Man 4820 3601 LC Vanquish UHPLC Man48203601 EN

thermoscientific
Vanquish
UHPLC and HPLC

Systems
Operating Manual
4820.3601-EN Revision 5.0 • August 2022
*4820.3601-EN-5.0*
Copyright © 2022 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Manual
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UHPLC and HPLC Systems Page 3

Operating Manual
Contacting Us
Page 4 UHPLC and HPLC Systems

Operating Manual
Contents
Contents
1 Using this Manual......................................................................... 9
1.1 About this Manual ............................................................................................... 10
1.2 Conventions ......................................................................................................... 11
1.2.1 Conventions for Safety Messages ............................................................ 11
1.2.2 Special Notices ......................................................................................... 11
1.2.3 Typographical Conventions ...................................................................... 12
1.3 Reference Documentation................................................................................... 13
2 Safety ......................................................................................... 15

2.1 Safety Symbols and Signal Words ........................................................................ 16
2.1.1 Safety Symbols and Signal Words in this Manual..................................... 16
2.1.2 Observing this Manual ............................................................................. 16
2.1.3 Safety Symbols on the System ................................................................. 17
2.2 Intended Use........................................................................................................ 18
2.3 Safety Precautions ............................................................................................... 19
2.3.1 General Safety Information...................................................................... 19
2.3.2 Qualification of the Personnel ................................................................. 19
2.3.3 Personal Protective Equipment................................................................ 21
2.3.4 General Residual Hazards......................................................................... 22
2.3.5 In Case of Emergency ............................................................................... 24
2.4 Solvent and Additive Information ........................................................................ 25
2.4.1 General Compatibility .............................................................................. 25
2.4.2 Piston Seal Compatibility.......................................................................... 25
2.4.3 Allowed pH Ranges................................................................................... 27
2.4.4 Allowed Concentrations ........................................................................... 27
2.4.5 Further Information ................................................................................. 27
3 System Overview........................................................................ 29

3.1 System Description (Standard Configuration)...................................................... 30
3.1.1 Solvent Rack ............................................................................................. 31
3.1.2 System Base ............................................................................................. 31
3.2 Operation............................................................................................................. 33

Operating Manual
Contents
4 Unpacking .................................................................................. 35

4.1 Unpacking ............................................................................................................ 36
4.2 Scope of Delivery ................................................................................................. 37
5 Installation ................................................................................. 39

5.1 Safety Guidelines for Installation ......................................................................... 40
5.2 Installing the System ............................................................................................ 41
5.3 Site Requirements................................................................................................ 43
5.3.1 Workbench............................................................................................... 43
5.3.2 Power Considerations .............................................................................. 44
5.3.3 Power Cord............................................................................................... 44
5.3.4 Condensation ........................................................................................... 45
5.3.5 Operating Conditions ............................................................................... 45
5.4 Setting Up the Hardware ..................................................................................... 47
5.4.1 System Stack Setup .................................................................................. 47
5.4.2 Moving the System Stack (Unlocking/Locking) ........................................ 52
5.4.3 Connecting the Waste Lines..................................................................... 55
5.4.4 Attaching the Column Compartment to the System Stack ...................... 62
5.4.5 Signal Cable Connections ......................................................................... 65
5.4.6 Connecting Power Cables......................................................................... 71
5.4.7 Guiding Cables through the Cable Clips ................................................... 72
5.5 Setting Up the Flow Connections......................................................................... 73
5.5.1 General Information and Guidelines........................................................ 73
5.5.2 Flow Connections Overview..................................................................... 74
5.5.3 Guiding Capillaries and Tubing Through the System................................ 75
5.5.4 Connecting Fittings, Capillaries, and Tubing ............................................ 77
5.6 Turning On the System......................................................................................... 79
5.7 Setting Up the System in the Software ................................................................ 80
5.8 Flushing the System ............................................................................................. 82
6 Operation................................................................................... 83
6.1 Introduction to this Chapter ................................................................................ 84
6.2 Safety Guidelines for Operation........................................................................... 85
6.3 Power On/Off Control.......................................................................................... 86
6.4 Preparing the System for Operation .................................................................... 87
6.5 Use of Solvents and Additives.............................................................................. 89

Operating Manual
Contents
6.6 Operating the System from the Software............................................................ 91

6.6.1 Starting the Instrument Controller and Client ......................................... 91
6.6.2 Controlling the System from the ePanel Set ............................................ 92
6.6.3 Monitoring the Baseline........................................................................... 93
6.6.4 Running Automated Sample Analysis....................................................... 94
6.7 Shutting Down the System................................................................................... 96
7 Maintenance and Service ........................................................... 99

7.1 Introduction to Maintenance and Service ......................................................... 100
7.2 Safety Guidelines for Maintenance and Service ................................................ 101
7.3 General Rules for Maintenance and Service...................................................... 103
7.4 Routine and Preventive Maintenance ............................................................... 104
7.4.1 Maintenance Plan .................................................................................. 104
7.4.2 Cleaning or Decontaminating the System .............................................. 105
7.5 Transporting or Shipping the System................................................................. 107
8 Troubleshooting ....................................................................... 111

8.1 General Information about Troubleshooting..................................................... 112
8.2 System Troubleshooting .................................................................................... 113
8.2.1 Peak Shape ............................................................................................. 113
8.2.2 Ghost Peaks, Negative Peaks and Spikes ............................................... 114
8.2.3 Peak Area Precision................................................................................ 115
8.2.4 Flow........................................................................................................ 117
8.2.5 Pressure.................................................................................................. 118
8.2.6 Retention Time Variation ....................................................................... 119
8.2.7 Baseline .................................................................................................. 119
8.2.8 Temperature Control ............................................................................. 121
8.2.9 Power and Communication.................................................................... 122
8.2.10 System Diagnostics................................................................................. 123
9 Modifying the System for Specific Applications ........................ 127

9.1 Normal-Phase Compatible Solvents and Additives............................................ 128
9.2 Modifying the System Modules ......................................................................... 128
9.3 Considerations with Normal-Phase Compatible Solvents and Additives ........... 130

Operating Manual
Contents
10 Specifications ........................................................................... 133

10.1 System Specifications......................................................................................... 134
10.2 Solvent Rack and System Base Specifications .................................................... 135
11 Accessories, Consumables and Replacement Parts ................... 137

11.1 General Information .......................................................................................... 138
11.2 Ship Kit ............................................................................................................... 139
11.3 Optional Accessories.......................................................................................... 141
11.4 Consumables and Replacement Parts................................................................ 143
11.4.1 Capillaries and Tubing ............................................................................ 143
11.4.2 Solvents and Wash Systems ................................................................... 144
11.4.3 Fuses and Cables .................................................................................... 145
11.4.4 Other Parts ............................................................................................. 145
12 Appendix.................................................................................. 147
12.1 Compliance Information .................................................................................... 148
12.1.1 Declarations of Conformity .................................................................... 148
12.1.2 WEEE Compliance .................................................................................. 149
12.1.3 FCC Compliance...................................................................................... 149
12.1.4 Manual Release History.......................................................................... 150
Index ........................................................................................ 151

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 provides instructions for installation, set up, start up, shut
down, operation, maintenance and troubleshooting of your system.
This manual also contains safety messages, precautionary statements,

and special notices. Follow these properly to prevent personal injury,
damage to the system, or loss of data.
Note the following:
• The descriptions in this manual refer to a standard one-stack

VanquishTM system configuration. Not all descriptions necessarily
apply to your particular system.
• Illustrations in this manual are provided for basic understanding.

They can vary from the actual model of the system. However, this
does not influence the descriptions. No claims can be derived from
the illustrations in this manual.

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 system 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 system.

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
refer to the viewpoint of a person that is facing the system 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 modules of the Vanquish system
• 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 system.

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 system.
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 system, read this manual carefully

to be familiar with the system and this manual. The manual contains
important information with regard to user safety as well as use and
care of the system.
• Always keep the manual near the system 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 System

For a list of the safety symbols that appear on a Vanquish system
module or on labels affixed to a module, refer to the Operating Manual
of the module. Follow the safety notices in these manuals to prevent the
risk of operator injury or damage to the system.
Safety Symbols on the System Base
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.
Indicates a power button that switches the system between on and

off states.

Operating Manual
2 • Safety
2.2 Intended Use

The intended use of the Vanquish system is to analyze mixtures of
compounds in sample solutions.
The system is for use by qualified personnel and in laboratory

environment only.
The Vanquish system and its modules 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 system.
If the system is used in a manner not specified by Thermo Fisher

Scientific, the protection provided by the system could be impaired.
• Operate the system only within its technical specifications.
• Use only the replacement parts and additional components, options,
and peripherals specifically authorized and qualified for the system
by Thermo Fisher Scientific.
• Perform only the procedures that are described in this operating
manual and in supporting documents for the system. Follow all
instructions step by step and use the tools recommended for the
procedure.
• Open the enclosure of the system 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 system. If there is any question regarding appropriate usage,
contact Thermo Fisher Scientific before proceeding.
2.3.2 Qualification of the Personnel

Observe the information below on the proper qualification of the
personnel installing and/or operating the system.

Operating Manual
2 • Safety
Installation
System configuration without Charger
Only skilled personnel are permitted to install the system 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 system, the installer is responsible for
ensuring the safety of the system.
System configuration with Charger: Installation by Service Engineer

only
Service personnel certified by Thermo Fisher Scientific must perform the

installation (for brevity, referred to as Thermo Fisher Scientific service
engineer).
Operation
General Operation
The system is designed to be operated only by trained and qualified

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

Operating Manual
2 • Safety
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.
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.

Operating Manual
2 • Safety
2.3.4 General Residual Hazards

Pay attention to the following general residual hazards when working
with the system:
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 system 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 system in the presence of flammable gases or
fumes.
CAUTION—Escape of Hazardous Substances from PEEK Capillaries

Some capillaries in the system are made of PEEK. Swelling or attack by
acids can cause PEEK capillaries to start leaking or to burst. Certain
chemicals, for example, trichlormethane (CHCl3), dimethyl sulfoxide
(DMSO), or tetrahydrofuran (THF) can cause PEEK to swell. Concentrated
acids, such as sulfuric acid and nitric acid, or a mixture of hexane, ethyl
acetate, and methanol, can attack PEEK.
• Swelling or attack is not a problem with brief flushing procedures.
• For more information, refer to the technical literature on the
chemical resistance of PEEK.
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.

Operating Manual
2 • Safety
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.
2.3.5 In Case of Emergency
WARNING—Safety Hazard
In case of emergency, disconnect the system modules 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. See Normal-Phase Compatible Solvents and
Additives (} page 128).
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
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.
VH‑pumps The pump is shipped with UHMW-PE piston seals. Using
tetrahydrofuran, ketones, or ammonium hydroxide as
prolonged exposure.

Operating Manual
2 • Safety
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.
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 information about the materials that are used in the flow path of
the Vanquish system, refer to the Specifications chapter in the
Operating Manual for each module.
• Observe the general guidelines and recommendations on the use of
solvents and additives in the chromatography system (see Use of
Solvents and Additives (} page 89)).
• 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

Operating Manual
3 • System Overview
3 System Overview
This chapter introduces you to the system and the main components.

Operating Manual
3.1 System Description (Standard Configuration)

The Vanquish system is designed for use in high performance liquid
chromatography (HPLC) and ultra-high performance liquid
chromatography (UHPLC) applications. The table shows the standard
configurations of three Vanquish systems as an example:
Module Core system Flex system Horizon system
Solvent rack Vanquish solvent rack

1
Detector VC-D40 VF-D40 VH-D10
Column VC-C10 VH-C10 VH-C10
compartment2
Autosampler VC-A12 VF-A10 VH-A10
Pump VC-P20 Quaternary: Binary: VH-P10
VF-P20 VF-P10
System base Vanquish system base
1
The appropriate flow cell has to be ordered separately.
2
In the standard configuration, the Vanquish system includes one column
compartment, installed to the right side of the system. For other configurations, see
System Stack Setup (} page 47).
For a description of the solvent rack and system base, see further down
in this chapter. For a description of the other modules, refer to the
Operating Manuals for these modules.
TIP
If your system configuration is a non-standard system configuration
including modules other than those listed in the table, for example, a
fluorescence detector or a charged aerosol detector, refer to the
Operating Manual for the module.

Operating Manual
3.1.1 Solvent Rack

The solvent rack provides a secure location for placing solvent
reservoirs. It can store, for example, 6 x 1 L of solvent and 2 x 0.25 L of
wash liquid as shown in the figure. The maximum volume for an
individual reservoir should not exceed 5 L.
Figure 1: Solvent rack (front view)
The front side of the solvent rack is magnetic. Here, you can attach a
magnetic label holder, for example, to show a user-specific system
name. Labels are included in the system ship kit.
3.1.2 System Base

The system base is a mandatory part of the Vanquish system. It is the
bottom part of the system stack and carries the pump, autosampler, and
detector in a standard configuration.
The system base provides:
• Power button for power on/off control of all modules
• Drawer to store tools and small system parts
• Drain port for connecting a system waste line
• Locks to toggle between moveable and stationary mode
• Dedicated mounting space for optional Vanquish System Controller

Operating Manual
Figure 2: System base (front and rear view)
No. Description
1 Blind cap/Vanquish System Controller power button

If a Vanquish system controller is installed, the power button allows power on/
off control of the system controller.
2 System power button
Allows power on/off control for all modules of the system that are connected
to the system base via the System Interlink port.
3 Drawer for tools
Allows storing any tools that are necessary to install or maintain the Vanquish
system. Push the drawer front to open or close the drawer.
4 Detector waste outlet
For guiding the waste line from the detector to waste.
5 System drain port
For connecting the system waste line.
6 Locks - on the left and right side of the system base
Allows toggling between movable and stationary.
7 System Interlink port
Allows connecting the other modules for power on/off control from the
Vanquish system base.
8 VSC port
Allows connecting the optional system controller.

Operating Manual
3.2 Operation
The system 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, see Operating the System from
the Software (} page 91).
TIP The system 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.
Keypads are available inside the system modules, allowing you to

perform certain basic functions directly from each module.

Operating Manual

Operating Manual
4 • Unpacking
4 Unpacking
This chapter provides information for unpacking the system 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 system for any signs of mechanical damage that
might have occurred during shipment.
If you suspect that the system 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 Solvent Rack and System Base

To unpack the solvent rack and system base, follow these steps:
1. Place the shipping container on the floor and open it.
2. Remove the ship kit.
3. Carefully remove the solvent rack and liquid reservoirs from the
shipping container.
4. Place the solvent rack on a stable surface.
5. Carefully remove the system base from the shipping container.
6. If applicable
Remove any additional packing material.
7. Place the system base on a stable surface.
TIP Keep the shipping container and all packing material. These items
will be needed if the system is transported to a new location or shipped.
Unpacking the System Modules

For details on unpacking and moving the system modules, refer to the
Operating Manual of each module.

Operating Manual
4 • Unpacking
4.2 Scope of Delivery

The following items are included in the delivery:
• System base
• Solvent rack
• Solvent reservoirs
• Ship Kit
For details about the kit content, see Ship Kit (} page 139).
• System operating manual (downloadable from customer manual

web site)

Operating Manual
4 • Unpacking

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 system.

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 19).

in the Safety Guidelines for Installation section in the Operating Manual
for the individual modules of the Vanquish system.

Operating Manual
5 • Installation
5.2 Installing the System

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.
The following description refers to the standard system configuration,

see System Description (Standard Configuration) (} page 30).
If your system configuration is a non-standard system configuration and

includes, for example, a fluorescence detector or a charged aerosol
detector, refer to the Operating Manual for the module for installation
and operation details.
If personnel other than a Thermo Fisher Scientific service engineer

installs the system, follow the steps below.
1. Pay attention to the safety guidelines and observe all site

requirements.
For the safety guidelines when installing the system, see Safety
Guidelines for Installation (} page 40). For the site requirements, see
Site Requirements (} page 43).
2. Set up the system hardware. See Setting Up the Hardware

(} page 47).
3. Set up the flow connections. See Setting Up the Flow Connections

(} page 73).
4. Turn on the system. See Turning On the System (} 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 system in the software. See Setting Up the System in the
Software (} page 80).
6. Flush the system. See Flushing the System (} page 82).

Operating Manual
5 • Installation
7. 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.
NOTICE
If the system 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.
8. Recommended: Perform Operational Qualification.

The qualification kit includes all materials required for the
qualification and detailed instructions.

Operating Manual
5 • Installation
5.3 Site Requirements

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

Note the following:
• Make sure that the installation site has enough power outlets for all
devices in the system.
• Operate the system only under appropriate laboratory conditions
• For specifications, see Specifications (} page 133).
5.3.1 Workbench
The Vanquish system is designed to be placed on a workbench. If the
workbench shall carry a complete Vanquish system and possibly other
instruments, the bench must be capable to bear the weight of all devices
and instruments, including solvents.
For dimensions and weight, see Specifications (} page 133).
Workbench Requirements
Part Requirements
Workbench • Sturdy
• A height that ensures convenient access to the
interior of each device in the system.
• The bench top must be dry, clean, and resistant to
chemicals.
• If the system stack is to be stabilized with the
Bench Clamp kit, the workbench top must fulfill
one of the following requirements:
¨ Thickness: Between 15 and 50 mm
or
¨ Material: Soft enough for wood screws
Site for the workbench The workbench must stand in a secure and level
position that is free of vibrations.

Operating Manual
5 • Installation
System Clearance Requirements
Side Requirements
On the sides • Allow sufficient free space for electrical

connections and for proper air circulation
• At least 5 cm of clearance on each side
• If the system includes a Charger or a Vanquish
Display, allow at least 10 cm of clearance on the
left side.
On the rear • Allow sufficient free space for electrical
connections and for proper air circulation
• At least 15 cm of clearance
Top At least 30 cm of clearance above the top
5.3.2 Power Considerations
CAUTION—Electric Shock or Damage to 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.
5.3.3 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.

Operating Manual
5 • Installation
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.
5.3.4 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.
5.3.5 Operating Conditions

When operating the system, make sure that the installation site meets
these general environmental and operating conditions. For specified
ambient temperature and humidity, see Specifications (} page 133).
Temperature
Temperature fluctuations can affect the performance of the system.
Avoid locations with significant changes in temperature and strong air
drafts. For example, do not place the system in the direct sunlight, near
heating or cooling sources, or under an air duct.
Humidity
The relative humidity of the operating environment is important for the
performance of the system. Operate the system in the specified
humidity range, with no condensation.
When the humidity is too high, condensation may occur, causing

damage to the electronic components in the system. When the humidity
is too low, static electricity may accumulate and discharge, shortening
the life of the electronic components.

Operating Manual
5 • Installation
Ventilation
Make sure that the installation site is well ventilated at any time to avoid
potential health hazards and safety risks, which may be caused by
handling hazardous substances, volatiles or gases.
Vibration and mechanical shocks

Vibrations and mechanical shocks may affect the performance of the
system. Therefore, the installation site should be free of vibrations.
Avoid mechanical shocks and avoid placing the system in locations
where vibrations are caused by other instruments.
Electromagnetic interference
Electromagnetic sources of strong interference may affect the
performance of the system. In close proximity to the system, avoid
operating equipment generating strong electric or magnetic fields and
only operate certified laboratory equipment. Do not connect equipment
that may cause power disturbances to the same power network used to
supply the system.

Operating Manual
5 • Installation
5.4 Setting Up the Hardware

This section describes how to set up the hardware and provides
information about the system connectors and cables.
1. Set up the system stack. For details, see System Stack Setup
(} page 47).
2. Connect the Waste Lines. For details, see Connecting the Waste
Lines (} page 55).
3. Attach the column compartment. For details, see Attaching the

Column Compartment to the System Stack (} page 62).
4. Connect the required signal cables. For details, see Signal Cable
Connections (} page 65).
5. Connect power cords to the power-inlet connectors of all modules.

For details, see Connecting Power Cables (} page 71).
5.4.1 System Stack Setup
CAUTION—Heavy Load, Bulky Device

The system modules are too heavy or bulky for one person alone to
handle safely. To avoid personal injury or damage to the system
modules, observe the following guidelines:
• Physical handling of the modules, including lifting or moving,
requires a team effort of two persons.
• A team effort is in particular required when lifting the modules into
the system stack or when removing them.
• Modules with carrying handles: Use the carrying handles that were
shipped with the modules to move or transport the modules. Never
move or lift the modules by the front doors. This will damage the
doors or the modules. Modules without carrying handles: To lift or
move the modules, grasp the modules by the sides. Do not move or
lift the modules by the front door. This will damage the door or the
modules.
The system modules are arranged in a system stack. The arrangement

depends on the system configuration.
The descriptions below refer to the standard Vanquish system (one-

stack configuration). The one-stack configuration is the standard
configuration, as it optimizes the flow path for minimum delay volume.

Operating Manual
5 • Installation
Figure 3: Vanquish system, standard configuration (example)
No. Description
1 Solvent Rack
2 Detector
3 Autosampler
4 Pump
5 System Base
6 Column Compartment

Operating Manual
5 • Installation
5.4.1.1 Safety Guidelines for Setting Up the System Stack

Observe the following safety message and the explanations below.
WARNING—Risk of tilting system stack

A one-stack configuration may exceed the maximum allowed height. If
the system configuration is higher, the system stack poses a tilting risk
which can entail personal injury.
If your configuration is higher, you need to stabilize the stack with one of
the following safety measures:
• Use a stack stabilization kit (see table below).
• Build up the system in two separate stacks.
The following table shows which stack stabilization kit you need for
which stack height. The heights are measured from the table surface to
the solvent rack railing. Due to production and installation tolerances,
the actual stack height can be up to 2 cm higher than the limit. This
tolerance is acceptable.
Stack height Stabilization required
Up to 100 cm None
Example: Configuration with pump, autosampler, diode array
detector and charged aerosol detector
Up to 123 cm One of the following kits:
• Bench clamp kit
• Stack stabilizer kit
• IonBench with stack mounting kit
Up to 139 cm Bench clamp kit
139 cm and higher Build up the system in two separate stacks

Operating Manual
5 • Installation
5.4.1.2 Installing the System Stack
NOTICE
Moving the Vanquish system stack after installation even over short
distances on the workbench can damage and impair the functionality of
the system base.
• Therefore, install the system stack at the final location.
• If you have to move the system after installation, see Moving the
System Stack (Unlocking/Locking) (} page 52).
1. Place the system base on the workbench.

2. Unlock the system base (see Unlocking the System Base
(} page 52)) to be able to shift the system base slightly for better
access to all system parts.
3. Only if you intend to guide the waste line of the system drainage
toward the system's rear:
Press the clips as shown in the left image and attach them onto the
system base at the positions shown in the right image.
Figure 4: Clip (left) and attaching the clips onto the system base (right)
4. Lift the pump by its carrying handles. Place the pump on the system
base approximately 5 cm before the end of the rails. Push the pump
towards the rear until the pump clicks into place.
5. Loosen the screws on the carrying handles, using a screwdriver

(TorxTM T20). Do not remove the screws from the carrying handles
completely.
Figure 5: Carrying handles
No. Component
1 Carrying handles
2 Attachment screw (one on each carrying handle)

Operating Manual
5 • Installation
6. Remove the two carrying handles by sliding them off the rails
toward the rear.
Figure 6: Sliding off the carrying handle from the left rail
7. Repeat the previous three steps for the autosampler and detector by
placing the autosampler on the pump, and the detector on the
autosampler.
8. Place the solvent rack on the detector approximately 5 cm before

the end of the rails. Push the solvent rack towards the rear until it
clicks into place.
9. Measure the stack height from the table surface to the solvent rack
railing and check whether a stack stabilization is needed (see Safety
Guidelines for Setting Up the System Stack (} page 49)). If necessary,
stabilize the stack.
10. Connect the waste lines (see Connecting the Waste Lines
(} page 55)).
TIP
System modules on the system stack have protective caps on the rear of
the housing. Remove them after installing the system stack and before
attaching the column compartment to the system stack.
11. Attach the column compartment to the system stack (see Attaching
the Column Compartment to the System Stack (} page 62)).
12. Loosen or remove any shipping locks. Refer to the Operating Manual
for each module for information on shipping locks that need to be
removed.

Operating Manual
5 • Installation
5.4.2 Moving the System Stack (Unlocking/Locking)

The system base has a locking mechanism. Before you move the system
base, for example, for installation and maintenance, you need to unlock
the system base. To prevent it from being moved during operation on
the workbench, lock it.
If your system configuration includes one column compartment, you can

switch between the moveable and stationary mode using the system
base locking tools shipped with the system base.
Figure 7: System base locking tool
If your system includes two or three column compartments or a Charger,

a Thermo Fisher Scientific service engineer must dismount the
mentioned modules before you can (un)lock the system base with the
locking tools.
5.4.2.1 Unlocking the System Base

1. Have the Charger and all but one column compartment dismounted
by a Thermo Fisher Scientific service engineer.
2. Insert one locking tool into another.
Figure 8: Extended locking tool
3. Insert the combined locking tools into the lock port on the side of
the system base where the column compartment is installed.
If the column compartment is installed on the right side, insert the
combined locking tools into the right lock port as shown in the figure
below.

Operating Manual
5 • Installation
4. Insert one locking tool into the lock port on the other side of the
system base.
Figure 9: Inserting locking tools into the system base (system base top
view)
5. Unlock the system base by turning the locking tools as shown below.
In the unlocked position, the locking tools cannot be removed from
the system base.
Figure 10: Unlocking the system base
6. Move the system.
7. Lock the system base (see Locking the System Base (} page 54)).
8. Have the additional column compartments and the Charger

mounted by a Thermo Fisher Scientific service engineer.

Operating Manual
5 • Installation
5.4.2.2 Locking the System Base

When the system base is in movable mode and one column
compartment is installed, locking tools are already inserted into the
system base. The following instructions and images assume that the
column compartment is installed on the right side of the system.
1. Move the system to the operating position.
2. Lock the system base by turning the locking tools as shown below.
Figure 11: Locking the system base (system base top view)
3. Remove the locking tools and store them in a safe place, for
example, in the system base drawer.
4. Have the column compartment(s) and Charger re-installed by a

Thermo Fisher Scientific service engineer.

Operating Manual
5 • Installation
5.4.3 Connecting the Waste Lines
5.4.3.1 Waste Connections Overview
WARNING—Escape of Hazardous Substances

Hazardous substances can escape from waste lines and waste containers
if connections and waste containers are not properly installed. Exposure
to these substances can pose health and safety risks.
Verify the correct installation of connections and containers by testing
the drain system (see Testing the Drain System (} page 59)).
The Vanquish system has been designed for optimized and simple leak
liquid and waste handling:
• Leak liquid from the solvent rack, detector, autosampler, and pump
flows through pipes from the modules to the system base drain port.
• Seal wash and needle wash liquids from the pump and autosampler,
as well as condensate from the autosampler, are also guided to the
system base drain port.
• Leak liquid from the column compartment flows to the column
compartment drain port.
• Waste from the detector can also be routed through the system
base.

Operating Manual
5 • Installation
Figure 12: Overview of waste lines in the system (example)
No. Description
1 Drainage from the modules in the stack to the system base

1a System drain port
1b Waste line for system drainage
2 Module waste lines:
2a Detector waste line
2b Pump waste line (here in VH-P10 pump)
3 Drainage from the column compartment:
3a Column compartment drain port
3b Waste line for column compartment drainage

Operating Manual
5 • Installation
Make the following connections:
• Connect a waste line to the system drain port (see Connecting the
Waste Line to the System Drain Port (Drain Tubing) (} page 58)).
• When the waste line is set up, test the drain system (see Testing the
Drain System (} page 59)).
• Install a detector waste line that connects the flow cell outlet
through the detector waste outlet to the waste. For installation
instructions, see Installing the Detector Waste Line (} page 60).
TIP
Make sure that you guide the detector waste line through the separate
outlet in the system base, which is located next to the drain port in the
system base.
Figure 13: Funnel and waste outlets on the system base
No. Description
1 Funnel for system drainage

2 Detector waste outlet
2a Detector waste line
3 System drain port (hidden behind the elbow connection)
3a System waste line
• If you have to cut tubing to length, use a tubing cutter. Make sure
that the cut is at a right angle to the length of the tubing and that
the end is free of nicks or burrs.

Operating Manual
5 • Installation
5.4.3.2 Connecting the Waste Line to the System Drain Port (Drain Tubing)
Parts required
• Drain tubing from ship kit
• Elbow connection piece from ship kit
• Suitable waste container
Follow these steps
1. Push an elbow connection piece into the system drain port as far as
it goes in to establish a self-sealing connection.
2. Push the drain tubing into the elbow connection piece with your
hand as far as it goes in to establish a self-sealing connection.
3. Route the free end of the drain tubing into a waste container.
4. Only if guiding the drain tubing toward the system's rear: Insert the
drain tubing into the clips and make sure that the drain tubing does
not form a siphon.
Figure 14: Inserting the drain tubing into clips
TIP
If routing the drain tubing of the column compartment also toward the
system's rear, you can insert the drain tubing of the column
compartment into the clips as well.
5. Ensure proper drainage of waste (see next section).
Ensuring Proper Drainage of Waste
1. Position the waste container below the level of the system stack. To
prevent solvent vapors from evaporating back into the system, make
sure that the distance is sufficient.
2. Make sure the drain tubing is neither bent nor pinched.
3. To prevent liquid from flowing back into the system, the entire drain
tubing must remain below the drain port. Avoid the formation of
siphons.

Operating Manual
5 • Installation
4. To allow the waste liquid flowing off properly and avoid liquid
accumulation in the system base, the end of the waste line must not
be submerged in waste liquid (see figure below):
a) Shorten the tubing if required.
b) Observe the liquid level in the waste container and empty the
waste container as necessary.
Figure 15: Free end of waste line in waste container
5.4.3.3 Testing the Drain System

Check the drain system for proper drainage of waste:
1. Pour water or isopropanol into the drain in the solvent rack.
2. Verify that the liquid leaves the system at the system drain port and
into the waste container.
3. If a leak is visible, find and eliminate the problem.

Operating Manual
5 • Installation
5.4.3.4 Installing the Detector Waste Line

Parts required
• Detector waste line
TIP The detector waste line connects the flow cell outlet through the
detector waste outlet to the waste.
• For instructions on how to connect the waste line through the
detector waste outlet to the waste, follow the steps below.
• For instructions on how to connect the waste line from the flow cell
outlet, refer to the Operating Manual for your Vanquish detector.
• Suitable waste container
Follow these steps
1. Locate the outlet for the detector waste line in the system base (see
figure below).
2. Route the waste line through the detector waste outlet.
Figure 16: Routing the waste line through the outlet

Operating Manual
5 • Installation
3. Route the free end of the waste line into a waste container.
Figure 17: Guiding the waste line to the waste container

4. Ensure proper drainage of the waste from the detector. You may
need to cut the waste line to length.
5. Ensure proper drainage of waste (see next section).
Ensuring Proper Drainage of Waste
1. Position the waste container below the level of the system stack. To
prevent solvent vapors from evaporating back into the system, make
sure that the distance is sufficient.
2. Make sure the drain tubing is neither bent nor pinched.
3. To prevent liquid from flowing back into the system, the entire drain
tubing must remain below the drain port. Avoid the formation of
siphons.
4. To allow the waste liquid flowing off properly and avoid liquid
accumulation in the system base, the end of the waste line must not
be submerged in waste liquid (see figure below):
a) Shorten the tubing if required.
b) Observe the liquid level in the waste container and empty the
waste container as necessary.
Figure 18: Free end of waste line in waste container

Operating Manual
5 • Installation
5.4.4 Attaching the Column Compartment to the System Stack

In the standard configuration, the Vanquish system includes one column
compartment, installed to the right side of the system.
TIP An extended or left-side configuration of the column compartment is

also available. Observe the following notes:
• The extended configuration on the right side can include up to three
column compartments. For the extended configuration of the
column compartment, up to two conversion kits are required.
• The column compartment can also be installed to the left side of the
Vanquish system stack. For the left-side installation, one column
compartment requires one conversion kit. Each additional column
compartment on the left side requires an additional conversion kit. If
a Vanquish Charger or the Vanquish Display is used with the
Vanquish system, the column compartment must be attached to the
right side of the system.
• For ordering information, contact your local Thermo Fisher Scientific
sales organization.
Installation by Service Engineer only
Only service personnel certified by Thermo Fisher Scientific are

permitted to install the extended configuration with up to three column
compartments or to perform the left-side installation of the column
compartment.
For installation of the standard configuration, follow the instructions

below.
Parts required
• 4 T-slot nuts
• 2 crosspieces
• 4 screws
• 4 spacers
Tools required
Screwdriver, Torx T20

Operating Manual
5 • Installation
Follow these steps
1. Align the screw holes of the two T-slot nuts, the spacers and the
crosspiece.
Figure 19: Mounting bar
No. Description
1 Spacer
2 Groove
3 Screw
4 T-slot nut
5 Crosspiece
2. With the screws, fix the T-slot nuts and the spacers onto the
crosspiece.
The T-slot nuts must face each other, as shown above.
3. Slide the T-slot nuts of the mounting bar in the rail on the system
housing and push until stop.
The grooves on the mounting bars must face upwards. Make sure,
that the orientation of the crosspiece is as indicated on the picture.

Operating Manual
5 • Installation
4. Tighten the screws on the mounting bars.
Figure 20: Installing the mounting bars on the system housing
No. Description
1 Rail
2 Mounting bar
5. Lift the column compartment into vertical position.

Operating Manual
5 • Installation
6. To insert the holding knobs in the grooves on the mounting bar,

grasp the column compartment by its sides and slightly lift the
column compartment up.
Figure 21: Attaching the column compartment to the system stack
7. Connect a waste line to the column compartment drain port. For

instructions, refer to the Operating Manual for the column
compartment.
See also
2 Connecting the Waste Lines (} page 55)
5.4.5 Signal Cable Connections

This section provides details on the cables and interfaces used to
connect the system to a computer or other devices, and details on how
to interlink the system modules with each other.

Operating Manual
5 • Installation
5.4.5.1 Connector Overview

The following connectors are provided on the system modules for power
line connection and for signal connections:
Figure 22: Connectors (here: pump)
No. Description
1 System Interlink port

Allows power on/off control for the system from the Vanquish system base
and device communication
Note: Do not connect cables other than the provided system interlink cables
to these ports, as this may damage the electronics.
For details on system interlink connections, see System Interlink
Connections (} page 69).
2 Digital I/O ports (not available in all modules)
Allow exchange of digital signals with external instruments
For information on connection and pin assignment, refer to the Operating
Manual for the related module.
3 USB (Universal Serial Bus) hub ("A"-type connector) (not available in all
modules)
Allows connection to other modules in the Vanquish system
4 USB port ("B" type connector)
Allows connection to other modules in the Vanquish system or the
computer on which the chromatography data system is installed.
For details on USB connections, see USB Connections (} page 67).
5 Main power switch (on/off control)
6 Fuse holder
7 Power inlet connector
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
5.4.5.2 USB Connections

All USB connections require standard USB A-to-B type cable.
Figure 23: USB cable
The flat, rectangular end of the cable is the "A" connector. The smaller,
hexagonal end is the "B" connector.
TIP
• The USB standard limits the USB cable length to 5 meters. Each USB
device can be separated from the computer or next USB hub by no
more than 5 meters.
• After connecting the USB cables and before turning on the power to
a device for the first time, verify that the chromatography software
is installed on the computer. When the power is turned on, the
required USB drivers are automatically found and the WindowsTM
operating system can detect the device.

Operating Manual
5 • Installation
Connecting the USB Cables
USB Cable Overview
Figure 24: USB cable connections (example)
No. Description
- USB connection:
1 From pump to detector
2 From autosampler to pump
3 From column compartment to detector
4 From detector to computer

Operating Manual
5 • Installation
Follow these steps 1. On the autosampler, pump, and column compartment, connect the
"B" connector of a USB cable to the USB port.
2. Connect the "A" connector of the USB cable from the pump to the
USB hub on the UV/VIS detector. Connect the "A" connector of the
USB cable from the other modules to the USB hub on the UV/VIS
detector or pump.
3. Connect the "B" connector of a USB cable to the USB port on the
UV/VIS detector, and connect the "A" connector of the USB cable to
a USB port (2.0 or higher) on the computer.
In order to control the modules that use a USB hub on another module,
the module that provides the hub must be turned on.
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 system.
5.4.5.3 System Interlink Connections

The system interlink connections require a special system interlink cable
(Cat. 6 cable).
Figure 25: System interlink cable

Operating Manual
5 • Installation
Connecting the System Interlink Cables
System Interlink Cable

Overview
Figure 26: USB and system interlink cable connections (example)
No. Description
- System interlink connection:

1 From system base to pump
2 From pump to autosampler
3 From autosampler to detector
4 From detector to column compartment

Operating Manual
5 • Installation
Follow these steps 1. Connect one end of the system interlink cable to the System
Interlink port on the system base, and the other end to a System
Interlink port on the pump.
2. Connect one end of the system interlink cable to the free System
Interlink port on the pump, and the other end to a System Interlink
port on the autosampler.
Interlink port on the autosampler, and the other end to a System
Interlink port on the detector.
Interlink port on the detector, and the other end to a System
Interlink port on the column compartment.
5.4.6 Connecting Power Cables

This section provides details on how to connect the modules to the
power source. Do not turn on the system or modules yet.
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.
Follow these steps
1. Verify that the power switch on each device is set to OFF.
2. Connect the power cord to the power-inlet connector on each

device.
3. Connect the free end of the power cords to an appropriate power

source.
4. Insert the signal and power cables into the cable clips (see Guiding
Cables through the Cable Clips (} page 72)).
5. If necessary, move the system to its final position.
6. Lock the system base against moving (see Locking the System Base
(} page 54)).

Operating Manual
5 • Installation
5.4.7 Guiding Cables through the Cable Clips

The cable clips can be used to guide signal and power cables in an
orderly fashion. The pump and the detector each have one cable clip on
each side and the autosampler has two cable clips on each side. The
location of the cable clips is shown below.
Figure 27: Cable clips in the autosampler and detector

Operating Manual
5 • Installation
5.5 Setting Up the Flow Connections

5.5.1 General Information and Guidelines
This section gives an overview of the flow connections to and from the
system. For details on tubing and capillary connections within and
between the modules, refer to the Operating Manual of each module.
Flow connections can be filled with hazardous substances. Observe the

warning messages and precautionary statements presented in Safety
Precautions (} page 19).
• 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.
• The system uses the Viper™ fitting system. For installation

instructions and guidelines and for handling recommendations, see
Connecting Fittings, Capillaries, and Tubing (} page 77).

Operating Manual
5 • Installation
5.5.2 Flow Connections Overview

The picture illustrates the liquid flow path through the system:
Figure 28: Flow connections in the Vanquish system (example)
Setting up the System Flow Connections
1. Set up the flow connections for the pump. For details, refer to the
Operating Manual of the pump.
2. Set up the flow connections for the autosampler. For details, refer to
the Operating Manual of the autosampler.

Operating Manual
5 • Installation
3. Set up the flow connections for the column compartment except the
column. For details, refer to the Operating Manual of the column
compartment.
¨ Connect the pre-heater from port 2 on the autosampler
injection valve to the column outlet tubing using a Viper union.
The union replaces the column for the flushing procedure.
¨ Do not install the column yet!
¨ Connect a waste tubing to the outlet from the column
compartment, for example, post-column cooler (if applicable) or
the detector inlet capillary (depending on system configuration),
and column switching valve (if applicable) and route it to waste.
¨ Do not install a flow cell yet.
4. Turn on the system (see Turning On the System (} page 79)).
5. Set up the system in the chromatography data system (see Setting

Up the System in the Software (} page 80)).
6. Flush the system without column (see Flushing the System

(} page 82)).
7. Install a column. For details, refer to the Operating Manual of the

column compartment. Route the column outlet to waste.
8. Flush the system without flow cell (see Flushing the System
(} page 82)).
9. Install a flow cell, if applicable. For details, refer to the Operating

Manual of your Vanquish detector.
10. Flush the system again with flow cell (see Flushing the System
(} page 82)).
See also
2 Connecting the Waste Lines (} page 55)
5.5.3 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.

Operating Manual
5 • Installation
Each guide can hold up to three tubes or lines. In each module, push the
tube (or line) into the appropriate guide.
Figure 29: 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
Tubing Brackets
Tubing brackets are available for holding the tubing in place. Slip the
bracket side onto the drain pipe.
Figure 30: 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.

Operating Manual
5 • Installation
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.
5.5.4 Connecting Fittings, Capillaries, and Tubing

This section provides information about how to connect and handle
capillaries, fittings, and tubing.
5.5.4.1 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.
• 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.
5.5.4.2 Connecting Viper Capillaries

This section describes how to connect Viper™ capillaries. All Viper flow
connections in the Vanquish system are designed to be finger-tight.
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.

Operating Manual
5 • Installation
Figure 31: Viper fitting with knurl
No. Description
1 Knurl
2 Capillary
3 Slot
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.
3. Check whether the connection leaks. If leakage exists, follow the

steps further down.
TIP
Depending on the modules used in the system, you may also find other
fitting connections. Refer to the Operating Manual for the respective
module for information on how to handle these types of fittings.
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.
4. Reinstall the capillary.
5. If the connection continues to leak, install a new Viper capillary.

Operating Manual
5 • Installation
5.6 Turning On the System

Preparations
1. Verify that any shipping locks have been properly loosened or

removed.
NOTICE—System damage
Shipping locks must be properly loosened or removed before operation
to avoid damage to the system.
2. Lock the system base (see Locking the System Base (} page 54)).
3. 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 system modules.
Follow these steps
1. Turn on each system module with its main power switch. Verify that
the autosampler is turned on before the pump flow is on and
pressure builds up.
2. If optional system controller is installed: Turn on the system

controller by pressing the upper push button on the front left of the
system base.
3. Turn on the system power by pressing the lower push button on the
front left of the system base (system power button).
TIP Turn a module off 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 module
completely.
See also
2 Power On/Off Control (} page 86)

Operating Manual
5 • Installation
5.7 Setting Up the System in the Software

This section describes the basic steps for operating the Vanquish system
with the Chromeleon 7 software. For additional information, refer to the
Help and documents provided with the software.
This manual assumes that the Chromeleon software is already installed

on the data system computer and a valid license is available.
TIP In order to start the Chromeleon Instrument Controller, you must log
on under Windows with local administrator privileges, or as a member
of the Windows Chromeleon Operators user group.
Loading the USB Drivers
1. Turn on the power to the data system computer if it is not yet

already on.
2. Turn on the power to all system modules.

Windows will automatically detect the new devices and perform the
USB installation. If Windows fails to detect the devices and launches
a wizard instead, this indicates that you connected the devices to
the computer and turned on the power for the first time before you
installed the Chromeleon software. In this case, cancel the wizard,
install the software, and then repeat the steps.
Starting the Instrument Controller and Instrument Configuration Manager
1. Start the Chromeleon Instrument Controller.

Right-click the Chromeleon tray icon on the Windows taskbar (the
icon is crossed out in red) and click Start Chromeleon Instrument
Controller. The icon changes to gold, indicating that the Instrument
Controller Service is starting. The icon changes to gray when the
Instrument Controller Service is running (idle).
If the Chromeleon tray icon is not available on the Windows taskbar,
click Start > All Programs (or Programs, depending on the operating
system) >Thermo Chromeleon 7 > Services Manager > Start
Instrument Controller.
2. Start the Chromeleon 7 Instrument Configuration Manager.

Click Start > All Programs (or Programs, depending on the operating
system) > Thermo Chromeleon 7 > Instrument Configuration
Manager.

Operating Manual
5 • Installation
Adding the Vanquish System
1. On the Edit menu, click Add Instrument to add a new instrument

(system).
2. Select the new instrument and click Add Module on the Edit menu
to add the first module.
3. In the Add module to instrument dialog box, on the Manufacturers

list, select Thermo Scientific HPLC: Vanquish and on the Modules
list, select the module you want to add, for example, Vanquish
Binary Pump. Repeat this step for each module of the system.
4. On the General configuration page for each module, make sure that
simulation mode is deactivated and click Browse to select the
module address.
The Chromeleon software connects to the module and transfers the
settings from the device firmware to the software. Check and
change the settings on the other configuration pages if necessary.
For information about the settings, click Help or press the F1 key.
Figure 32: Software configuration: select module address (here: pump)
5. On the File menu, click Save Installation and then close the
Instrument Configuration Manager.

Operating Manual
5 • Installation
5.8 Flushing the System

This section describes how to flush the Vanquish system after
installation. As certain system components are filled with isopropanol
during shipment, flushing is required before the system can be
operated.
Flushing the System without Column

Follow these steps:
NOTICE
To avoid damage to other modules in the Vanquish system, verify the
following before you begin:
• The detector is not connected to the flow path.
• No column is installed in the column compartment.
1. Purge the pump.
2. Have the pump deliver the solvent used for purging for a short time.
Flushing the System with Column Installed

Flush the system again for a short time after connecting the column with
a solvent suitable for your application. Follow these steps:
1. Verify that the detector is not connected to the flow path.
2. Have the pump deliver the solvent for a short time. Observe the
pressure limit and other properties of the column.
Flushing the System with Column and Flow Cell Installed

Flush the system again for a short time after connecting the flow cell
with a solvent suitable for your application. Observe the guidelines for
flow cells in the Operating Instructions of the detector.
NOTICE
• When the charged aerosol detector is connected in the system flow
path, flush the detector only when the detector gas flow is turned
on.
• Flush the detector with flow from the pump.

Operating Manual
6 • Operation
6 Operation
This chapter 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
system has already been completed. If this is not the case, refer to the
instructions in Installation (} page 39).
Software descriptions in this manual refer to Chromeleon 7.

Terminology may be slightly different with other software versions.

Operating Manual
6 • Operation
6.2 Safety Guidelines for Operation

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


in the Safety Guidelines for Operation section in the Operating Manual
for the individual modules of the Vanquish system.
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 Power On/Off Control

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.

Operating Manual
6 • Operation
6.4 Preparing the System for Operation

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

Prepare the system 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.
Follow the instructions in Flushing the System (} page 82).
• Some components of the system are filled with isopropanol when
the system is shipped from the manufacturing site. When operating
the system for the first time, use solvents that are miscible with
isopropanol. If they are not, use an appropriate intermediate
solvent.
• Verify that any air bubbles are completely flushed out of the system
flow path.
Refer to the Operating Manual for each system module for any steps
that may be required before initial operation.
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.
• Close the doors of all modules in the Vanquish system, if not already
done.
• Make sure that the chromatography system is properly equilibrated

(see further down).

Operating Manual
6 • Operation
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
6.5 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. See Normal-Phase Compatible Solvents and
Additives (} page 128).
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.
• If a charged aerosol detector is connected in the system flow path:
Observe the specific mobile phase guidelines for the detector in the
Vanquish Charged Aerosol Detector Operating Manual.

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 Operating the System from the Software

This section describes the basic steps for operating the Vanquish system
with the Chromeleon software. For additional information, refer to the
Help and documents provided with the software that you are using.
6.6.1 Starting the Instrument Controller and Client

1. Start the Chromeleon Instrument Controller.
Right-click the Chromeleon tray icon on the Windows taskbar (the
icon is crossed out in red) and click Start Chromeleon Instrument
Controller. The icon changes to gold, indicating that the Instrument
Controller Service is starting. The icon changes to gray when the
Instrument Controller Service is running (idle).
If the Chromeleon tray icon is not available on the Windows taskbar,
click the Start button, then select Thermo Chromeleon 7 > Services
Manager > Start Instrument Controller.
2. Start the Chromeleon 7 client.

Click the Start button, then select Chromeleon 7.

Operating Manual
6 • Operation
6.6.2 Controlling the System from the ePanel Set

When the chromatography system is not running an automated analysis,
you can control the system modules from the ePanel Set. Use the ePanel
Set to view status information and perform commands.
To access the ePanel Set:
1. On the Console, click the Instruments Category Bar.
2. In the Navigation Pane, click the instrument that you want to

control.
The Chromeleon software connects to the instrument and displays
the ePanel Set.
The ePanel Set opens to the Home panel, which shows basic status
information about each module in the system and provides access to
the instrument Audit Trail.
Figure 33: Chromeleon 7 ePanel for a Vanquish system (example)
3. On the ePanel Set, click the tab for a module.
4. Use the controls (for example, buttons, sliders) to perform

commands.

Operating Manual
6 • Operation
5. If a function that you want to perform is not available on a panel,

press the F8 key to open the Command window. From this window,
you can access all commands that are available for the system.
TIP
The commands and parameters that are available in the Command
window may vary, depending on the user level in the Command window
(Normal, Advanced, or Expert). To change the user level, right-click in
the commands list and select a different user level.
6.6.3 Monitoring the Baseline

When an instrument is idle, you can monitor the baseline signals
without starting a sequence. During baseline monitoring, the monitored
signals are displayed on the real-time signal plot on the ePanel for the
module. You may have to add the signal to the plot in the Plot Properties
(for details, refer to the Help).
To monitor the baseline signals:
1. Open the ePanel Set.
2. On the toolbar above the ePanel Set, click Monitor Baseline:
Figure 34: Monitor Baseline icon
3. In the Select Channels to Monitor dialog box, select the signals that
you want to monitor.
4. To stop monitoring the baseline, click Stop on the toolbar.
TIP
Monitor baseline data is overwritten each time baseline monitoring is
started. If you want to save the data permanently, define the location in
the Monitor Baseline Save Preferences dialog box. For details, refer to
the Help.

Operating Manual
6 • Operation
6.6.4 Running Automated Sample Analysis

Automated sample analysis with the chromatography system involves
creating and running a sequence. In a sequence, you determine how the
injections of a sample are analyzed and in which order they are
processed. Each injection of a sequence is processed by using an
instrument method, which defines the property values and timed
control commands for each module. For details how to create an
instrument method using the Instrument Method Wizard, refer to the
Help.
Chromeleon 7 supports several methods for creating a new sequence.

The most important are:
TIP
If no eWorkflows are available, you can create a new eWorkflow as
described in the Help. As an alternative, use the Sequence Wizard to
create the sequence.
• eWorkflows (preferred method)

eWorkflows provide a set of predefined templates and rules for
creating a new sequence.
• Sequence Wizard
Creating a Sequence via eWorkflows
1. On the Console, click the eWorkflows Category Bar.
2. In the Navigation Pane, click the eWorkflow name.
3. In the Work Area, click the instrument name, and then click Launch.
4. The eWorkflow Wizard guides you through the process. Complete

the steps in the wizard. For detailed information about a wizard
page, click the Help icon.
After you finish the wizard, the sequence is displayed in the Data
view of the Console.
Creating a Sequence via Sequence Wizard
1. On the Console menu bar, click Create > Sequence.
2. The Sequence Wizard guides you through the process. Complete the
steps in the wizard. Specify the number of samples and/or
standards, the instrument method, processing method, and report
template that you want to use. For detailed information about a
wizard page, click the Help icon.
After you finish the wizard, the sequence is displayed in the Data
view of the Console.

Operating Manual
6 • Operation
Starting the new sequence

For details how to control sequences, assign them to instruments, start
the sequence run, and manage queues, refer to the Chromeleon Help.

Operating Manual
6 • Operation
6.7 Shutting Down the System

If the system will not be operated for some time, observe the general
guidelines outlined below.
Interrupting Operation of the System for a Short Period

To interrupt operation of the system 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.
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.

Operating Manual
6 • Operation
Interrupting Operation of the System for a Longer Period

To interrupt operation for a longer period, follow the instructions below.
Also observe the instructions and guidelines for the long-term shutdown
for the other system modules in the Operating Manual for each module.
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, see the information
about the flushing liquid in Considerations with Normal-Phase
Compatible Solvents and Additives (} page 130).
Situation after Shutdown If no additive is used If an additive is used
System remains in the Flush the system, for Flush the system with
laboratory after example with methanol. several volumes of
shutdown 100% acetonitrile should methanol and water (50:50)
not be used. (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.
System 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.
3. Turn off the system with the system power button on the system
base.
If one of the modules shall be removed 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.
If the system shall be transported or shipped after shutdown, follow the
instructions in Transporting or Shipping the System (} page 107).

Operating Manual
6 • Operation

Operating Manual
7 • Maintenance and Service
7 Maintenance and
Service
This chapter gives general guidelines on maintenance and transport of
the system.

Operating Manual
7.1 Introduction to Maintenance and Service

This chapter describes the routine maintenance that the user may
perform for the system.
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).

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
High voltages are present inside the device that could cause an electric
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—Hot Surfaces
Surfaces inside the system may become hot during operation. Touching
hot parts might cause burns.
Allow hot surfaces to cool down before starting replacement or
maintenance procedures.
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. Refer to the Operating Manual for the
pump.
• Retighten the reservoir caps.
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
7.3 General Rules for Maintenance and Service

For successful maintenance and service procedures, follow the rules and
recommendations below.
General Rules
• Use only the replacement parts specifically authorized and qualified

for the device by Thermo Fisher Scientific.
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.
Depot Repair
• If you need to return a system module for depot repair, follow the
instructions in section Transporting or Shipping the System
(} page 107).
See also
2 Consumables and Replacement Parts (} page 143)

Operating Manual
7.4 Routine and Preventive Maintenance

Optimum system performance, maximum uptime of the system, and
accurate results can be obtained only if the system is in good condition
and properly maintained.
7.4.1 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 system.
Frequency What you should do...
Daily • Inspect the flow connections for signs of leakage or blockage.

• When you use buffers or salt solutions, flush the system
thoroughly after use with an appropriate solvent that does not
contain buffers or salts.
Regularly • Solvent line filter frits: regularly check the filter frits for
permeability. Replace the filter frits at regular intervals. This is
especially important when using aqueous solvents. Aqueous
solvents may contaminate the filters with algae and other
microorganisms that deposit on the filter frits. Therefore, also
replace the solvents at regular intervals. Rinse the reservoirs
thoroughly before refilling them.
• Empty the waste container or containers.
• Inspect the flow connections for damage, such as cracks, nicks,
cuts, or blockage.
• Check the drain system for blockage (see Testing the Drain System
(} page 59)). If a leak alarm is triggered or if a leak is visible, find
and eliminate the blockage.
• Clean the system (see Cleaning or Decontaminating the System
(} page 105)).
• Check that all warning labels are still present on the system and
clearly legible. If they are not, contact Thermo Fisher Scientific for
replacement.
Annually Have Thermo Fisher Scientific service personnel perform preventive
maintenance once a year.

Operating Manual
7.4.2 Cleaning or Decontaminating the System

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 system. Use a suitable
cleaning detergent or disinfectant to ensure that the treatment renders
the system 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 system 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.

Operating Manual
7.5 Transporting or Shipping the System

NOTICE
Moving the Vanquish system stack even over short distances on the
workbench can damage and impair the functionality of the system base.
• Configuration with one column compartment: Before moving the
system stack, unlock the system base using the locking tools.
• Configuration with two or three column compartments or a Charger:
Before moving the system stack, dismount the system stack (for
instructions, see below).
Dismounting the system stack
Preparations 1. Turn off all modules with their main power switch.
2. Remove the solvent reservoirs and solvent lines from the solvent
rack.
3. Remove all flow connections between the modules within the

Vanquish system and all waste lines.
4. Remove all signal cables and power cords.
5. Grasp the system by its sides and slightly lift the column
compartment up and out of the grooves on the mounting bars.
6. Lift the front part of the solvent rack and remove the solvent rack by
pulling it towards the front.
7. Remove the detector, autosampler, and pump as described in the

next section.

Operating Manual
Removing the System 1. Slide the carrying handles that were installed when the system was
Modules shipped on the rails at the right and left of the module from the rear
as shown in the figure below.
The final position of the handles must match the foam spacers used
for transport (15 cm from the rear of the module to the center of
the handle).
Figure 35: Sliding the carrying handle on the left rail
2. Fix the attachment screws on the carrying handles as shown below.
Figure 36: Carrying handles attached
No. Description
1 Carrying handles
2 Attachment screw (one on each carrying handle)
CAUTION—Risk of Injury and Device Damage

Handles can slide off the device if the attachment screws are not fixed
properly. Also, the slide-in module can fall out if not fixed properly. This
could cause personal injury and damage to the device. Verify the
following before lifting a device:
• The handles are fixed properly and cannot slide off the device.
• The four screws on the slide-in module are tightened and the slide-in
module cannot fall out (for the location of the screws, refer to the
operating manual of the respective system module).
3. Lift the front part of the module by using the carrying handles.
Remove the module from the stack towards the front and carefully
place it on a stable surface.

Operating Manual
Shipping the Solvent Rack and System Base

To ship the solvent rack and/or system base, 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 solvent rack or system base to Thermo

Fisher Scientific, contact your local Thermo Fisher Scientific support
organization for the appropriate procedure.
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.
Transporting or Shipping other System Modules

For details on transporting or shipping the other system modules, refer
to the Transporting or Shipping section in the Operating Manual of each
module.

Operating Manual

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

Operating Manual
8.1 General Information about Troubleshooting

This section gives information about operating issues that might occur
during the operation of a Vanquish system.
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 (Light Emitting Diodes) on the front side of
each module and the STATUS LED on the keypad inside each module
provide quick visual feedback on the operational status of the module. If
the firmware detects a problem, the status indicators are red.
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
recommended remedial actions, see the Messages section in the
Operating Manual of the module that is in error state.

Operating Manual
8.2 System Troubleshooting

This section is a guide to troubleshooting issues that may arise during
operation of the Vanquish system.
Locate the tables in the following sections for the type of symptom you
have, find the possible cause, and use the description of the solution to
help you solve your problem quickly.
TIP
For information on troubleshooting issues that may arise during
operation with the Vanquish charged aerosol detector and the Vanquish
fluorescence detector, refer to the respective Operating Manual for the
detector.
This section provides information on symptoms and causes directly

related to the Vanquish system modules and connections between the
modules. For information on general chromatography and application
troubleshooting, refer to the technical literature.
8.2.1 Peak Shape

Peak tailing
Possible Cause Remedial Action
Extra column volume too Use short capillary connections with a suitable inner diameter. Use appropriate
large Viper capillaries.
Improper capillary Check fittings for correct placement. Loosen and retighten Viper fittings (refer to
connections the Viper Installation and Operation Guide). Use only the appropriate fittings (see
Connecting Fittings, Capillaries, and Tubing (} page 77)).
Peak broadening
Flow cell volume too Use a smaller volume flow cell.

large
Extra-column volume • If early peaks are broader than later eluting ones, check the capillary I.D. and
too large length, sample loop size, flow cell, for example.
• Use a capillary with a smaller volume for the connection between column
compartment and detector.
Temperature gradient • Use a pre-heater.
in column • If forced air mode is used, consider switching to still air mode (refer to Column
Compartment Operating Manual).
Detector response time Select a suitable response time and/or data collection rate.
too long and/or data
collection rate too low

Operating Manual
Capillaries clogged Replace the capillaries.

Sample loop clogged Replace the sample loop (refer to Split Sampler Operating Manual).
Solvent selector/ Contact Technical Support.
proportioning valve
defective
8.2.2 Ghost Peaks, Negative Peaks and Spikes

Ghost peaks
Contamination Flush the system using an appropriate solvent.

(typically injection unit
or column)
Improper reference The sample must not absorb in the range of the reference wavelength. Consider
wavelength using a method without reference wavelength.
Selected bandwidth too Select a lower bandwidth.
high
Degassing channels Purge the pump (all channels) to rinse the degassing channels (refer to Pump
contaminated Operating Manual).
Negative peaks
Wrong polarization of If you are using analog output, check the analog output polarization.
analog output
Spikes
Air trapped in flow cell • Check all fluid connections for tightness, in particular in the intake path.
• Degas the mobile phase.
• Install a restrictor at the flow cell outlet, observing the pressure specification of
the respective flow cell and the general guidelines for the flow cell.
Note: Excessive backpressure will destroy flow cells!
Particles in flow cell • Flush the system (see Flushing the System (} page 82)). If you suspect that a
capillary is contaminated with particles, in particular between the column and the
flow cell, replace the capillary.
• Flush the flow cell with different flows if particles are trapped in flow cell.
• Check if the column is defective.
UV/VIS lamp old, Check if the lamp is properly seated. Replace the lamp (refer to Detector Operating
defective, or not Manual).
properly installed

Operating Manual
Electrical interferences Avoid operation of equipment generating strong electric or magnetic fields in close
from other instruments proximity. Do not connect equipment that may cause power disturbances to the
same power network used to supply the system.
Column temperature • Install a restrictor at the flow cell outlet, observing the pressure specification of
significantly above the respective flow cell and the general guidelines for the flow cell.
boiling point of mobile Note: Excessive backpressure will destroy flow cells!
phase • Install a post-column cooler (refer to Column Compartment Operating Manual).
8.2.3 Peak Area Precision

Contamination or carry-over
Contamination in the Flush the system using an appropriate solvent.

system
Autosampler carry-over The needle may be contaminated. Wash the needle in the wash port. If carry-over
persists, replace the needle seat (refer to Split Sampler Operating Manual).
Environmental conditions
Unstable Make sure that the temperature and air humidity are constant. Use column
environmental thermostatting. Avoid draft. Use insulation on the capillary from the column
conditions compartment to the detector.
Capillary problems
Capillary connections Properly install the capillary connections. Tighten the capillary connections. Replace
not installed properly capillary.
or not tight, dead
volumes in capillary
connections

Operating Manual
Pump problems
Piston seals in pump Replace the seals (refer to Pump Operating Manual).
leaking
Air trapped in pump Purge the pump (refer to Pump Operating Manual).
head
Baseline fluctuations See "Periodic baseline fluctuations" in Baseline (} page 119).
Pump pulsation or flow See "Pressure pulsation or inconstant pressure" in Pressure (} page 118).
fluctuations
Irreproducible gradient Change the gradient.
Check the solvent line filters for permeability. Replace the filter frits if necessary
(refer to Pump Operating Manual).
Inappropriate detector settings
Improper wavelength, Choose a detection wavelength that is located near the apex of the spectrum.
e.g., in a UV spectrum
flank
Detector response time Select a longer response time.
too short
Detector response time Peaks are eventually not separated any more. Select a shorter response time.
too long
Injection volume variation
Autosampler draws air There is not enough amount of sample in the vial, the needle height setting is
from vial incorrect, or there are too many replicates.
Air trapped in Perform a wash cycle. Check that the injection valve is in Inject position and the
autosampler flow path flow components of the autosampler are flushed with solvent.
Draw speed too high Select a lower draw speed.
Gas content of sample Reduce the draw speed. Degas the sample if possible.
too high or saturated
Needle clogged or Replace the needle (refer to Split Sampler Operating Manual).
needle tip deformed
Piston seals in Replace the metering device head (refer to Split Sampler Operating Manual).
autosampler metering
device leaking
Injection valve or other Inspect the autosampler and the connections on the injection valve. Tighten leaking
autosampler connections. Replace leaking parts (refer to Split Sampler Operating Manual).
components leaking
Needle seat worn out Replace the needle seat (refer to Split Sampler Operating Manual).

Operating Manual
8.2.4 Flow
No flow
Leak in system Find and eliminate the leak.

Inlet and/or outlet Clean the inlet check valve or outlet check valve, and replace the check valve if
check valve necessary (refer to Pump Operating Manual).
contaminated or
defective
Air trapped in pump Purge the pump (refer to Pump Operating Manual) and check in the
heads chromatography data system whether the degasser has reached the operating
vacuum (Degasser Vacuum = OK).
Air trapped in Perform a wash cycle (refer to Split Sampler Operating Manual).
autosampler flow path
Column temperature Select a lower column temperature (refer to Column Compartment Operating
too high – eluent Manual).
evaporating
Flow fluctuations
Pump inlet path Check the solvent inlet lines, solvent line filters, and solvent selectors/proportioning
clogged valve, for example, for signs of clogging.
Air trapped in pump • Purge the pump.
inlet path • Inspect the degasser for indications for leakage. Check in the chromatography
data system whether the degasser has reached the operating vacuum
(Degasser Vacuum = OK). Degassing may not work properly if the flow rate is too
high.
• Inspect the capillary and solvent line connections for leakage; tighten loose fitting
connections.
contaminated or
defective
Piston seals not sealing Replace the piston seals (refer to Pump Operating Manual).
tightly

Operating Manual
8.2.5 Pressure
Pressure pulsation or inconstant pressure
Air trapped in the Purge the pump (refer to Pump Operating Manual).
system
contaminated or
defective
Pump inline filter (or Check the permeability of the inline filter (or static mixer). Replace the inline filter
static mixer) clogged (or static mixer) if necessary (refer to Pump Operating Manual).
Solvent line filter Check the solvent line filters for permeability. Replace the filter frits if necessary
clogged (refer to Pump Operating Manual).
Pump head Check the compression values and take remedial action (refer to Pump Operating
compression values not Manual).
reached
System clogged with Samples and insufficient solvent purity are frequently the source for particles
particles clogging the system. Follow the instructions for resolving clogging in the
autosampler (refer to Split Sampler Operating Manual).
High backpressure
One or more capillaries Check the capillaries in the system systematically from the detector to the pump.
in the system clogged Replace the capillaries as needed.
or damaged by bending
Pump inline filter (or Check the permeability of the inline filter (or static mixer). Replace the inline filter
static mixer) clogged (or static mixer) if necessary (refer to Pump Operating Manual).
Pre-heater clogged Rinse the pre-heater capillary in reverse direction, using an appropriate solvent. If
necessary, replace the pre-heater (refer to Column Compartment Operating
Manual).
Column switching valve Check the valve for indications of blockage. Replace the valve if necessary (refer to
clogged Column Compartment Operating Manual).
Post-column cooler Rinse the post-column cooler capillary in reverse direction using an appropriate
clogged or defective solvent. If necessary, replace the post-column cooler (refer to Column
Flow cell clogged Clean the flow cell. Replace the flow cell if necessary (refer to Detector Operating
Manual).
Contamination in the Flush the system with an appropriate solvent.
system
Low backpressure
Leak in system Find and eliminate the leak.

Operating Manual
8.2.6 Retention Time Variation

Decreasing retention times
Improper mobile phase Check premixed mobile phase. Perform an OQ gradient accuracy test. A solvent
composition selector/proportioning valve may be defective. Contact Technical Support.
Increasing flow rate Check flow rate settings. Perform OQ flow precision test.
Increasing retention times
Improper mobile phase Check premixed mobile phase. Perform an OQ proportioning test. A solvent
composition selector/proportioning valve may be defective. Contact Technical Support.
Decreasing flow rate Check capillary connections for leaks. Check flow rate settings.
Piston seal leakage Check the pump for piston seal leakage (refer to Pump Operating Manual).
Scattering retention times
Imprecise solvent • Perform an OQ eluent proportioning test.

proportioning • Clean the inlet check valve or outlet check valve, and replace the check valve if
necessary (refer to Pump Operating Manual).
• A solvent selector/proportioning valve may be defective. Contact Technical
Support.
Pressure fluctuations • Purge the pump.
from pump • Check the compression values and take remedial action (refer to Pump Operating
Manual).
• Check the pump for piston seal leakage (refer to Pump Operating Manual).
• Check the solvent line filters for permeability. Replace the filter frits if necessary
(refer to Pump Operating Manual).
8.2.7 Baseline
High baseline drift
System not sufficiently Flush the system until equilibration. Usually, a volume of 5–10 times the column
equilibrated volume will be sufficient.
Unstable 1. Make sure that the temperature and the humidity are constant. You can
environmental determine temperature fluctuations by recording the temperature channels.
conditions 2. Verify on the detector that the lamp house cover is properly installed and that the
front doors are closed. Avoid draft.
Flow cell contaminated Clean the flow cell. Replace the flow cell if necessary (refer to the Detector
Operating Manual).

Operating Manual
UV/VIS lamp not stable Allow the lamp and optics to warm up for at least 60 minutes. If the lamp is old, you
may need to replace the detector lamp (refer to the Detector Operating Manual).
A new lamp may need burn-in time before the first analysis. For details, refer to the
Detector Operating Manual.
Absorption of eluent Absorbing additives may change the absorption spectrum, depending on the
changes when gradient solvent. Consider varying additive concentrations to level the drift.
is run
Non-periodic baseline fluctuation, high noise
Pressure fluctuations • Purge the pump (refer to the Pump Operating Manual).
from pump • Perform a basic tightness test (see Basic Tightness Test (} page 124)), or test the
pump for leakage as described in the Pump Operating Manual.
• Clean the check valves (refer to the Pump Operating Manual).
Air trapped in the Purge the system as necessary (refer to the Pump Operating Manual).
system
UV/VIS lamp old or not Check that the lamp is correctly installed. Replace the lamp (refer to the Detector
properly installed Operating Manual).
Detector response time Select a suitable response time.
too short
Improper wavelength Select an appropriate wavelength.
or optical bandwidth Select a higher bandwidth in particular with critical conditions (low absorption, few
light).
Flow cell not properly Check that the flow cell is installed properly (refer to the Detector Operating
installed Manual).
Detector defective Contact Technical Support.
Optical transmission of Check the lamp age and replace the lamp, if necessary. Use the Cell Transmission
the flow cell too low Check / Flow Cell Wash button on the ePanel for the module and follow the
(Vanquish system with instructions. For this procedure, a diagnostic cell for the VH‑D10 is required. If you
VH-D10 detector only) do not have a diagnostic cell, compare the cell transmission (light intensity) values
of the flow cell before and after a wash procedure and check whether the cell
transmission (light intensity) has increased. If it has not increased, perform an
extended wash cycle and check whether the cell transmission (light intensity) has
increased.

Operating Manual
Periodic baseline fluctuation, pulsation
Pressure fluctuations • Purge the pump (refer to the Pump Operating Manual).
from pump • Perform a basic tightness test (see Basic Tightness Test (} page 124)), or test the
pump for leakage as described in the Pump Operating Manual.
• Clean the check valves (refer to the Pump Operating Manual).
Air trapped in the Purge the system (refer to the Pump Operating Manual).
system
UV/VIS lamp defective Check that the lamp is correctly installed. Replace the lamp (refer to the Detector
or not properly Operating Manual).
installed
Piston calibration value Verify that the calibration value of the piston (imprinted on the rear of the piston)
mismatch corresponds to the related piston calibration value in the chromatography data
system. Adapt the value in the data system if necessary.
8.2.8 Temperature Control

Column compartment temperature does not change although the set point has not been
reached
Ambient temperature Reduce the ambient temperature (for example, by ventilating the room).
too high or setpoint
lower than the
specified difference to
the ambient
temperature
Temperature control Check the setting for TempCtrl in the chromatography data system (TempCtrl=On
turned off turns temperature control on).
Ventilation grid Make sure that the ventilation grids of the column compartment are not obstructed
obstructed in any way.
Ambient air enters • Improper sealing of the column chamber may impair the heating and cooling
column chamber performance of the column compartment and lead to a considerable amount of
condensed water.
• When guiding capillaries through the column chamber cover seal, make sure that
the cover seals properly. If the chamber cover seal is damaged, replace the
chamber cover (refer to Column Compartment Operating Manual).
• Also, make sure that the front door is properly closed.
Column compartment Contact Technical Support.
defective

Operating Manual
Pre-heater does not reach set temperature
Pre-heater not The performance may be impaired if the thermal contact is imperfect, or if the pre-
installed correctly heater inlet and outlet are exchanged. Reinstall the pre-heater (refer to Column
Pre-heater defective Replace the pre-heater (refer to Column Compartment Operating Manual).
Post-column cooler does not reach set temperature
Post-column cooler not Verify that the post-column cooler screws are tightened and the post-column
installed correctly cooler is seated properly.
Autosampler does not reach set temperature
Ambient temperature Reduce the ambient temperature (for example, by ventilating the room), and/or
or humidity too high ambient humidity.
8.2.9 Power and Communication

Entire system has no power (all LED bars off (dark))
System power button Turn on the system with the power button on the front left of the system base.
turned off
Single module has no power (LED bar off (dark))
Module power turned Turn on the module with its main power switch.
off
Module not connected Connect the power cord.
to the mains
Fuse has blown Replace the fuses (refer to Operating Manual of the module).
Error in electronic Contact Technical Support.
system
One or more modules cannot be turned off from the power button on the system base
System power Check the system interlink connections between the system base and the system
connection modules, see Signal Cable Connections (} page 65).
interrupted

Operating Manual
Module cannot be operated from the chromatography data system
No connection • Check the USB connections from the system to the computer, see Signal Cable
between module and Connections (} page 65). If the module uses a USB hub on another module, check
computer that the module that provides the hub is turned on.
• Check the USB port on the computer. USB standard 2.0 is required.
Repeated unexpected Install a USB Isolator. For ordering information, see Optional Accessories
disconnects in the (} page 141).
chromatography data
system
8.2.10 System Diagnostics

For the Vanquish system modules, diagnostics features are supported in
the Chromeleon software. With these features, the user can check and
monitor the performance and reliability of certain components.
Manual Testing
You can run the following tests from Chromeleon:
Test Available for Remarks
Basic Tightness Pump and autosampler Depending on the Vanquish

Test system configuration, the
available tests may vary. If a
Grating Motor Variable wavelength detector
test is grayed out in the
Test
Chromeleon software, the
Intensity Test Variable wavelength detector test is currently not available.
When a test is running, the
Shutter Motor Variable wavelength detector
LED bar on the module shows
Test
a blue running light.
Automatic Testing
You can set up a schedule in Chromeleon for automatic testing.
Automatic testing is possible only for tests and functions that can run
unattended, without further user interaction, for example the Basic
Tightness Test.
Test Failed
To ensure that you run sequences only on fully operational modules, the
Chromeleon software prevents you from starting a sequence if a
diagnostic test has failed. If a test failed, take remedial action and repeat
the test. A user with special control privileges in the Chromeleon
software can override the failed test result. Refer to the Chromeleon
Help.
See also
2 Basic Tightness Test (} page 124)
2 Grating Motor Test (} page 124)
2 Intensity Test (} page 125)
2 Shutter Motor Test (} page 125)

Operating Manual
8.2.10.1 Basic Tightness Test
The Basic Tightness Test checks the tightness of the pump and
autosampler.
Follow these steps
1. Run the test from the Chromeleon software. Refer to the

Chromeleon Help.
The test runs automatically without further user interaction.
2. If the test fails, check the Instrument Audit Trail for a message. For
remedial actions refer to the Troubleshooting section in the
Operating Manual for the module for which the test failed.
8.2.10.2 Grating Motor Test
The Grating Motor Test checks the mechanical stability of the grating
drive.
Follow these steps
1. Install the diagnostic cell in the detector.

Chromeleon Help.
3. Depends on the test result:
Test result Action
Passed Reinstall the flow cell of your application.

Failed Contact Thermo Fisher Scientific Technical Support.

Operating Manual
8.2.10.3 Intensity Test
The Intensity Test is a test to measure the intensity of the detector lamp
and the transmission performance ("intensity") of the optics. The test is
available for the diode array detector and for the variable wavelength
detector.
Follow these steps
2. Turn on the detector lamps (one or both) that you want to test.

Chromeleon Help.
Test result Action

Failed 1. Replace the lamp. Refer to the Operating Manual
for the detector.
2. If the test fails with the new lamp, the optics may
be defective. Contact Thermo Fisher Technical
Support.
8.2.10.4 Shutter Motor Test
The Shutting Motor Test checks the mechanical stability of the shutter
motor and filter paddle.
Follow these steps
2. Turn on the detector lamps (one or both).

Chromeleon Help.
Test result Action

Failed Contact Thermo Fisher Scientific Technical Support.

Operating Manual

Operating Manual
9 • Modifying the System for Specific Applications
9 Modifying the
System for Specific
Applications

Operating Manual
9.1 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 are modified with the
components from the Normal-Phase (NP) kit.
9.2 Modifying the System Modules

This section applies to Vanquish Core system modules.
When
To use very non-polar and harsh organic solvents, such as 100%
acetonitrile, n-hexane, tetrahydrofuran, and similar solvents.
Parts required
• Normal phase (NP) kit, including the parts and instructions for
modifying the pump and autosampler and for replacing the detector
waste line.
• Tubing cutter
• Pistons (for pumps VC-10, VC-P20, VC-P32, VC-P40)

Modifying the pump includes replacing the UHMW-PE piston seals
with PTFE seals. 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.
Additional parts required as applicable
• NP-compatible VC-detector flow cell

If you need assistance on the NP compatibility of your flow cell,
contact your local Thermo Fisher Scientific sales organization.
• NP column switching valve for column compartment
Preparations
1. Turn off the pump flow and wait until the system pressure is down
to zero.
2. Unscrew the cap of the seal wash reservoir.
3. Together with the cap, remove the seal wash line from the reservoir.
4. 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
1. Modify the system components with the components from the NP

kit. Follow the instructions in the installation guide that comes with
the kit.
2. As applicable:
a) Replace the pump pistons. Refer to the Operating Manual for
the pump.
b) Replace the flow cell with an NP-compatible flow cell. Refer to
the Operating Manual for the detector.
c) Replace the column switching valve with an NP-compatible
valve. Refer to the Operating Manual for the column
compartment.
3. Observe the specific information for operation in Considerations

with Normal-Phase Compatible Solvents and Additives (} page 130).

Operating Manual
9.3 Considerations with Normal-Phase Compatible

Solvents and Additives
After the installation of the NP kit, the system remains compatible with
reversed-phase applications. The pH range of the system is not affected
by application of the NP kit, see Allowed pH Ranges (} page 27).
When running applications with normal-phase compatible solvents and

additives, observe the information in this section on:
• Seal wash liquid
• Long-term shutdown
• Routine and preventive maintenance
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.
For NP applications, ammonium formate in isopropanol (2 mmol/L)
is recommended.
Interrupting Operation of the System for a Longer Period

To interrupt operation for a longer period and restart operation
afterward, follow the instructions in Shutting Down the System
(} page 96).
Use the following liquids for flushing:
Situation Action
No additive is used Flush the system with isopropanol. 100% acetonitrile

should not be used.
Flushing liquids should be minimum HPLC-grade.
Additive is used 1. Flush the system with several volumes of an
appropriate pure solvent (for example, 1.0 mL/min for
10 minutes with the standard system).
2. Flush the system with isopropanol.
Flushing liquids should be minimum HPLC-grade.

Operating Manual
Routine and Preventive Maintenance
• Observe the information in the Routine and Preventive Maintenance

section in the Operating Manuals for the system modules.
• Depending on the application, slightly increased abrasion may be

observed with normal-phase piston seals. Therefore, consider
testing the static mixer for permeability at shorter intervals. Refer to
the Operating Manual for the pump.

Operating Manual

Operating Manual
10 • Specifications
10 Specifications
This chapter provides important system specifications.

Operating Manual
10.1 System Specifications

The physical conditions of a standard system are specified as follows:
Type Specification
Materials in the flow path For materials in the flow path, refer to the Operating Manuals for the
modules in your system.
For solvent and additive information, see Solvent and Additive
Information (} page 25).
Biocompatibility Core system in the standard Horizon/Flex system in the
configuration: No standard configuration: Yes
Control System base power button
Chromeleon 7
The system can be operated also with other data systems. For details,
contact the Thermo Fisher Scientific sales organization.
Good Laboratory Practice (GLP) Predictive Performance functions for scheduling maintenance
features procedures based on the actual operating and usage conditions of the
system.
All system parameters logged in the Chromeleon Audit Trail.
Safety features Leak detection and safe leak handling
Range of use Indoor use only
Ambient operating temperature 5 °C - 35 °C
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
Emission sound pressure level System with one column compartment, without Charger:
Typically approx. 55 dB(A), max. approx. 75 dB(A)
System dimensions System with one column compartment, without Charger:
(height x width x depth) 82 cm x 55 cm x 62 cm
System weight Vanquish Core Vanquish Flex: Vanquish Horizon:
With one column compartment, Approx. 80 kg Approx. 90 kg Approx. 110 kg
without Charger

Operating Manual
10.2 Solvent Rack and System Base Specifications

The physical conditions of the solvent rack and system base (without the
Vanquish System Controller) are specified as follows. For specifications
of the other modules in the Vanquish system, refer to the Specifications
section in the Operating Manual for each module.
Type Specification
System Interlink 1 System Interlink port (RJ45-8 connector)

Max. volume of an individual 5 L
solvent reservoir
Solvent rack dimensions 12 cm x 42 cm x 62 cm
(height x width x depth)
Solvent rack weight 4 kg
System base dimensions 6 cm x 42 cm x 42 cm
(height x width x depth)
System base weight 5 kg
System base user input System base power button

Operating Manual

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

Operating Manual
11.1 General Information

The system 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
11.2 Ship Kit

This section lists the content of the ship kit. 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 system is shipped.
For reordering information, see Consumables and Replacement Parts

(} page 143).
Ship Kit for Vanquish Core system
Item Quantity in
shipment
Fuses kit, Vanquish system 1

The kit includes the appropriate fuses for the Vanquish system
modules.
Viper union 1
Tubing connector, straight, for tubing I.D. 1.0 – 2.0 mm, set of 5 1
Tubing connector, tapered, I.D. 1/16" 5
Viper capillary kit, Vanquish Core system, including: 1
• Capillary pump-autosampler, stainless steel, I.D. x length
0.18 x 350 mm length
• Passive pre-heater, stainless steel, I.D. x length 0.18 x 530 mm
Drainage kit, Vanquish system, including: 1
• L piece (elbow, pack of 4, different sizes)
• Drain tubing, 6.25 m length
• Clip (set of 2)
Paper label for magnetic label holder 1
System interlink cable 1
Screwdriver, Torx T10 1
Reservoir cap 6

Operating Manual
Ship Kit for Vanquish Flex and Horizon system
Item Quantity in
shipment
Fuses kit, Vanquish system 1

modules.
Viper inline filter 1
Viper union 1
Tubing connector, straight, for tubing I.D. 1.0 – 2.0 mm, set of 5 1
Tubing connector, tapered, I.D. 1/16" 5
Viper capillary kit, Vanquish Horizon and Flex system, including: 1
• Capillary pump-autosampler, MP35N, I.D. x length 0.1 x 350 mm
length
• Active pre-heater, MP35N, I.D. x length 0.1 x 380 mm
• Passive pre-heater, MP35N, I.D. x length 0.1 x 530 mm
Drainage kit, Vanquish system, including: 1
• Clip (set of 2)
Paper label for magnetic label holder 1
Screwdriver, Torx T10 1
System interlink cable 1
Reservoir cap 6

Operating Manual
11.3 Optional Accessories

Stack Stabilizers
Item Part No.
Bench clamp kit 6036.1740

Stabilizes system stacks with a height of max. 139 cm
Stack stabilizer kit 6036.1710
IonBench including stack mounting kit 6036.1720
Vanquish Solvent Monitor
Description Part No.
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
Vanquish User Interface
Item Part No.
Vanquish User Interface 6036.1170

Consists of the Vanquish System Controller and the Vanquish
Display.
Can be used to display and monitor the vital parameters of the
overall system and of attached modules.
Method Development and Transfer Kits
Item Part No.
Extension Kit for Automated Method Scouting 6036.0100

Kit including solvent reservoirs, flow connection components and
a 10-position 11-port solvent selection valve extending the
number of supported solvents for method scouting.
Method Transfer Kit 6036.2100
Contains a loop capillary kit and a switching valve to adjust the
system gradient delay volume to the desired HPLC method.
Strong solvent loop Vanquish (for Vanquish Core systems) 6036.2200
Loop to increase the volume between autosampler and column
for successful transfer of applications using strong-eluting sample
solvents.

Operating Manual
Normal-Phase Kits
Normal-Phase (NP) kit 6036.3972

In a Vanquish Core system, normal-phase (NP) compatible
solvents and additives may be used only if the system modules
have been modified for NP applications.
The Vanquish NP kit is designed for the use of the Vanquish Core
HPLC system with normal phase applications, e.g. based on n-
hexane or tetrahydrofuran. The system remains compatible with
reverse phase applications after the modification. Also, the pH-
range of the system is not affected by the NP kit.
The kit includes the parts and instructions for modifying the pump
and autosampler and for replacing the detector waste line.
NOTE: Depending on the system configuration, additional parts
may be required. See Modifying the System Modules
(} page 128).
Normal-Phase (NP) tubing kit 6036.3973
The kit includes the replacement tubing and tubing connectors,
for replacing the following:
• All seal wash lines from the seal wash reservoir to the seal wash
pump and from the seal wash pump to the pump heads and on
to the seal wash detector (opaque white tubing)
• The peristaltic tubing in the seal wash pump (light yellow tubing)
• The needle wash line from the needle wash reservoir to the
needle wash pump and from the needle wash pump to the wash
port (clear tubing)
• The detector waste line (capillary and fitting)
For device-specific replacement parts, refer to the Operating Manual for the module.
Miscellaneous
Item Part No.
Manual injection valve 6230.1600

Includes all parts needed for manual sample injection: System
fixture, 20 µL sample loop, and syringe.
Capillary, Viper, MP35N, I.D. x length 0.13 x 350 mm (for Horizon 6083.2410
and Flex systems)
Capillary, Viper, MP35N, I.D. x length 0.13 x 500 mm (for Horizon 6083.2411
and Flex systems)
USB isolator 6287.0540
The USB Isolator improves the reliability of the USB connection
between the USB port of an HPLC system module and the data
system computer.

Operating Manual
11.4 Consumables and Replacement Parts

11.4.1 Capillaries and Tubing
Single Parts
Capillary pump-autosampler, stainless steel, I.D. x length 6040.2375

0.18 x 350 mm (for Core systems)
Capillary pump-autosampler, MP35N, I.D. x length 0.1 x 350 mm 6042.2340
(for Horizon and Flex systems)
Active pre-heater1, MP35N, I.D. x length 0.1 x 380 mm (for Horizon 6732.0110
and Flex systems)
Passive pre-heater1, stainless steel, I.D. x length 0.18 x 530 mm 6732.0170
(for Core systems)
Passive pre-heater1, MP35N, I.D. x length 0.1 x 530 mm (for 6732.0174
Horizon and Flex systems)
Vanquish system drainage L pieces, set of 4, different sizes 6036.0003
Viper inline filter 6036.1045
Installed between a column and a Viper capillary to filter particles
bigger than 0.5 µm
Viper union 6040.2304
1
: For more information about column compartment-specific parts, refer to the
Accessories, Consumables and Replacement Parts section in the Operating Manual for
the column compartment.
Drainage Kit
Drainage kit, Vanquish system, including: 6036.1120

• Clip (set of 2)

Operating Manual
Viper Capillary Kits

Vanquish Core Description Part No.
System
Viper capillary kit, Vanquish Core system, including (parts are 6036.2302
available separately, see table in section Single Parts):
• Capillary, stainless steel, I.D. x length 0.18 x 350 mm
• Passive pre-heater, stainless steel, I.D. x length 0.18 x 530 mm
Vanquish Horizon Description Part No.

and Flex System
Viper capillary kit, biocompatible, Vanquish Flex system, including 6036.2303A
(parts are available separately, see table in section Single Parts):
• Capillary, MP35N, I.D. x length 0.1 x 350 mm
• Active pre-heater, MP35N, I.D. x length 0.1 x 380 mm
• Passive pre-heater, MP35N, I.D. x length 0.1 x 530 mm
11.4.2 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 plug to close open holes in the reservoir cap (pack of 10)
• Retaining guide to keep the liquid line in place in the reservoir
cap (pack of 5)
Solvent Lines and Solvent Line Filters

For information about the solvent lines and solvent line filters, refer to
the Consumables and Replacement Parts section in the Operating
Manual for the pump.

Operating Manual
11.4.3 Fuses and Cables
Fuses kit, Vanquish system 6036.0002

modules.
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
11.4.4 Other Parts
Base module (system base), (all Vanquish systems) 6036.1100

Packing material 6036.7005
Solvent rack 6036.1350
System base locking tool 6036.1160

Operating Manual

Operating Manual
12 • Appendix
12 Appendix
This chapter provides additional information about compliance.

Operating Manual
12 • Appendix
12.1 Compliance Information

Thermo Fisher Scientific performs complete testing and evaluation of its
products to ensure full compliance with applicable domestic and
international regulations.
For details on compliance, also see the Compliance Information section

in the Operating Manual for each module in the Vanquish system.
12.1.1 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

Operating Manual
12 • Appendix
UKCA Declaration of Conformity

The device has satisfied the requirements for the UKCA mark and is
12.1.2 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 37: 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.
12.1.3 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
12 • Appendix
12.1.4 Manual Release History

Revision Covering
5.0 Vanquish Core system with system base VC‑S01‑A‑02, Vanquish

Flex system and Vanquish Horizon system with system base
VF‑S01‑A‑02
4.0 Vanquish Core system with system base VC‑S01‑A‑02, Vanquish
Flex system with system base VF‑S01‑A‑02, Vanquish Horizon
system with system base VH‑S01‑A‑02
3.0a Vanquish Flex system with system base VF‑S01‑A‑02, Vanquish
Horizon system with system base VH‑S01‑A‑02
3.0 Vanquish Flex system with system base VF‑S01‑A‑02, Vanquish
Horizon system with system base VH‑S01‑A‑02
2.0 Vanquish Flex system (103 MPa) with system base VF‑S01,
Vanquish system (151 MPa) with system base VH‑S01
1.0 Vanquish system (151 MPa) with system base VH‑S01
The instructions were prepared in English (original instructions). Other

language versions are translations based on the English original
instructions.

Operating Manual
Index
Index
A connectors ....................................................... 66
consumables.................................................. 143
additives ........................................................... 25
information ................................................. 25 D
use............................................................... 89
algae ................................................................. 89 decontamination ........................................... 105
audit trail........................................................ 112 delivery ............................................................ 37
Diagnostics..................................................... 123
B digital I/O ......................................................... 66
drainage........................................................... 55
buffer use ......................................................... 89
buffers .............................................................. 25 E
concentration.............................................. 25
information ................................................. 25 EAC mark ....................................................... 148
use............................................................... 89 ePanel Set ........................................................ 92
equilibration .................................................... 88
C eWorkflow ....................................................... 94
cable connections............................................. 65 F
capillaries
guide ........................................................... 75 FCC................................................................. 149
install........................................................... 77 flow connections
Viper............................................................ 77 drain system ............................................... 55
CE mark .......................................................... 148 overview ..................................................... 74
charged aerosol detector ........................... 30, 41 waste lines.................................................. 55
chloride concentration ..................................... 27 fluorescence detector................................ 30, 41
Chromeleon................................................ 33, 91 flushing ............................................................ 82
audit trail................................................... 112
instrument configuration ............................ 80 G
Smart Shutdown.......................................... 96
gloves............................................................... 21
Smart Standby............................................. 96
guide hole ........................................................ 75
Smart Startup .............................................. 88
guidelines
system setup ............................................... 80
installation.................................................. 40
Chromeleon 7................................................... 91
maintenance............................................. 101
automated module control ......................... 94
operation .................................................... 85
client............................................................ 91
ePanel Set.................................................... 92
eWorkflow................................................... 94 I
Instrument Configuration Manager ............ 80 installation
Instrument Controller ........................... 80, 91 capillaries and tubing ................................. 75
module control............................................ 92 flow connections ........................................ 73
monitor baseline ......................................... 93 flushing ....................................................... 82
Sequence Wizard ........................................ 94 hardware setup .......................................... 47
cleaning .......................................................... 105 power connections ..................................... 71
condensation.............................................. 45, 71 safety guidelines......................................... 40
signal cable connections............................. 65

Operating Manual
Index
site requirements........................................ 43 P
software setup ............................................ 80
system ......................................................... 41 peak shape..................................................... 113
system stack................................................ 50 pH range .......................................................... 27
waste lines................................................... 55 power connections .......................................... 71
Instrument Audit Trail .................................... 112 power considerations ...................................... 44
intended use..................................................... 18 power cord ...................................................... 44
Interlink ...................................................... 32, 66 power on/off ................................................... 86
protective clothing........................................... 21
L
R
leak liquid ......................................................... 55
LED bar ........................................................... 112 regulatory compliance................................... 148
locking the system............................................ 54 replacement parts ......................................... 143
long-term shutdown ........................................ 97 requirements
long-term shutdown (NP)............................... 130 power cord ................................................. 44
system clearance ........................................ 44
M workbench.................................................. 43
RoHS mark ..................................................... 148
maintenance ............................................ 99, 104
cleaning ..................................................... 105 S
decontamination....................................... 105
general rules.............................................. 103 safety glasses ................................................... 21
interval ...................................................... 104 safety guidelines
interval (NP) .............................................. 131 case of emergency...................................... 24
introduction .............................................. 100 general........................................................ 19
maintenance (NP) ..................................... 131 general hazards .......................................... 22
safety guidelines ....................................... 101 installation.................................................. 40
maintenance............................................. 101
operation .................................................... 85
N
power cord ................................................. 44
normal-phase compatible solvents and additives protective equipment................................. 21
.................................................................. 128 qualification of personnel........................... 19
servicing.................................................... 101
O safety symbols ................................................. 16
scope of delivery.............................................. 37
operating conditions ........................................ 45
seal wash system
electromagnetic interference ..................... 46
seal wash liquid (NP) ................................ 130
humidity ...................................................... 45
Sequence Wizard ............................................. 94
mechanical shocks ...................................... 46
service.............................................................. 99
temperature................................................ 45
setup
ventilation ................................................... 46
hardware .................................................... 47
vibration ...................................................... 46
software ..................................................... 80
operation.......................................................... 33
ship kit ........................................................... 139
Chromeleon................................................. 91
shipping ......................................................... 107
interrupt...................................................... 96
short-term shutdown ...................................... 96
power on/off ............................................... 86
shutdown
preparation ................................................. 87
long-term.................................................... 97
safety guidelines ......................................... 85
long-term (NP).......................................... 130
overview (functional) ....................................... 29
short-term .................................................. 96

Operating Manual
Index
signal cable connections .................................. 65 troubleshooting ............................................. 111

signal words ..................................................... 16 baseline .................................................... 119
site requirements ............................................. 43 communication......................................... 122
condensation......................................... 45, 71 flow........................................................... 117
operating conditions ................................... 45 general information.................................. 112
power considerations.................................. 44 ghost peaks............................................... 114
Smart Shutdown............................................... 96 negative peaks.......................................... 114
Smart Standby .................................................. 96 peak area precision .................................. 115
Smart Startup ................................................... 88 power ....................................................... 122
solvent pressure.................................................... 118
chloride concentration................................ 27 retention time variation ........................... 119
information ................................................. 25 spikes........................................................ 115
pH range...................................................... 27 temperature control................................. 121
use............................................................... 89 tubing............................................................... 77
solvent rack ...................................................... 31 tubing bracket ................................................. 75
ship............................................................ 107 tubing chase .................................................... 75
transport ................................................... 107 tubing guides ................................................... 75
specifications.................................................. 133
solvent rack ............................................... 135 U
system ....................................................... 134
system base............................................... 135 UKCA mark..................................................... 149
startup.............................................................. 88 Universal Serial Bus ......................................... 66
status indicator unlocking the system....................................... 52
LED bar ...................................................... 112 unpack ............................................................. 36
STATUS LED ............................................... 112 USB .................................................................. 66
STATUS LED .................................................... 112 USB drivers ...................................................... 80
system
configuration............................................... 30 V
dismount ................................................... 107 Viper fitting system ......................................... 77
installation................................................... 50
locking ......................................................... 54 W
preparing for operation .............................. 87
troubleshooting......................................... 113 waste container ............................................... 58
unlocking ..................................................... 52 waste lines ....................................................... 55
system arrangement ........................................ 47 WEEE.............................................................. 149
system base...................................................... 31 workbench requirements ................................ 43
installation................................................... 50
safety symbols............................................. 17
ship............................................................ 107
system base lock .............................................. 52
system clearance requirements ....................... 44
system equilibration......................................... 88
System Interlink.......................................... 32, 66
T
transport ........................................................ 107
troubleshoot system ...................................... 113

Operating Manual
www.thermofisher.com
Thermo Fisher Scientific Inc.

168 Third Avenue
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Massachusetts 02451
USA

Man 4820 3601 LC Vanquish UHPLC Man48203601 EN

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thermoscientific

UHPLC and HPLC

Original Operating Manual

Printed manual version only

UHPLC and HPLC Systems Page 3

Page 4 UHPLC and HPLC Systems

2 Safety ......................................................................................... 15

3 System Overview........................................................................ 29

UHPLC and HPLC Systems Page 5

4 Unpacking .................................................................................. 35

5 Installation ................................................................................. 39

Page 6 UHPLC and HPLC Systems

6.6 Operating the System from the Software............................................................ 91

7 Maintenance and Service ........................................................... 99

8 Troubleshooting ....................................................................... 111

9 Modifying the System for Specific Applications ........................ 127

UHPLC and HPLC Systems Page 7

10 Specifications ........................................................................... 133

11 Accessories, Consumables and Replacement Parts ................... 137

Index ........................................................................................ 151

Page 8 UHPLC and HPLC Systems

1 Using this Manual

UHPLC and HPLC Systems Page 9

1.1 About this Manual

This manual also contains safety messages, precautionary statements,

Note the following:

• The descriptions in this manual refer to a standard one-stack

• Illustrations in this manual are provided for basic understanding.

Page 10 UHPLC and HPLC Systems

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

UHPLC and HPLC Systems Page 11

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)

Page 12 UHPLC and HPLC Systems

1.3 Reference Documentation

• Operating manuals for the modules of the Vanquish system

• Instrument Installation Qualification Operating Instructions

Go to the following web site: www.thermofisher.com/HPLCmanuals

• Chromeleon™ Help and documents

• Instrument Configuration Manager Help

• Quick Start Guide

UHPLC and HPLC Systems Page 13

Page 14 UHPLC and HPLC Systems

UHPLC and HPLC Systems Page 15