, and quaternary pump
Dual pump: The capillaries to use depend on the application
workflow and are provided in the respective Workflow Solution
Kits. For details refer to the documentation that comes with the
kit.

Operating Manual
12.4 Consumables and Replacement Parts

The following consumables and replacement parts are available for the
pump.
12.4.1 Maintenance Kits

The maintenance kits that are available for the pumps include all parts
that are required for routine maintenance.
• See Maintenance Kits (VC-Pumps) (} page 270).
• See Maintenance Kits (VF-Pumps) (} page 272).
12.4.1.1 Maintenance Kits (VC-Pumps)
TIP Maintenance kits can include parts that are not required for your
specific pump. These parts are marked accordingly in the contents lists
for the kits.
VC-P10
Maintenance kit for VC-P10, including: 6040.1953A

• Pump head seal (2 PTFE seals (2 each), different sized)
• Silicone tubing (clear tubing)
• Peristaltic tubing (light yellow tubing)
• Tubing connector (straight) (pack of 5)
• Tubing connector (90°-angled)
• Seal wash seal (pack of 4)
• Piston seal (pack of 4)
• Valve cartridge, ceramics (pack of 2)
• Solvent line filter (4 filter holders and filter frits)
• Cleaning swab (pack of 5)
• Tubing clip (self-adhesive) (pack of 3)
Not required with VC-P10: Support ring

Operating Manual
VC-P20

• Pump head seal (2 PTFE seals, different sized)
• Valve cartridge, ceramics
VC-P32


Operating Manual
VC-P40

• Solvent line filter (1 filter holder and filter frits)
12.4.1.2 Maintenance Kits (VF-Pumps)
VF-P10
Maintenance kit for VF-P10, including: 6040.1956B


Operating Manual
VF-P20
Maintenance kit for VF-P20, including: 6040.1954A

VF-P32
Maintenance kit for VF-P32, including: 6040.1955B


Operating Manual
12.4.2 Pump Heads and Components

• See Pump Heads and Components (VC-Pumps) (} page 274).
• See Pump Heads and Components (VF-Pumps) (} page 275).
12.4.2.1 Pump Heads and Components (VC-Pumps)
VC-P10
Pump head (complete assembly), including spacing tool 6045.3205

Piston seal (RP) (pack of 2)* 6040.0304
Seal wash seal (pack of 2)* 6040.0033
Support ring (pack of 2) 6040.0012
Piston, sapphire (pack of 2) 6040.0042
Check valve, valve nut kit, including: 6035.1965
• Nut for inlet check valve
• Nut for outlet check valve
Check valve, cartridge, ceramics 6041.2301
Identical for inlet check valve and outlet check valve
Pump head seals (PTFE O-rings, sizes: 32x1.5 and 9x1.5; 5 each) 6040.2208
Capillary kit, pump head, including: 6045.3000
• U-tube (pack of 2)
• Capillary from right pump head to purge/sensor unit
• Capillary from left pump head to purge/sensor unit
Seal-handling tool 6040.7158
* With pump modified for NP applications: Seals (pack of 2) for 6040.0306
use as both piston seals and seal wash seals
VC-P20, VC-P32, and VC-P40

Piston seal (RP) (pack of 2)* 6040.0304
Seal wash seal (pack of 2)* 6040.0033

Operating Manual
• Capillary from pump head to purge/sensor unit (pack of 2)
* With pump modified for NP applications: Seals (pack of 2) for 6040.0306
use as both piston seals and seal wash seals
VC-P21 and VC-P33

Seals (pack of 2) for use as both seal wash seals and piston seals 6040.0306
12.4.2.2 Pump Heads and Components (VF-Pumps)
VF-P10

Piston seal (RP) and seal wash seal (pack of 2 each) 6044.0295

Operating Manual
• Capillary from right pump head to purge/sensor unit
• Capillary from left pump head to purge/sensor unit
Installation tool for Viper capillaries with torque toothing 6040.2314
VF-P20 and VF-P32

Piston seal (RP) and seal wash seal (pack of 2 each) 6044.0295
Installation tool for Viper capillaries with torque toothing 6040.2314

Operating Manual
12.4.3 Solvents and Wash Systems

Reservoirs for solvents and wash liquids
Reservoir, 1 L, including cap 2270.0012

Reservoir, 0.25 L, including cap 2270.0026
Cap for reservoirs, screw-cap (pack of 4) 6270.0013
Cap plug to close open holes in the reservoir cap (pack of 20) 6000.0047
Retaining guide to keep the liquid line in place in the reservoir cap 6000.0042
(pack of 5)
Plugs and retaining guides for reservoir caps, kit including 6030.9101
cap (pack of 5)
Seal wash system
Peristaltic and wash tubing kit 6044.1150

The kit includes peristaltic tubing (PharMed), silicone tubing, and
tubing connectors for use in
• Seal wash system in the pump and in the autosampler
• Needle wash system in the autosampler
• Drain pump in the autosampler
NOTICE: Use the thick silicone tubing (and related tubing
connectors) in the autosampler. Use the thin silicone tubing (and
related tubing connectors) in the pump. Use the screwable
connectors for the pump head. The screwable tubing connectors
are not used with the VC‑pumps and VF‑pumps.
NOTE: For a Vanquish Core system that has been modified for NP
applications, order the Normal-Phase (NP) tubing kit. For ordering
details and kit content, refer to the Vanquish System Operating
Manual.
Seal wash detector (drop detector) with funnel 6044.1898
Seal wash detector (drop detector) with funnel, NP 6044.1902
Seal wash seals
VF‑pumps: Seal wash seal (pack of 2 seal wash seals and 2 piston 6044.0295
seals (RP))
VC‑pumps – all VC‑pumps except VC‑P21 and VC‑P33: Seal wash 6040.0033
seal (pack of 2 seal wash seals)
VC‑P21, VC‑P33, and VC-pumps modified for NP applications: Seals 6040.0306
(NP) (pack of 2) for use as both seal wash seals and piston seals

Operating Manual
Solvent line filters, solvent lines and tubing
Solvent line filter, filter holder (pack of 6) (no filter frits included) 6268.0115
Solvent line filter, filter frits, 10 µm (pack of 10) for
VF‑pumps (biocompatible frits) 6268.0111
VC‑pumps (stainless steel frits) 6268.0110
Solvent lines to connect the solvent reservoirs to the pump inlet
Quaternary pump: Solvent lines to connect the solvent reservoirs 6036.1703
to the degasser inlet ports
Dual pump: Solvent lines to connect the solvent reservoirs to the 6036.1704
degasser inlet ports
Binary pump: Solvent lines to connect the solvent reservoirs to the 6036.1701
solvent selectors
Isocratic pump: Solvent line to connect the solvent reservoir to 6036.1705
the pump head
Solvent lines to connect the pump inlet to the pump heads
Quaternary pump: Tubing kit, including: 6044.8017
• Solvent lines from degasser to proportioning valve
• Solvent line from proportioning valve to pump head
Dual pump: Tubing kit, including: 6044.8005
• Solvent lines from degasser to proportioning valve
• Solvent line from proportioning valve to pump head
Binary pump: Tubing kit, including: 6044.8006
• Solvent lines from solvent selectors to degasser
• Solvent lines from degasser to pump heads

Operating Manual
12.4.4 Mixing Systems

system.
The tables list the reordering part numbers for the components with
which the pump is shipped from the factory. Mixing systems with other
volumes are available as an option. For ordering information, see
Optional Accessories (} page 267).
Static mixers

(standard in binary VC-pump, quaternary pumps and dual pumps)
(standard in binary VF- pump and isocratic pumps)
Capillary mixers
Capillary mixer (volume: 50 µL) for use with static mixers

(volumes: 150 µL, 350 µL, 750 µL, and 1500 µL) for:
VC-pumps 6044.3015
VF-pumps 6044.5026
12.4.5 Miscellaneous Parts
Capillary, nanoViper (length: 750 mm, inner diameter: 75 µm) 6041.5780

To be used, for example, when running in new piston seals.
Cleaning swabs (pack of 25) 6040.0007
Diagnostics tool kit 6040.3099
The kit includes a fitting plug (Viper, biocompatible) and
backpressure capillaries (2 capillaries with 15 m length each).
Fitting plug, Viper, biocompatible 6040.2303
Front door kit, including right door and left door 6044.1920
Fuses kit, Vanquish system 6036.0002
The kit includes the appropriate fuses for the Vanquish system
modules. For the pump, use only the 3.15 AT 250 V AC, slow-blow
fuses.
Packaging material for pump 6084.7001
Purge valve knob (with integrated seals) 6040.2035

Operating Manual
Syringe and tubing kit, including 6000.0010

• 12 mL plastic syringe (pack of 5)
• Silicone tubing (O.D. x I.D. 2.8 x 1.3), 3 m
Tool kit, including 6007.9304
• Spacing tools, pump head and pistons
For system capillaries and tubing, refer to the Vanquish System
Operating Manual.
For system capillaries and tubing for special applications, refer to
the related application documentation.
12.4.6 Interface Cables and Power Cords

Interface cables
Digital I/O signaling cable, 6-pin, cable length: 5 m 6036.0006

System interlink cable (RJ45), 0.5 m 6036.0004
USB cable, type A to type B, high-speed, USB 2.0 6035.9035A
Cable length: 1 m
USB cable, type A to type B, high-speed, USB 2.0 6911.0002A
Cable length: 5 m
Power cords
Power cord, Australia 6000.1060

Power cord, China 6000.1080
Power cord, Denmark 6000.1070
Power cord, EU 6000.1000
Power cord, India, SA 6000.1090
Power cord, Italy 6000.1040
Power cord, Japan 6000.1050
Power cord, UK 6000.1020
Power cord, USA 6000.1001
Power cord, Switzerland 6000.1030

Operating Manual
13 • Appendix
13 Appendix
This chapter provides additional information about compliance and the
use of the digital I/O ports.

Operating Manual
13 • Appendix
13.1 Compliance Information

13.1.1 Declarations of Conformity
CE Declaration of Conformity
The device has satisfied the requirements for the CE mark and is
compliant with the applicable requirements.
EAC Declaration of Conformity

The device has satisfied the requirements for the EAC mark and is
RoHS Compliance
This product complies with the RoHS (Restrictions of Hazardous
Substances) directives:
• European RoHS Directive

Directive on the restriction of the use of certain hazardous
substances in electrical and electronic equipment
The CE mark on the device indicates that the product is compliant
with the directive.
• China RoHS regulations

Measures for Administration of the Pollution Control of Electronic
Information Products
One of the following logos may be present on the device if
applicable:
Logo Description
The green logo marks items that do not contain the hazardous
substances identified by the regulations.
The orange logo including a one-digit or two-digit number marks

items that contain hazardous substances identified by the
regulations. The number indicates the environment-friendly use
period (EFUP) of the item. During this period, the item (when used as
intended) will not cause serious damage to human health or
environment.
For more information, go to http://www.thermofisher.com/us/en/
home/technical-resources/rohs-certificates.html
UKCA Declaration of Conformity

The device has satisfied the requirements for the UKCA mark and is

Operating Manual
13 • Appendix
UL/CSA 61010-1 Compliance

The label of the NRTL Lab on the device (for example, cTUVus or CSA
mark) indicates that the device has satisfied the requirements of the
applicable standards.
13.1.2 WEEE Compliance

This product is required to comply with the European Union’s Waste
Electrical & Electronic Equipment (WEEE) Directive. It is marked with the
following symbol:
Figure 83: WEEE symbol
Thermo Fisher Scientific has contracted with one or more recycling or

disposal companies in each European Union (EU) Member State, and
these companies should dispose of or recycle this product. For further
information, contact Thermo Fisher Scientific.
13.1.3 FCC Compliance

This equipment has been tested and found to comply with the limits for
a Class A digital device, pursuant to part 15 of the U.S. FCC Rules.
These limits are designed to provide reasonable protection against

harmful interference when the equipment is operated in a commercial
environment. This equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the
instructions, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause
harmful interference, in which case the user will be required to correct
the interference at his expense.

Operating Manual
13 • Appendix
13.1.4 Manual Release History
Revision Covering
4.0 and 5.0 VC‑P10‑A, VC‑P20‑A, VC‑P21‑A, VC‑P32‑A, VC‑P33‑A, VC‑P40‑A,

VF‑P10‑A, VF‑P20‑A, VF‑P32‑A
3.0 VF‑P10‑A, VF‑P20‑A, VF‑P32‑A
2.0 and 2.0a VF‑P10‑A, VF‑P20‑A
1.1 and 1.2 VF‑P20‑A
The instructions were prepared in English (original instructions). Other

language versions are translations based on the English original
instructions.

Operating Manual
13 • Appendix
13.2 Digital I/O

The digital I/O ports (Dig I/O) can be used to exchange digital signals
with external devices. Each port provides:
• one digital input
• one relay output
• one bidirectional input/output
Pin Assignment
Figure 84: Digital I/O port
Pin Description — Signal Name
1 Bidirectional input/output
2 Relay output — Relay_NC (Normally Closed contact)
3 Ground — GND
4 Digital input — Input
5 Relay output — Relay_COM
COM is the common contact for NO and NC. If the relay is not activated or if
the device is turned off, the connection is between COM and NC. If the relay
is activated, the connection is between COM and NO.
6 Relay output — Relay_NO (Normally Open contact)
The next table lists the functions assigned to the connector pins and the
color of the cable wire connected to each pin.
Pin Wire Color Signal Name Signal Level Remarks
1 Pink Input/output Input (low active): Configure as either input or output.

On: 0-0.4 V Reference potential is ground. Note
Off: 2.2-5 V the following:
Open Collector Output: • The maximum input voltage at the
0-5 V, 0-2 mA input must not exceed +5 V with
Pull-up resistor: 47 kΩ to 5 V reference to ground.
• The minimum input voltage must
not be lower than the ground
potential.
2 Gray Relay output Potential free Opening contact
— Relay_NC 0-24 V, 0-100 mA

Operating Manual
13 • Appendix
Pin Wire Color Signal Name Signal Level Remarks
3 Green Ground — Ground Reference potential

GND
4 Yellow Digital input — Input (low active): Digital input; reference potential is
Input On: 0-0.4 V ground. Note the following:
Off: 2.2-5 V • The maximum input voltage at the
Pull-up resistor: 47 kΩ to 5 V input must not exceed +5 V with
reference to ground.
• The minimum input voltage must
not be lower than the ground
potential.
5 White Relay output Potential free Common contact for NO and NC
— Relay_COM
6 Brown Relay output Potential free Closing contact
— Relay_NO 0-24 V, 0-100 mA
Prerequisites
To use the digital I/O functionality, the following must be fulfilled:
• The digital I/O port is connected to the external device with the
digital I/O signaling cable.
• The inputs and outputs that you want to use are selected in the
Instrument Configuration Manager.
Connecting a Digital I/O Port
1. Plug the 6-pin connector of the cable into the digital I/O port that
you want to use.
2. For each relay output or digital input to be used, connect the

appropriate signal wire and ground wire to the corresponding
connectors on the external device. For details, refer to the
documentation provided with the external device.
Selecting the inputs and outputs in the chromatography data system
1. In the dialog box for the pump, on the Inputs and Outputs pages,
select the inputs (Pump_Input_X) and outputs (Pump_Relay_X) that
you want to use. The numbering in the dialog box corresponds to
the port numbers on the pump.
2. To configure the bidirectional input/output (Pump_IO_X), select the

related check box on either the Inputs or Outputs page, depending
on the preferred usage.

Operating Manual
Index
Index
A cleaning ......................................................... 124
compression .................................................... 98
accessories ..................................................... 259 compression values ....................................... 211
optional ..................................................... 267 condensation ............................................. 50, 54
ship kit....................................................... 261 connection
additives ........................................................... 26 power cord ................................................. 54
information ................................................. 26 connectors ....................................................... 53
use............................................................... 90 consumables.......................................... 259, 270
air bubbles (remove) .............................. 101, 105 cTUVus mark.................................................. 283
algae ................................................................. 90 curve ................................................................ 98
audit trail........................................................ 199
Audit Trail messages ...................................... 200 D
B decontamination ........................................... 124
degasser mode ................................................ 98
Basic Tightness Test ....................................... 177 delivery ............................................................ 44
buffer use ......................................................... 90 device
buffers .............................................................. 26 optimization ............................................. 107
concentration.............................................. 26 preparing for operation.............................. 92
information ................................................. 26 restart after long-term shutdown ............ 113
use............................................................... 90 shutdown.................................................. 110
Dig I/O...................................................... 53, 285
C Digital I/O................................................. 53, 285
capillaries Dock (button)................................................... 85
conventional (non-Viper) ............................ 61 door ................................................................. 51
guide ........................................................... 56 open............................................................ 51
install........................................................... 57 remove ..................................................... 116
Viper............................................................ 58 replace...................................................... 185
capillary mixer .................................................. 37 unhinge............................................. 116, 185
replace....................................................... 167 drain system .................................................... 62
CE mark .......................................................... 282 drainage........................................................... 62
charged aerosol detector ............................... 198 drop detector.......................... 218, 219, 228, 233
check valve drop detector (replace) ................................. 132
clean.......................................................... 164 dual pump...................................................... 217
maintenance ............................................. 159 specifics .................................................... 225
replace....................................................... 159 dwell volume .................................. 222, 231, 236
CheckValvesServiceDone ............................... 126
chloride concentration ..................................... 28 E
Chromeleon...................................................... 39 EAC mark ....................................................... 282
audit trail................................................... 199 equilibration .................................................... 93
device setup ................................................ 80 ExceptionLogClear (Chromeleon) .................. 199
module setup .............................................. 80
Predictive Performance............................. 125 F
Smart Shutdown........................................ 110
Smart Standby........................................... 110 FCC................................................................. 283
Smart Startup .............................................. 93 filter permeability.......................................... 213

Operating Manual
Index
firmware failure.............................................. 199 L
firmware update ............................................ 183
flow .................................................................. 94 leak detection ............................................ 38, 98
Flow (button).................................................... 86 leak sensor..................................................... 210
flow acceleration.............................................. 94 leak sensor mode............................................. 98
flow connections .............................................. 55 leak test
flow deceleration ............................................. 94 automatic testing ..................................... 177
Flow LEDs ......................................................... 86 Basic Tightness Test.................................. 177
flow ramp ......................................................... 94 manual testing.......................................... 178
flush piston seals ....................................... 156, 210
pump ................................................. 122, 123 pump ................................................ 177, 210
fuses ............................................................... 181 purge valve knob ...................................... 210
seal wash system .............................. 128, 210
G leakage........................................................... 210
LED bar................................................ 84, 86, 198
gloves ............................................................... 23 liquid leaks..................................................... 210
gradient delay volume.................... 222, 231, 236 liquid level monitoring..................................... 96
guide hole......................................................... 56 long-term shutdown...................................... 111
guidelines
installation................................................... 46 M
maintenance ............................................. 117
operation..................................................... 83 main power fuses .......................................... 181
maintenance.......................................... 115, 120
I cleaning .................................................... 124
decontamination ...................................... 124
inlet check valve doors......................................................... 185
clean.......................................................... 164 firmware update....................................... 183
replace....................................................... 159 fuses ......................................................... 181
inline filter .............................................. 237, 268 general rules............................................. 119
permeability ...................................... 166, 213 internal ..................................................... 120
replace............................................... 166, 213 interval ..................................................... 120
installation........................................................ 45 introduction.............................................. 116
capillaries and tubing .................................. 56 predictive performance............................ 125
safety guidelines ......................................... 46 safety guidelines....................................... 117
site requirements........................................ 49 messages ....................................................... 200
system ......................................................... 47 MixerChanged ............................................... 126
Instrument Audit Trail .................................... 199 mixing system .................................................. 37
intended use..................................................... 20 available volumes ..................................... 237
interior view ..................................................... 34 exchange (change to different volume) ... 239
Interlink ............................................................ 53 permeability ............................................. 166
internal maintenance ..................................... 120 replace...................................................... 166
isocratic pump................................................ 233 move................................................................ 48
Mute Alarm...................................................... 85
K
keypad.............................................................. 84 N
non-Viper capillaries........................................ 61
normal-phase compatible solvents and additives
.................................................................. 249

Operating Manual
Index
O pump head
maintenance............................................. 134
operating parameters ...................................... 94 parts overview.......................................... 135
operating principle ........................................... 33 pump head seals....................................... 154
operation.................................................... 39, 81 replace...................................................... 136
control elements ......................................... 84 pump head bushing ....................................... 135
interrupt.................................................... 110 pump head seals
power on/off ............................................... 89 replace...................................................... 154
safety guidelines ......................................... 83 pump inlet ............................................. 221, 230
optimization ................................................... 107 pump outlet.... 218, 220, 221, 229, 230, 233, 234
guidelines .................................................. 107 pump pressure (record)................................... 95
outlet check valve purge ............................................................... 98
clean.......................................................... 164 automatic ................................................. 101
replace....................................................... 161 changing solvents ..................................... 102
overview (functional) ....................................... 31 empty solvent lines .................................. 102
first time operation .................................. 102
P manual...................................................... 102
peristaltic tubing remove air bubbles................................... 102
replace....................................................... 130 Purge (button) ................................................. 85
permeability purge settings ................................................ 100
static mixer................................................ 166 purge valve ............................... 36, 218, 219, 233
permeability test ............................................ 213 purge valve knob (replace) ............................ 175
pH range........................................................... 27 purge/sensor unit ............................................ 36
piston purging........................................................... 100
clean.......................................................... 144
replace....................................................... 142 Q
piston seal QualificationDone.......................................... 126
leak test..................................................... 156 quaternary pump........................................... 217
replace....................................................... 145
run-in......................................................... 149 R
piston seal wash cycle ...................................... 99
piston seal wash system..................... 35, 69, 127 rating plate ...................................................... 19
PistonsChanged.............................................. 126 rear seal wash cycle......................................... 99
power considerations................................. 49, 50 rear seal wash system......................... 35, 69, 127
power cord ................................................. 50, 54 regulatory compliance..................................... 29
power on/off .................................................... 89 remove slide-in module................................. 190
power up .......................................................... 79 reordering...................................................... 259
Predictive Performance.................................. 125 replacement parts ................................. 259, 270
preparation requirements
remove module......................................... 190 power cord ................................................. 50
pressure limits.................................................. 95 restart device after long-term shutdown ...... 113
pressure range ................................................. 95 return
protective clothing ........................................... 22 slide-in module ......................................... 192
Pump .............................................................. 224 RoHS mark ..................................................... 282
pump (flush) ........................................... 122, 123
pump block LED.................................. 84, 87, 198

Operating Manual
Index
S shutdown....................................................... 110
long-term.................................................. 111
safety class ....................................................... 21 short-term ................................................ 110
safety glasses.................................................... 23 signal words..................................................... 18
safety guidelines site requirements ............................................ 49
case of emergency ...................................... 25 condensation ........................................ 50, 54
electrical safety ........................................... 23 power considerations ........................... 49, 50
general ........................................................ 21 slide-in module .............................................. 190
general hazards ........................................... 24 install ........................................................ 192
installation................................................... 46 remove ..................................................... 190
maintenance ............................................. 117 return........................................................ 192
operation..................................................... 83 Smart Shutdown ............................................ 110
power cord .................................................. 50 Smart Standby ............................................... 110
protective equipment ................................. 22 Smart Startup .................................................. 93
qualification of personnel ........................... 22 solvent
servicing .................................................... 117 chloride concentration ............................... 28
safety symbols............................................ 18, 19 information................................................. 26
scope of delivery .............................................. 44 pH range ..................................................... 27
seal wash body ............................................... 135 use .............................................................. 90
seal wash cycle ..................................... 79, 89, 99 solvent composition ........................................ 96
seal wash detector (replace) .......................... 132 solvent consumption ............................... 96, 226
seal wash seal (replace).................................. 151 solvent line filter...................................... 63, 169
seal wash system........................................ 35, 69 assemble............................................. 64, 174
flush............................................................. 76 replace...................................................... 173
maintenance ............................................. 127 solvent lines............................................. 63, 169
replace....................................................... 129 connect....................................................... 63
seal wash detector .................................... 132 empty ....................................................... 169
seal wash liquid ........................................... 69 replace...................................................... 170
setup ........................................................... 70 shut-off valves .......................................... 107
test for leakage ......................................... 128 solvent monitoring .......................................... 96
SealsChanged ................................................. 126 solvent name ................................................... 96
Select (button).................................................. 85 solvent reservoir (share)................................ 226
Select LEDs ....................................................... 85 solvent selection valve..................................... 32
self-test ...................................................... 79, 89 solvent selector ....................................... 32, 232
service ............................................................ 115 specifications ................................................. 251
ServiceDone ................................................... 126 performance............................................. 252
setup physical..................................................... 258
hardware..................................................... 52 startup ............................................................. 93
software ...................................................... 80 static filter............................... 166, 213, 237, 268
system arrangement ................................... 52 static mixer ...................................................... 37
ShareEluentBottles......................................... 226 permeability ..................................... 166, 213
ShareWasteBottles......................................... 227 replace...................................................... 167
ship................................................................. 187 status indicator
slide-in module.......................................... 192 LED bar .......................................... 84, 86, 198
ship kit ............................................................ 261 Status LED...................................... 84, 86, 198
short-term shutdown ..................................... 110 Status LED ........................................... 84, 86, 198

Operating Manual
Index
support ring.................................................... 145
SyncWithPump ......................................... 99, 224
system arrangement ........................................ 52
system equilibration......................................... 93
System Interlink................................................ 53
system pressure sensor.................................... 36
T
transport ........................................................ 187
troubleshooting.............................................. 197
check compression values......................... 211
general information .................................. 198
leakage ...................................................... 209
messages................................................... 200
pressure issue ........................................... 211
retention time shift ................................... 211
tubing ............................................................... 57
tubing bracket .................................................. 56
tubing chase ..................................................... 56
tubing guides.................................................... 56
type label.......................................................... 19
U
UKCA mark ..................................................... 282
UL/CSA compliance ........................................ 283
Universal Serial Bus .......................................... 53
unpack.............................................................. 42
USB ................................................................... 53
V
Viper
knurl ............................................................ 58
torque toothing........................................... 58
W
waste ................................................................ 62
waste container (share) ................................. 227
waste level ..................................................... 227
waste level monitoring..................................... 97
WEEE .............................................................. 283

Operating Manual
www.thermofisher.com
Thermo Fisher Scientific Inc.

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Massachusetts 02451
USA

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Original Operating Manual

Printed manual version only

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2 Safety ......................................................................................... 17

3 Device Overview......................................................................... 31

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3.5 Purge/Sensor Unit................................................................................................ 36

4 Unpacking .................................................................................. 41

5 Installation ................................................................................. 45

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7 Maintenance and Service ......................................................... 115

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7.6 Pump Head......................................................................................................... 134

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8 Troubleshooting ....................................................................... 197

9 Pump-Specific Information ....................................................... 215

10 Modifying the Pump for Specific Applications........................... 235

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11 Specifications ........................................................................... 251

12 Accessories, Consumables and Replacement Parts ................... 259

Index ........................................................................................ 287

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1 Using this Manual

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1.1 About this Manual

This manual also contains safety messages, precautionary statements,

Note the following:

• The device configuration may vary; therefore, not all descriptions

• If some detail applies to only one model or variant, the model or

• Illustrations in this manual are provided for basic understanding.

• The pump is also referred to as device in this manual. If some detail

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1.2.1 Conventions for Safety Messages

• Safety messages or precautionary statements that apply to the

• Safety messages or precautionary statements that apply to an entire

• Safety messages that apply to only a particular section or procedure

1.2.2 Special Notices

TIP Highlights information of general interest or helpful information that

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1.2.3 Typographical Conventions

Data Input and Output

• Buttons that you click on the screen

• Commands that you enter by the keyboard

• Names of, for example, dialog boxes, properties, and parameters

References and Messages

• References to additional documentation appear italicized.

• Messages that appear on the screen are identified by quotation

Particularly Important Words

Electronic Manual Version (PDF)

• Table of contents entries

• Cross-references (in blue text)

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1.3 Reference Documentation

• Chromeleon™ Help and documents

• Instrument Configuration Manager Help

• Quick Start Guide

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