LTQ Orbitrap Discovery Hardware

LTQ Orbitrap Discovery™
Hardware Manual
Revision A - 122 5850
For Research Use Only

Not for use in Diagnostic Procedures
Part of Thermo Fisher Scientiﬁc

LTQ Orbitrap Discovery™
Hardware Manual
Revision A - 122 5850
For Research Use Only

Not for use in Diagnostic Procedures
© 2007 Thermo Fisher Scientific Inc. All rights reserved.
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Printing History: Revision A printed in September 2007.
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Read This First
Welcome to the Thermo Scientific, LTQ Orbitrap Discovery™ system!
The LTQ Orbitrap Discovery is a member of the family of LTQ™ mass
spectrometer (MS) hybrid instruments.
Who uses this Guide This LTQ Orbitrap Discovery Hardware Manual is intended for all
personnel that need a thorough understanding of the instrument (to
perform maintenance or troubleshooting, for example). This manual
should be kept near the instrument to be available for quick reference.
Scope of this Guide This LTQ Orbitrap Discovery Hardware Manual contains a description
of the modes of operation and principle hardware components of your
LTQ Orbitrap Discovery instrument. In addition, this manual provides
step-by-step instructions for cleaning and maintaining your instrument.
This manual includes the following chapters:
• Chapter 1: “Functional Description” describes the principal

components of the LTQ Orbitrap Discovery.
• Chapter 2: “Basic System Operations” provides procedures for

shutting down and starting up the LTQ Orbitrap Discovery.
• Chapter 3: “User Maintenance” outlines the maintenance

procedures that you should perform on a regular basis to maintain
optimum MS detector performance.
• Chapter 4: “Replaceable Parts” lists the replaceable parts for the

MS detector and data system.
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual i

Read This First
Changes to the Manual
Changes to the To suggest changes to this manual, please send your comments to:
Manual
Editors, Technical Documentation
Thermo Fisher Scientific
Hanna-Kunath-Str. 11
28199 Bremen
Germany
[email protected]
You are encouraged to report errors or omissions in the text or index.

Thank you.
ii LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First
Typographical Conventions
Typographical Typographical conventions have been established for Thermo Fisher

Conventions Scientific manuals for the following:
• Data input
• Admonitions
• Topic headings
Data Input Throughout this manual, the following conventions indicate data input
and output via the computer:
• Messages displayed on the screen are represented by capitalizing the

initial letter of each word and by italicizing each word.
• Input that you enter by keyboard is identified by quotation marks:

single quotes for single characters, double quotes for strings.
• For brevity, expressions such as “choose File > Directories” are used
rather than “pull down the File menu and choose Directories.”
• Any command enclosed in angle brackets < > represents a single

keystroke. For example, “press <F1>” means press the key labeled
F1.
• Any command that requires pressing two or more keys

simultaneously is shown with a plus sign connecting the keys. For
example, “press <Shift> + <F1>” means press and hold the <Shift>
key and then press the <F1> key.
• Any button that you click on the screen is represented in bold face
letters. For example, “click on Close”.
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual iii

Read This First
Typographical Conventions
Admonitions Admonitions contain information that is important, but not part of the
main flow of text.
Admonitions can be of the following types:
• Note – information that can affect the quality of your data. In

addition, notes often contain information that you might need if
you are having trouble.
• Caution – information necessary to protect your instrument from

damage.
• Warning – hazards to human beings. Each Warning is accompanied

by a Warning symbol.
Topic Headings The following headings are used to show the organization of topics
within a chapter:
Chapter Name
The following headings appear in the left column of each page:
Second Level Topics
Third Level Topics
Fourth Level Topics
iv LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First
Safety and EMC Information
Safety and EMC In accordance with our commitment to customer service and safety, this
Information instrument has satisfied the requirements for the European CE Mark
including the Low Voltage Directive.
Designed, manufactured and tested in an ISO9001 registered facility,

this instrument has been shipped to you from our manufacturing facility
in a safe condition.
Caution This instrument must be used as described in this manual. Any

use of this instrument in a manner other than described here may result
in instrument damage and/or operator injury. ▲
Identifying Safety The LTQ Orbitrap Discovery Hardware Manual contains precautionary
Information statements that can prevent personal injury, instrument damage, and
loss of data if properly followed. Warning symbols alert the user to check
for hazardous conditions. These appear throughout the manual, where
applicable, and are defined in Table i.
Table i. Warning Symbols

Symbol Description
General This general symbol indicates that a hazard is present, which if
not avoided, could result in injuries.
The source of danger is described in the accompanying text. ▲

Electric Shock High voltages capable of causing personal injury are
used in the instrument. The instrument must be shut down and
disconnected from line power before service or repair work is
performed. ▲
Noxious This symbol alerts to hazards resulting from noxious
fumes. ▲
Hot Surface / Heat Allow heated components to cool down before

servicing them! ▲
Instrument-Specific Every instrument has specific hazards, so be sure to read and comply
Hazards with the following precautions. They will help ensure the safe,
long-term use of your system.
1. Before plugging in any of the instrument modules or turning on the

power, always make sure that the voltage and fuses are set
appropriately for your local line voltage.
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual v

Read This First
2. Only use fuses of the type and current rating specified. Do not use
repaired fuses and do not short-circuit the fuse holder.
3. The supplied power cord must be inserted into a power outlet with a
protective earth contact (ground). When using an extension cord,
make sure that the cord also has an earth contact.
4. Do not change the external or internal grounding connections.

Tampering with or disconnecting these connections could endanger
you and/or damage the system.
Caution The instrument is properly grounded in accordance with

regulations when shipped. You do not need to make any changes to the
electrical connections or to the instrument’s chassis to ensure safe
operation. ▲
5. Never run the system without the housing on. Permanent damage
can occur.
6. Do not turn the instrument on if you suspect that it has incurred

any kind of electrical damage. Instead, disconnect the power cord
and contact a Service Representative for a product evaluation. Do
not attempt to use the instrument until it has been evaluated.
(Electrical damage may have occurred if the system shows visible
signs of damage, or has been transported under severe stress.)
7. Damage can also result if the instrument is stored for prolonged

periods under unfavorable conditions (e.g., subjected to heat, water,
etc.).
8. Always disconnect the power cord before attempting any type of

maintenance.
9. Capacitors inside the instrument may still be charged even if the

instrument is turned off.
10. Never try to repair or replace any component of the system that is
not described in this manual without the assistance of your service
representative.
vi LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First
Safety Advice for Possible Hazardous Material Might Contaminate Certain Parts of Your
Contamination System During Analysis.
In order to protect our employees, we ask you to adhere to special

precautions when returning parts for exchange or repair.
If hazardous materials have contaminated mass spectrometer parts,

Thermo Fisher Scientific can only accept these parts for repair if they
have been properly decontaminated. Materials, which due to their
structure and the applied concentration might be toxic or which in
publications are reported to be toxic, are regarded as hazardous.
Materials that will generate synergetic hazardous effects in combination
with other present materials are also considered hazardous.
Your signature on the Repair-Covering letter confirms that the

returned parts have been decontaminated and are free of hazardous
materials.
The Repair-Covering letter can be ordered from your service engineer or

downloaded from the Customer Information Service (CIS) site. Please
register under http://register.thermo-bremen.com/form/cis.
Parts contaminated by radioisotopes are not subject to return to Thermo

Fisher Scientific – either under warranty or the exchange part program.
If parts of the system may be possibly contaminated by hazardous
material, please make sure the Field engineer is informed before the
engineer starts working on the system.
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual vii

Contents
Chapter 1 Functional Description.............................................................1-1
General Description .......................................................... 1-2
Specifications ................................................................. 1-5
Control Elements.............................................................. 1-6
System Status LEDs ....................................................... 1-6
Control Panels ............................................................... 1-7
Linear Ion Trap............................................................... 1-12
Orbitrap Analyzer ........................................................... 1-13
Measuring Principle ..................................................... 1-13
Curved Linear Trap ..................................................... 1-13
Extraction of Ion Packets ............................................. 1-14
Ion Detection............................................................... 1-15
Active Temperature Control ........................................ 1-17
HCD Collision Cell..................................................... 1-17
Vacuum System .............................................................. 1-19
Turbopumps ................................................................ 1-20
Forevacuum Pumps...................................................... 1-21
Vacuum System Controls............................................. 1-22
Vacuum System Heating during a System Bakeout ...... 1-23
Gas Supply...................................................................... 1-24
Vent Valve of the Linear Ion Trap ............................... 1-26
Cooling Water Circuit .................................................... 1-27
Recirculating Chiller .................................................... 1-28
Properties of Cooling Water......................................... 1-28
Printed Circuit Boards .................................................... 1-29
Linear Ion Trap Electronics.......................................... 1-30
Electronic Boards at the Right Side of the Instrument.. 1-31
Electronic Boards on the Left Side of the Instrument ... 1-44
Chapter 2 Basic System Operations ........................................................2-1

Shutting Down the System in an Emergency .................... 2-2
Behavior of the System in Case of a Main Failure........... 2-2
Placing the System in Standby Condition ......................... 2-4
Shutting Down the System ............................................... 2-5
Starting Up the System after a Shutdown.......................... 2-7
Starting Up the Instrument............................................ 2-7
Setting Up Conditions for Operation............................. 2-8
Resetting the System ....................................................... 2-10
Resetting the Tune and Calibration Parameters to their
Default Values ................................................................ 2-11
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual ix

Contents
Chapter 3 User Maintenance.................................................................... 3-1

General Remarks............................................................... 3-2
Returning Parts .............................................................. 3-2
Cleaning the Surface of the Instrument .......................... 3-3
Baking Out the System ..................................................... 3-4
Bakeout Procedure ......................................................... 3-4
Maintaining the Vacuum System ...................................... 3-6
Exchanging the Lubricant Reservoir of the Turbopumps 3-6
Maintenance of the Recirculating Chiller .......................... 3-7
Reservoir ........................................................................ 3-7
Fluid Bag Filter .............................................................. 3-7
Condenser Filter ............................................................ 3-7
Chapter 4 Replaceable Parts .................................................................... 4-1

Parts Basic System............................................................. 4-2
Parts Orbitrap Analyzer.................................................. 4-3
Parts Pumping System Orbitrap..................................... 4-3
Parts Gas and Water Supply........................................... 4-5
Electronic Parts ................................................................. 4-7
Electronics - Right Panel ................................................ 4-7
Electronics - Left Panel .................................................. 4-8
Electronics Analyzer ....................................................... 4-8
Electronics Main Supply ................................................ 4-9
Glossary .................................................................................... G-1
Index ............................................................................................ I-1
x LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Figures
LTQ Orbitrap Discovery front view ...................................................... 1-2

Schematic view of the LTQ Orbitrap Discovery .................................... 1-3
Top lid opened ...................................................................................... 1-4
System status LEDs ............................................................................... 1-6
Right side of the LTQ Orbitrap Discovery ............................................ 1-7
Upper control panel .............................................................................. 1-8
Power control panel with power control LEDs and switches ................. 1-9
Main power switch .............................................................................. 1-10
External connections to the LTQ Orbitrap Discovery ......................... 1-11
Schematic view of the Orbitrap cell and example of a stable ion
trajectory ............................................................................................. 1-13
Layout of the instrument, also showing the applied voltages ................ 1-14
Principle of electrodynamic squeezing of ions in the Orbitrap as the field
strength is increased ............................................................................ 1-15
Approximate shape of ion packets of different m/q after stabilization of
voltages ............................................................................................... 1-16
HCD collision cell and C-Trap ........................................................... 1-17
Schematical view of vacuum system (C-Trap compartment not
shown) ................................................................................................ 1-19
Vacuum components on the left instrument side ................................ 1-20
Vacuum components on the right instrument side .............................. 1-20
Forepumps cabinet .............................................................................. 1-21
Schematical view of the gas supply ...................................................... 1-24
Valve for HCD collision gas ................................................................ 1-25
Nitrogen pressure regulator and gas flow divider ................................. 1-26
Schematical view of cooling water circuit ............................................ 1-27
Electronic connections to linear trap (covers removed) ........................ 1-30
Electronic boards on the right side of the instrument .......................... 1-31
Preamplifier board ............................................................................... 1-32
Data Acquisition unit (covers removed) .............................................. 1-33
Data Acquisition Digital PCI board .................................................... 1-34
Data Acquisition Analog board ........................................................... 1-35
Instrument Control board ................................................................... 1-37
Power Distribution board ................................................................... 1-38
Power Supply 1 board ......................................................................... 1-43
Electronic boards on the left side of the instrument ............................. 1-44
Ion Optic Supply board ...................................................................... 1-45
Central Electrode Pulser board ............................................................ 1-46
Temperature Controller board ............................................................ 1-47
CLT RF unit (cover removed) ............................................................. 1-49
Central Electrode Power Supply board ................................................ 1-50
High Voltage Power Supply board (cover removed) ............................ 1-52
High Voltage Power Supply board with SPI Bus Termination board .. 1-53
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual xi

Figures
Main power switch in Off position ....................................................... 2-2

Bakeout timer ....................................................................................... 3-4
xii LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Tables
System status LEDs of the LTQ Orbitrap Discovery ............................. 1-6

Circuit breakers of the LTQ Orbitrap Discovery ................................... 1-8
Diagnostic LEDs on the Preamplifier board ........................................ 1-33
Diagnostic LEDs of the Data Acquisition Digital PCI board .............. 1-35
Diagnostic LEDs of the Data Acquisition Analog board ...................... 1-36
Diagnostic LEDs of the Power Supply 2 board ................................... 1-36
Diagnostic LEDs of the Instrument Control board ............................. 1-37
Software status LEDs of the Instrument Control board ....................... 1-38
Status LEDs of the Power Distribution board ..................................... 1-40
Working modes of the Power Distribution board ................................ 1-41
Operating states of the Power Distribution board ............................... 1-41
Diagnostic LEDs of the Power Supply 1 board ................................... 1-43
Diagnostic LEDs of the Ion Optic Supply board ................................. 1-46
Diagnostic LEDs of the Central Electrode Pulser board ...................... 1-47
Diagnostic LEDs of the Temperature Controller board ....................... 1-48
Diagnostic LEDs of the CLT RF Main board ..................................... 1-49
Diagnostic LEDs of the Central Electrode Power Supply board .......... 1-51
Diagnostic LEDs of the High Voltage Power Supply board ................ 1-53
User maintenance procedures ................................................................ 3-2
Parts for the LTQ Orbitrap Discovery .................................................. 4-1
Parts LTQ Orbitrap Discovery; 50 Hz (P/N 072 3720) ........................ 4-1
Parts basic system Orbitrap-2 (P/N 122 4790) ...................................... 4-2
Parts Upgrade kit Orbitrap HCD option (P/N 122 4800) .................... 4-2
Parts Orbitrap Installation Kit (P/N 118 8120) .................................... 4-2
Parts Orbitrap-2 chamber; complete (P/N 122 4780) ........................... 4-3
Parts pumping system Orbitrap (P/N 118 4490) .................................. 4-3
Parts pump kit Orbitrap (P/N 117 5000) ............................................. 4-3
Parts pump system Orbitrap (P/N 117 5010) ....................................... 4-4
Parts gas supply (P/N 117 7881) ........................................................... 4-5
Upgrade kit gas supply LTQ Orbitrap XL (P/N 122 4820) .................. 4-5
Parts water supply (P/N 117 8460) ...................................................... 4-6
Kit gas-water assembly (P/N 208 7351) ................................................ 4-6
Electronic parts Orbitrap-2 (P/N 800 1110) ......................................... 4-7
Parts Orbitrap-2 electronics; right panel (P/N 208 1010) ...................... 4-7
Parts Unit data acquisition (P/N 206 4132) .......................................... 4-8
Parts Orbitrap-2 electronics; left panel (P/N 208 1020) ........................ 4-8
Parts electronics analyzer Orbitrap-2 (P/N 210 0160) ........................... 4-8
Parts electronics main supply Orbitrap (P/N 208 1040) ........................ 4-9
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual xiii

Chapter 1 Functional Description
This chapter provides an overview of the functional elements of the

LTQ Orbitrap Discovery. It contains the following topics:
• “General Description” on page 1-2
• “Control Elements” on page 1-6
• “Linear Ion Trap” on page 1-12
• “Orbitrap Analyzer” on page 1-13
• “Vacuum System” on page 1-19
• “Gas Supply” on page 1-24
• “Cooling Water Circuit” on page 1-27
• “Printed Circuit Boards” on page 1-29
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-1

Functional Description
General Description
General Description LTQ Orbitrap Discovery is a hybrid mass spectrometer incorporating

the LTQ XL™ linear trap and the Orbitrap™. Figure 1-1 shows a front
view of the instrument.
LTQ XL Linear Ion Trap
Figure 1-1. LTQ Orbitrap Discovery front view
Figure 1-2 on page 1-3 shows the schematic view of the LTQ Orbitrap
Discovery. The LTQ Orbitrap Discovery consists of three main
components, which are described in the following topics:
• A linear ion trap (Thermo Scientific LTQ XL) for sample ionization,
selection, fragmentation, and AGC™.
• An intermediate storage device (curved linear trap) that is required

for short pulse injection.
• An Orbitrap analyzer for Fourier transformation based analysis.
A collision cell for performing HCD (Higher Energy Collisional

Dissociation) experiments is available as option for LTQ Orbitrap
Discovery. The feature will be not available if the instrument is not
equipped with this option.
1-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

1
C-Trap
HCD collision cell1
Lens stack
Figure 1-2. Schematic view of the LTQ Orbitrap Discovery
1HCD
is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option.

General Description
Wheels at the bottom side of the instrument facilitate positioning the

LTQ Orbitrap Discovery at the intended place in the laboratory. The
instrument is designed to be placed with its rear panel against a wall. To
ensure a sufficient air flow for cooling the instrument, spacers on the
rear panel provide for minimum distance to the wall.
The mains inlet as well as a power outlet for peripheral devices (data
system, for example) are located at the right side of the instrument.
Rotary pumps are hidden under the linear trap and accessible from the
front. The left side panel and the front panel are mounted on hinges and
the right side panel is removable.
The top lid opens upwards to allow easy access for Field Engineers from
the top. See Figure 1-3.
Figure 1-3. Top lid opened
A stand-alone recirculating water chiller is delivered with the

instrument. It is connected to the right side of the instrument.

General Description
Specifications The LTQ Orbitrap Discovery has the following measuring properties:
Resolution (apodized)30000 (FWHM) @ m/z 400

with a detect time of 400 ms
Minimum resolution 7500,
maximum resolution 30000 @ m/z 400
Mass Range m/z 50–2000; m/z 200–4000
Mass Accuracy <5 ppm RMS for 8 h period with external
calibration,
<2 ppm RMS with internal calibration
Dynamic Range >10000 between mass spectra,
>4000 between highest and lowest detectable
mass in one spectrum
MS/MS MS/MS and MSn scan functions

Control Elements
Control Elements The LTQ Orbitrap Discovery is mainly operated from the desktop
computer (data system). Some control elements for important system
functions are located directly on the instrument. They are described in
the following sections.
System Status LEDs Figure 1-4 shows the system status LEDs at the front of the instrument.
Five LEDs indicate the main functions of the system. (See also
Figure 1-5 on page 1-7.) While the Power LED is directly controlled by
the 3 × 230 V input, all other LEDs are controlled by the power
distribution board (Refer to topic “Power Distribution Board” on
page 1-38). Table 1-1 explains the function of the various LEDs.
Figure 1-4. System status LEDs
The system status LEDs at the front panel of the linear ion trap are
described in the LTQ XL Hardware Manual.
Table 1-1. System status LEDs of the LTQ Orbitrap Discovery

LED Status Information
Power Green Main switch on
Off Main switch off
Vacuum* Green Operating vacuum reached
Yellow Insufficient vacuum or Vacuum Pumps switch off
Communication Green Communication link between instrument and data system
established
Yellow Communication link starting up or Vacuum Pumps switch off
System* Green System ready
Yellow FT Electronics switch off or Vacuum Pumps switch off
Detect Blue Instrument is scanning
Off Instrument is not scanning
* These
LEDs are flashing when a system bakeout is performed. See topic “Baking Out the System” on
page 3-4.

Control Elements
Control Panels Figure 1-5 shows the right side of the LTQ Orbitrap Discovery. Located
here are the control panels, switches, and the ports for the external
connections (mains supply, gases, Ethernet communication, and cooling
water).
System status LEDs System status LEDs of LTQ Orbitrap Discovery

of linear trap Bakeout timer
Cover lid for

bake out
controls
Switches and
control LEDs
Main power
switch
Power connector
Forepumps cabinet Power panel of linear trap
Figure 1-5. Right side of the LTQ Orbitrap Discovery
For more information about the external connections, refer to topic

“External Connections” on page 1-10.
Upper Control Panel The upper instrument control panel comprises the bakeout timer, the
bakeout control buttons, and three circuit breakers. To access the upper
control panel, swing open the small lid (opens from left to right). See
Figure 1-5 and Figure 1-6 on page 1-8.
The timer allows setting the duration for the bakeout of the system.
After the duration is set, the bakeout procedure is started by pressing the
green button on the right. A running bakeout procedure can be stopped
by pressing the orange button on the left side. For instructions about
performing a bakeout, refer to topic “Baking Out the System” on
page 3-4.

Control Elements
Bakeout timer Cover lid
Bakeout control
buttons
Circuit breakers
Figure 1-6. Upper control panel
Note The buttons themselves have no indicator function. A running

bakeout procedure is indicated by flashing Vacuum and System LEDs at
the front side of the instrument. See Figure 1-4 on page 1-6. ▲
Three circuit breakers are located at the bottom of this control panel.
Table 1-2 shows the parts of the LTQ Orbitrap Discovery that are
protected by the respective circuit breaker. The proper function of each
circuit breaker is signaled by a dedicated LED in the power control
panel (for example, F1 corresponds to L1).
Table 1-2. Circuit breakers of the LTQ Orbitrap Discovery

Circuit breaker Ampere LED Instrument parts
F1 10 L1 Power Distribution
F2 16 L2 Linear ion trap
F3 10 L3 Multiple socket outlets (Data system, LC, heater,
etc.)
Power Control Panel In addition to the system status LEDs at the front side (see Figure 1-4
on page 1-6), the LTQ Orbitrap Discovery has three power control
LEDs above the Vacuum Pumps switch at the right side. See Figure 1-7.
They indicate whether the corresponding circuit breaker is closed and
the respective parts of the instrument have power. (See Table 1-2 on
page 1-8.)

Control Elements
Power control LEDs
Vacuum Pumps switch
FT Electronics switch
Figure 1-7. Power control panel with power control LEDs and switches
The use of the switches below the power control LEDs changes the
working mode of the power distribution. (See topic “Working Modes of
the Power Distribution” on page 1-48.)
The Vacuum Pumps switch can be set into the positions ON or OFF.
When the switch is in the OFF position, everything but the multiple
socket outlet is switched off.
The FT Electronics switch can be set into the Operating Position (ON)
or into the Service Position (OFF). When the switch is in the Service
position, all components are switched off with exception of the
following:
• Fans
• Heater control
• Power distribution (Refer to the topic “Power Distribution Board”

on page 1-38)
• Pumps (Refer to the topic “Vacuum System” on page 1-19)
• Temperature controller (Refer to the topic “Temperature Controller

Board” on page 1-47)
• Vacuum control
The linear ion trap also remains on because it has a separate Service
switch.

Control Elements
Main Power Switch The main power switch must be turned 90° clockwise/anti-clockwise to
switch on/off the instrument (see Figure 1-8). Placing the main power
switch in the Off position turns off all power to the LTQ Orbitrap
Discovery (and linear ion trap as well, including the vacuum pumps).
On
Off
Figure 1-8. Main power switch
Note When the main power switch is in the Off position, you can secure
it with a padlock or a cable tie (to prevent unintended re-powering when
performing maintenance, for example). ▲
External Connections Figure 1-9 on page 1-11 shows the lower right side of the instrument
with the external connections for mains supply, gases, cooling water, and
Ethernet communication.
The power connector for the mains supply is located on the center. The
cooling water ports are located below the power connector. (See also
topic “Cooling Water Circuit” on page 1-27.) A Teflon® hose connects
the instrument to the nitrogen gas supply. An analogous port is used for
the HCD collision gas supply.1 Metal tubing connects the instrument
with the helium gas supply. (See also topic “Gas Supply” on page 1-24.)
Located at the top are two ports for Ethernet cables for connecting the
LTQ Orbitrap Discovery and the linear ion trap via an Ethernet hub
with the data system computer.
The exhaust hose from the rotary pumps is led backwards below the
instrument, comes out the back of the instrument, and connects the
pumps to the exhaust system in the laboratory.
1HCD
is an option for LTQ Orbitrap Discovery. The feature will be not available if the
instrument is not equipped with this option.

Control Elements
Ethernet ports
Power outlet for

peripheral devices
Power connector
Helium gas inlet

Cooling water inlet port
Collision gas inlet1
Inlet for nitrogen gas
Cooling water outlet port
Figure 1-9. External connections to the LTQ Orbitrap Discovery
The power outlet for peripheral devices (data system, for example) is
located above the mains supply port. The outlet provides the mains
supply for the peripherals via a multiple socket outlet.
Caution Do not connect the recirculating chiller to the peripherals

power outlet!
Furthermore, make sure that the maximum current drawn from the
power outlet does not exceed 16 A. Overloading it (by connecting to
many pieces of equipment to the multiple socket outlet, for example)
may destroy the outlet by excessive heating. ▲
1
Not used in the standard version of the LTQ Orbitrap Discovery.

Linear Ion Trap
Linear Ion Trap The LTQ Orbitrap Discovery system can utilize a variety of ionization
techniques such as ESI, APCI, or APPI. Maintenance of the API source,
as well as switching between ionization methods, is vent-free. Ions are
transferred by octapole and “square” quadrupole lenses into an ion trap
that is optimized for axial ion ejection into the curved linear trap. (See
Figure 1-2 on page 1-3.)
The linear ion trap is an independent MS detector (Thermo Scientific

LTQ XL), which can store, isolate, and fragment ions and then send
them either to the Orbitrap for further analysis or to an SEM detector.
The linear ion trap is a unique ion preparation and injection system for
Orbitrap MS, because it has greater ion storage capacity than
conventional 3D ion trap devices. The linear ion trap is completely
described in the LTQ XL Hardware Manual.
All the ion handling, selection and excitation capabilities of the ion trap
can be used to prepare ions for analysis in the Orbitrap. These features
include storage and ejection of all ions, storage of selected masses or
mass ranges, as well as ion isolation. Isolated ions can be excited and
then fragmented as necessary for MS/MS and MSn experiments. The
patented Automatic Gain Control (AGC) provides extended dynamic
range and insures optimized overall performance of the ion trap and
Orbitrap MS.
The linear ion trap and the transfer chamber are mounted on a table.
See Figure 1-1 on page 1-2. The table also serves as a housing for the
forepumps. See Figure 1-18 on page 1-21. The LTQ Orbitrap
Discovery provides power for the linear ion trap – and for the data
system.
The linear ion trap is delivered with power connector, gas lines (He, N2,
and collision gas), and vacuum tube lines extending to the ESI source.
On the rear side of the LTQ XL ion trap is a flange with an O-ring seal.
When the flange is removed, the Orbitrap transfer chamber is mounted
to the flange of the linear ion trap. The transfer chamber is held with
supports on the table. The components of the ion optics and the
Orbitrap are fixed to the transfer chamber.

Orbitrap Analyzer
Orbitrap Analyzer This section describes the basic principle of the Orbitrap analyzer. The
heart of the system is an axially-symmetrical mass analyzer. It consists of
a spindle-shape central electrode surrounded by a pair of bell-shaped
outer electrodes. See Figure 1-10. The Orbitrap employs electric fields
to capture and confine ions.
Figure 1-10. Schematic view of the Orbitrap cell and example of a stable
ion trajectory
Measuring Principle In the mass analyzer shown in Figure 1-10, stable ion trajectories rotate
around an axial central electrode with harmonic oscillations along it.
The frequency ω of these harmonic oscillations along the z-axis depends
only on the ion mass-to-charge ratio m/q and the instrumental
constant k:
q
w = m- × k
---
Two split halves of the outer electrode of the Orbitrap detect the image
current produced by the oscillating ions. By Fast Fourier Transformation
(FFT) of the image current, the instrument obtains the frequencies of
these axial oscillations and therefore the mass-to-charge ratios of the
ions.
Curved Linear Trap On their way from the linear trap to the Orbitrap, ions move through
the gas-free RF octapole (Oct 1) into the gas-filled curved linear trap
(C-Trap). See Figure 1-11 on page 1-14. Ions in the C-Trap are returned
by the trap electrode. Upon their passage, the ions loose enough kinetic
energy to prevent them from leaving the C-Trap through the Gate. The
nitrogen collision gas (bath gas) is used for dissipating the kinetic energy
of ions injected from the LTQ XL and for cooling them down to the axis
of the curved linear trap.

Orbitrap Analyzer
Voltages on the end apertures of the curved trap (Trap and Gate
apertures) are elevated to provide a potential well along its axis. These
voltages may be later ramped up to squeeze ions into a shorter thread
along this axis. The RF to the C-Trap (“Main RF”) is provided by the
CLT RF main board. (See page 1-48.) Trap and gate DC voltages as well
as RF voltages to octapole 1 are all provided by the ion optic supply
board. (See page 1-45.) High voltages to the lenses are provided by the
high voltage power supply board. (See page 1-51.)
1
HCD collision octapole1
Figure 1-11. Layout of the instrument, also showing the applied voltages
Extraction of Ion Packets For ion extraction, the RF on the rods of the C-Trap is switched off and
extracting voltage pulses are applied to the electrodes, pushing ions
orthogonally to the curved axis through a slot in the inner hyperbolic
electrode. Because of the initial curvature of the curved trap and the
subsequent lenses, the ion beam converges on the entrance into the
Orbitrap. The lenses form also differential pumping slots and cause
spatial focusing of the ion beam into the entrance of the Orbitrap. Ions
are electrostatically deflected away from the gas jet, thereby eliminating
gas carryover into the Orbitrap.
1HCD

Orbitrap Analyzer
Owing to the fast pulsing of ions from the curved trap, ions of each
mass-to-charge ratio arrive at the entrance of the Orbitrap as short
packets only a few millimeters long. For each mass/charge population,
this corresponds to a spread of flight times of only a few hundred
nanoseconds for mass-to-charge ratios of a few hundred Daltons/charge.
Such durations are considerably shorter than a half-period of axial ion
oscillation in the trap. When ions are injected into the Orbitrap at a
position offset from its equator (Figure 1-12), these packets start
coherent axial oscillations without the need for any additional excitation
cycle.
Figure 1-12. Principle of electrodynamic squeezing of ions in the Orbitrap

as the field strength is increased
The evolution of an ion packet during the increase of the electric field is
shown schematically on Figure 1-12. When the injected ions approach
the opposite electrode for the first time, the increased electric field
(owing to the change of the voltage on the central electrode) contracts
the radius of the ion cloud by a few percent. The applied voltages are
adjusted to prevent collision of the ions with the electrode. A further
increase of the field continues to squeeze the trajectory closer to the axis,
meanwhile allowing for newly arriving ions (normally, with higher m/q)
to enter the trap as well. After ions of all m/q have entered the Orbitrap
and moved far enough from the outer electrodes, the voltage on the
central electrode is kept constant and image current detection takes
place.
Ion Detection During ion detection, both the central electrode and deflector are
maintained at very stable voltages so that no mass drift can take place.
The outer electrode is split in half at z=0, allowing the ion image current
in the axial direction to be collected. The image current on each of half
of the outer electrode is differentially amplified and then undergoes
analog-to-digital conversion before processing using the fast Fourier
transform algorithm.

Orbitrap Analyzer
Figure 1-13. Approximate shape of ion packets of different m/q after

stabilization of voltages
As mentioned above, stable ion trajectories within the Orbitrap combine

axial oscillations along the z-axis with rotation around the central
electrode and vibrations in the radial direction. (See Figure 1-10 on
page 1-13.) For any given m/q, only the frequency of axial oscillations is
completely independent of initial ion parameters, while rotational and
radial frequencies exhibit strong dependence on initial radius and
energy. Therefore, ions of the same mass/charge ratio continue to
oscillate along z together, remaining in-phase for many thousands of
oscillations.
In contrast to the axial oscillations, the frequencies of radial and

rotational motion will vary for ions with slightly different initial
parameters. This means that in the radial direction, ions dephase orders
of magnitude faster than in the axial direction, and the process occurs in
a period of only 50–100 oscillations. After this, the ion packet of a given
m/q assumes the shape of a thin ring, with ions uniformly distributed
along its circumference. (See Figure 1-13.) Because of this angular and
radial smearing, radial and rotational frequencies cannot appear in the
measured spectrum. Meanwhile, axial oscillations will persist, with axial
thickness of the ion ring remaining small compared with the axial
amplitude. Moving from one half outer electrode to the other, this ring
will induce opposite currents on these halves, thus creating a signal to be
detected by differential amplification.

Orbitrap Analyzer
Active Temperature Active temperature control is achieved by monitoring temperature

Control directly on the Orbitrap assembly and compensating any changes in
ambient temperature by a thermoelectric cooler (Peltier element) on the
outside of the UHV chamber. A dedicated temperature controller board
is used for this purpose. See page 1-47.
Peltier Cooling To allow stable operating conditions in the UHV chamber, it can be
cooled or heated (outgassing) by means of a Peltier element located on
the outside. A second Peltier element is located on the back of the
CE power supply board. See Figure 1-32 on page 1-44.
The Peltier cooling is based on the Peltier Effect, which describes the
effect by which the passage of an electric current through a junction of
two dissimilar materials (thermoelectric materials) causes temperature
differential (cooling effect). The voltage drives the heat to flow from one
side of the Peltier element to the other side, resulting in cooling effects
on one side and heating effects on the other side.
To remove the heat from the hot side of the Peltier elements, they are
connected to the cooling water circuit of the LTQ Orbitrap Discovery.
See topic “Cooling Water Circuit” on page 1-27 for further
information.
HCD Collision Cell HCD is an option for LTQ Orbitrap Discovery. The feature will be not
available if the instrument is not equipped with this option.
HCD collision cell
C-Trap
Figure 1-14. HCD collision cell and C-Trap

Orbitrap Analyzer
The collision cell consists of a straight multipole mounted inside a metal

tube which is connected in direct line-of-sight to the C-Trap.
Figure 1-14 on page 1-17 shows a close-up view of the configuration.
It is supplied with a collision gas through the open split interface,

providing increased gas pressure inside the multipole. The choice of
collision gas is independent from the gas in the C-Trap. See topic “Gas
Supply” on page 1-24 for details. The front of the tube is equipped with
a lens for tuning transmission and ejection to/from the C-Trap. The ion
optic supply board provides the voltages for the collision cell. (See
page 1-45.)
For HCD (Higher Energy Collisional Dissociation), ions are passed

through the C-Trap into the collision cell. The offset between the
C-Trap and HCD is used to accelerate the parents into the gas-filled
collision cell.
The fragment spectra generated in the collision cell and detected in the
Orbitrap show a fragmentation pattern comparable to the pattern of
typical collisional quadrupole spectra. See the LTQ Orbitrap Discovery
Getting Started manual for more information.

Vacuum System
Vacuum System Figure 1-15 shows a schematic overview of the vacuum system. The
Orbitrap has the following vacuum compartments:
• CLT compartment in the aluminum vacuum chamber (pumped

by the same pump as the linear trap)
• Vacuum chamber (pumped by a water-cooled 60 L/s – for N2 –

turbopump TMH 071, TMP 1, manufacturer: Pfeiffer)
• Ultra high vacuum chamber (UHV chamber, pumped by a

water-cooled 60 L/s turbopump TMH 071, TMP 2, manufacturer:
Pfeiffer)
• Orbitrap chamber (pumped by a 210 L/s – for N2 – water-cooled

turbopump TMU 262, TMP 3, manufacturer: Pfeiffer)
The forepumps of the linear trap provide the forevacuum for the
turbopumps.
LTQ XL
UHV Chamber
Vacuum Chamber
Turbopump TMH 071
(TMP 2) Orbitrap
Chamber
Pirani Gauge
Cold Ion Gauge
LTQ XL
Fore Fore Turbopump TMU 262 Turbopump TMH 071

Pump Pump (TMP 3) (TMP 1)
Figure 1-15. Schematical view of vacuum system (C-Trap compartment not shown)*
* For an abridged version of the parts list, see Table 4-7 on page 4-3.

Vacuum System
Turbopumps All parts of the system except for the Orbitrap analyzer are mounted in a
aluminum vacuum chamber evacuated by a 60 L/s turbopump (TMP 1,
see Figure 1-16). The rotary vane pumps of the linear trap (see below)
provide the forevacuum for this pump. This chamber is bolted to a
stainless steel welded UHV chamber housing the Orbitrap, lenses, and
corresponding electrical connections.
Pirani gauge Turbopump vacuum chamber (TMP 1)
Figure 1-16. Vacuum components on the left instrument side
The UHV chamber is evacuated down to 10-8 mbar pressure range by a

60 L/s UHV turbopump (TMP 2, see Figure 1-17).
1
Preamplifier
HCD housing1
Cooling water
supply for Peltier
element
Cold Ion
Gauge
Turbopump
TMU 262 Turbopump TMH 071
(TMP 3) (TMP 2)
Figure 1-17. Vacuum components on the right instrument side
1HCD

Vacuum System
The Orbitrap itself is separated from the UHV chamber by differential

apertures and is evacuated down to 10-10 mbar by a 210 L/s turbopump
(TMP 3, see Figure 1-17 on page 1-20). All turbopumps are equipped
with TC 100 control units (manufacturer: Pfeiffer).
Linear Trap Turbopump A separate turbopump provides the high vacuum for the linear ion trap.
It it is mounted to the bottom of the vacuum manifold of the linear ion
trap. For more information, refer to the LTQ XL Hardware Manual.
Forevacuum Pumps The rotary vane pumps from the linear trap serve as forepumps for the
two smaller turbopumps (TMP 1 and TMP 2). The exhaust hose from
the forepumps is led to the back of the instrument and connects them to
the exhaust system in the laboratory. The forepumps are located on a
small cart in the forepumps cabinet below the linear trap. See
Figure 1-18.
Oil mist filters
Forepumps
Figure 1-18. Forepumps cabinet
To minimize the ingress of pump oil into the exhaust system, the outlets
of the forepumps are fitted to oil mist filters. See page 3-6 on
instructions about returning the collected oil to the forepumps.
The forevacuum pumps (forepumps) of the linear trap are powered by

the power panel of the linear ion trap.
Warning When analyzing hazardous materials, these may be present in

the effluent of the forepumps! The connection to an adequate exhaust
system is mandatory! ▲

Vacuum System
Leave the on/off switches of the forepumps always in the On position to

provide the control from the vacuum control panel. Before starting the
pumps, however, make sure that:
• The forevacuum pumps are filled with oil,
• They are connected to the power supply, and
• The gas ballast is shut.
For a detailed description of the forepumps, refer to the handbook of

the manufacturer.
Vacuum System Controls The power distribution board controls all turbopumps via voltage levels.
Refer to topic “Power Distribution Board” on page 1-38. An interface
for RS485 data via the instrument control board connects the
turbopumps with the linear ion trap. (Refer to topic “Instrument
Control Board” on page 1-36.) The linear ion trap has a separate
turbopump controller.
Vacuum Gauges The vacuum is monitored by several vacuum gauges:
• The forevacuum of the

LTQ Orbitrap Discovery is
monitored by an Active Pirani
gauge (TPR 280, manufacturer:
Pfeiffer) connected to the
LTQ Orbitrap Discovery
forevacuum line. See photo
right and Figure 1-16 on
page 1-20.
• The high vacuum of the LTQ Orbitrap Discovery is monitored by a

Cold Ion Gauge (IKR 270, manufacturer: Pfeiffer) connected to the
UHV chamber. See Figure 1-17 on page 1-20. Since the gauge
would be contaminated at higher pressures, it is only turned on
when the forevacuum has fallen below a safety threshold
(<10-2 mbar).
• The linear ion trap vacuum is monitored by a Convectron gauge

and an ion gauge. Refer to the LTQ XL Hardware Manual for more
information.
The vacuum gauges of the LTQ Orbitrap Discovery are connected to

the power distribution board that directly responds to the pressure
values. (Refer to the topic “Power Distribution Board” on page 1-38.)

Vacuum System
The analog values are digitized by the instrument control board. (Refer
to the topic “Instrument Control Board” on page 1-36.) They are then
sent as readout values to the data system.
Switching on the Vacuum System When the vacuum system is switched on, the following occurs:
1. After the Vacuum Pumps switch is switched On, the pumps of the
linear ion trap and the LTQ Orbitrap Discovery are run up. The
Pirani gauge (see above) controls the LTQ Orbitrap Discovery low
vacuum pressure as well as the pressure at the forevacuum pumps.
Within a short time, a significant pressure decrease must be
observed. The goodness of the vacuum can be estimated by means
of the rotation speed of the turbopumps (e.g. 80% after 15 min.).
2. If the working pressure is not reached after the preset time, the
complete system is switched off. At the status LED panel of the
power distribution board, an error message (Vacuum Failure) is put
out (see below).
3. The Cold Ion Gauge is only switched on after the low vacuum is
reached. It is then used to monitor the vacuum in the Orbitrap
region.
Vacuum Failure In case the pressure in the LTQ Orbitrap Discovery or the linear ion
trap exceeds a safety threshold, the complete system including linear ion
trap, electronics, and pumps is switched off. However, the power
distribution is kept under current and puts out an error message at the
LED panel. (Refer to the topic “Power Distribution Board” on
page 1-38.) It can be reset by switching the main power switch off and
on. (Refer to the topic “Main Power Switch” on page 1-10.)
Upon venting, the vent valves of the turbopumps on the Orbitrap

detector stay closed. Only the vent valve of the linear ion trap is used.
(Refer to the topic “Vent Valve of the Linear Ion Trap” on page 1-26.)
Vacuum System Heating After the system has been open to the atmosphere (e.g. for maintenance
during a System Bakeout work), the vacuum deteriorates due to contaminations of the inner parts
of the vacuum system caused by moisture or a power outage. These
contaminations must be removed by heating the vacuum system: a
system bakeout. Refer to the topic “Baking Out the System” on
page 3-4.

Gas Supply
Gas Supply Figure 1-19 shows a schematical view of the gas supply in the
instrument. The LTQ Orbitrap Discovery uses at least two gases for
operation:
• Nitrogen,
• Helium, and
• Argon (optional as HCD collision gas)1.

1
HCD collision gas1
Collision gas valve1
HCD collision cell1
Figure 1-19. Schematical view of the gas supply*

* For parts lists of the gas supply, refer to Table 4-10 on page 4-5.
The linear trap requires high-purity (99%) nitrogen for the API sheath
gas and auxiliary/sweep gas. The Orbitrap uses nitrogen as collision gas
(bath gas) for the curved linear trap. The linear trap requires ultra-high
1HCD

Gas Supply
purity (99.999%) helium for the collision gas.

Nitrogen is also used as collision gas for the optional HCD octapole. If
argon is used as HCD collision gas, it should be of high purity
(99.99%).
The laboratory gas supply is connected to the inlets at the right side of
the instrument. See Figure 1-9 on page 1-11. Within the instrument,
the helium gas is led from the helium port through a stainless steel
capillary to the right rear side of the linear trap. Nitrogen gas and
HCD collision gas are both led via Teflon tubing to the right side of the
LTQ Orbitrap Discovery.
Part of the nitrogen gas flow is directed through Teflon tubing via a
pressure regulator to the vent valve of the linear trap. (See below for
further information.) Another part of the nitrogen flow is directed
through Teflon tubing to the vacuum chamber of the Orbitrap.
Nitrogen gas pressure to the C-Trap is kept constant by using an
“open-split” interface (gas flow divider, see Figure 1-21). It contains a
capillary line from the nitrogen line of the instrument to atmosphere
(flow rate: ~20 mL/min), with another capillary leading from the point
of atmospheric pressure into the C-Trap (flow rate: ~0.2 mL/min). For
the nitrogen gas to the C-Trap, black PEEKSil™ tubing is used
(75 μm ID silica capillary in 1/16 in PEEK tubing).
Orbitrap
CLT RF Main board housing
Temperature controller board
Figure 1-20. Valve for HCD collision gas

Gas Supply
The HCD collision gas is also led to a gas flow divider. Part of the gas is
led through a capillary line to the atmosphere (flow rate: ~20 mL/min).
The other part of the gas (flow rate: ~0.5 mL/min) enters the IN port of
a three way valve. The gas leaves the valve through the OUT port and is
led to the collision octapole next to the curved linear trap.1 For the
HCD collision gas, red PEEKSil™ tubing is used (100 μm ID silica
capillary in 1/16 in PEEK tubing).
The valve is located at the left instrument side next to the temperature
controller board. See Figure 1-20 on page 1-25. It is switched by the
software via the power distribution board. (See page 1-38.)
Vent Valve of the Linear If the system and pumps are switched off, the system is vented. The vent
Ion Trap valve is controlled by the linear ion trap. The LTQ XL Hardware Manual
contains further information about the vent valve.
The instrument is vented with nitrogen from the same tubing that
supplies the LTQ XL sheath gas. See Figure 1-19 above. The vent valve
of the LTQ XL is attached to a pressure regulator that is set to a venting
pressure of 3–4 psi. The pressure regulator is located at the left side of
the LTQ Orbitrap Discovery. See Figure 1-21.
Gas flow divider
Nitrogen pressure regulator
Figure 1-21. Nitrogen pressure regulator and gas flow divider
1
The third port of the valve is closed.

Cooling Water Circuit
Cooling Water Circuit Figure 1-22 on page 1-27 shows a schematical view of the cooling water
circuit in the LTQ Orbitrap Discovery. Cooling water at a temperature
of 20 °C enters and leaves the instrument at the bottom of the right side.
See Figure 1-9 on page 1-11. First, the fresh water passes through the
turbopumps in the order TMP 3 → TMP 1 → TMP 2. Then it passes
through the heating element (Peltier element) that keeps constant
(±0.5 °C) the preset temperature of the analyzer. Before it leaves the
instrument, the water passes through the other Peltier element at the
back of the central electrode power supply board.
Figure 1-22. Schematical view of cooling water circuit*

* For a parts list of the cooling water circuit, refer to Table 4-12 on page 4-6.
A flow control sensor is connected to the power distribution board and

allows displaying the current flow rate of the cooling water in the
software.

Cooling Water Circuit
Recirculating Chiller A recirculating chiller (NESLAB Merlin M-33 or NESLAB

ThermoFlex 900) is delivered with the instrument, making the
LTQ Orbitrap Discovery independent from any cooling water supply. A
wall receptacle provides the electric power for the chiller. Two water
hoses (black), internal diameter 9 mm, wall thickness 3 mm, length
approx. 3 m (~10 ft) are delivered with the instrument.
For instruction about performing maintenance for the chiller, see topic
“Maintenance of the Recirculating Chiller” on page 3-7. See also the
manufacturer’s manual for the chiller.
Properties of Cooling The water temperature is not critical, but should be in the range of 20 to
Water 25 °C (68 to 77 °F). Lower temperatures could lead to a condensation of
atmospheric water vapor. It is recommended to use distilled water rather
than de-ionized water due to lower concentration of bacteria and
residual organic matter.
The water should be free of suspended matter to avoid clogging of the

cooling circuit. In special cases, an in-line filter is recommended to
guarantee consistent water quality.
The cooling water should meet the following requirements:
Hardness: <0.05 ppm

Resistivity: 1–3 MΩ/cm
Total dissolved solids: <10 ppm
pH: 7–8
Warning Danger of Burns!

If the water circuit fails, all parts of the water distribution unit may be
considerably heated up. Do not touch the parts!
Before disconnecting the cooling water hoses, make sure the cooling
water has cooled down! ▲

Printed Circuit Boards
Printed Circuit Boards The LTQ Orbitrap Discovery is controlled by a PC running the
Xcalibur software suite. The software controls all aspects of the
instrument. The main software elements are the communication with
the linear ion trap, the control of ion detection, and the control of the
Orbitrap mass analyzer.
The following pages contain a short overview of the various electronic

boards of the LTQ Orbitrap Discovery. For each board, its respective
location and function are given. If applicable, the diagnostic LEDs on
the board are described.
The electronics of the LTQ Orbitrap Discovery contains complicated

and numerous circuits. Therefore, only qualified and skilled electronics
engineers should perform servicing.
A Thermo Fisher Scientific Service Engineer should be called if servicing

is required. It is further recommended to use Thermo Fisher Scientific
spare parts only. When replacing fuses, only use the correct type. Before
calling a Service Engineer, please try to localize the defect via errors
indicated in the software or diagnostics. A precise description of the
defect will ease the repair and reduce the costs.
Warning Parts of the printed circuit boards are at high voltage.

Opening the electronics cabinet is only allowed for maintenance
purposes by qualified personal. ▲
Note Many of the electronic components can be tested by the

LTQ Orbitrap Discovery diagnostics, which is accessible from the Tune
Plus window. ▲

Linear Ion Trap The linear ion trap is connected to the LTQ Orbitrap Discovery main
Electronics power switch. The linear ion trap has a sheet metal back cover.
Figure 1-23 shows the electronic connections at the rear side of the
linear trap.
Cold Ion Gauge
Figure 1-23. Electronic connections to linear trap (covers removed)
The linear ion trap electronics has two connections with the
LTQ Orbitrap Discovery electronics:
• Data communication with the internal computer of the

LTQ Orbitrap Discovery. Refer to the topic “Electronic Boards at
the Right Side of the Instrument” on page 1-31.
• Signal communication (SPI bus) with supply information for the

instrument control board. Refer to the topic “Instrument Control
Board” on page 1-36.
For further information about the linear ion trap electronics, refer to the
LTQ XL Hardware Manual.

Electronic Boards at the Figure 1-24 shows the parts of the instrument when the right side panel
Right Side of the is opened. A transparent cover protects the lower part.
Instrument
Preamplifier
Computer
housing
Instrument Control
board housing
Power Supply 1 Power

board Distribution
board
Ground wire for Ground

side panel wire for
side
panel
Figure 1-24. Electronic boards on the right side of the instrument
The side panel is connected to the instrument frame by two

green/yellow ground wires. See bottom of Figure 1-24. The connectors
on the panel are labeled with green-yellow PE (for Protective Earth)
signs. See photo left. Do not forget to reconnect them before closing the
panel!

Preamplifier Figure 1-25 shows the preamplifier (P/N 207 8900)1. The preamplifier
is located in a housing next to the Cold Ion Gauge.
Cooling water supply

for Peltier element
Cold Ion Gauge
Figure 1-25. Preamplifier board
This board is a broadband preamplifier with differential

high-impedance inputs. It serves as a detection amplifier and impedance
converter for the image current created by the oscillating ions. The
output current is transferred to the data acquisition board. It has an
amplification factor of about 60 dB and covers the frequency range from
15 kHz to 10 MHz.
The diagnostic LEDs on the preamplifier are listed in Table 1-3 on

page 1-33. The positions of the diagnostic LEDs on the board are
indicated by white rectangles in Figure 1-25.
1
Part number of complete unit.

Table 1-3. Diagnostic LEDs on the Preamplifier board

No. Name Color Description Normal Operating
Condition
LD1 Overload Yello RF output is overloaded Off
w
LD2 +5 V Green +5 V input voltage present On
LD3 +15 V Green +15 V input voltage present On
LD4 -5 V Green -5 V input voltage present On
LD5 Input off Yello RF inputs are shortened On, off during
w (protection) Detect
Internal Computer Figure 1-26 shows the components of the data acquisition unit
(P/N 206 4132). The unit is mounted in a housing located at the right
side of the instrument.
Power Supply 2 board
Location of
Data Acquisition Analog board
Data Acquisition
Digital PCI board
Computer housing
Instrument Control board
Figure 1-26. Data Acquisition unit (covers removed)
The internal computer (P/N 207 6470) contains a computer mainboard

with an ATX power supply. The data acquisition digital PCI board is
directly plugged into the mainboard. The data acquisition analog board
is mounted on top of the computer mainboard.

Data Acquisition Figure 1-27 shows the data acquisition digital PCI board
Digital PCI Board (P/N 206 0501). It is an add-on board to the internal computer (See
Figure 1-26 on page 1-33.).
Figure 1-27. Data Acquisition Digital PCI board
This board is used to convert detected ion signals to digital form and to
interface to the computer mainboard. The board has two 16 bit parallel
connections to the DAC and the ADC on the data acquisition analog
board, which is used for controlling and reading-back signals. A
high-speed link port channel is also on the board that is used to
communicate with the electronics in the linear ion trap.
While precision timing is derived from the data acquisition analog

board, events with lower requirements use the timer in the internal
computer. This timer is used to check at regular intervals whether the
foreground process works as expected.
Communication takes place not only between the ion trap and the
internal computer of the LTQ Orbitrap Discovery system, but also
between the ion trap and the data system computer. For further
information about the data system, refer to the LTQ XL Hardware
Manual.
The diagnostic LEDs listed in Table 1-4 on page 1-35 show the status of
the board. The position of the LEDs on the board is indicated by a
white rectangle in Figure 1-27.

Table 1-4. Diagnostic LEDs of the Data Acquisition Digital PCI board
Name Color Description Normal Operating Condition
+5 V Green +5 V voltage present On
+3.3 V Green +3.3 V voltage present On
Data Acquisition Analog Board Figure 1-28 shows the data acquisition analog board (P/N 206 4150).
Figure 1-28. Data Acquisition Analog board
This board is an add-on board to the mainboard of the internal

computer. See Figure 1-26 on page 1-33. It is used to convert analog to
digital signals for Orbitrap experiments, especially for detecting the ions.
The board contains an ADC for the detection of the transient signal,
with a frequency range from 10 kHz to 10 MHz. Three anti-aliasing
filters for the low, middle and high mass range are automatically selected
by the software.
The data acquisition board provides precision timing to control the
acquisition. Events with lower timing requirements on accuracy are
controlled by the linear ion trap.
The diagnostic LEDs listed in Table 1-5 on page 1-36 show the status of
the voltages applied to the board. The position of the LEDs on the
board is indicated by a white rectangle in Figure 1-28.

Table 1-5. Diagnostic LEDs of the Data Acquisition Analog board

+5 V Green +5 V voltage present On
-5 V Green -5 V voltage present On
Power Supply 2 Board The power supply 2 board (P/N 206 1440) provides the supply voltages
for the data acquisition analog board. It is mounted to the back inside
the housing of the internal computer. See Figure 1-26 on page 1-33.
The diagnostic LEDs listed in Table 1-6 show the status of the voltages
applied to the board.
Table 1-6. Diagnostic LEDs of the Power Supply 2 board

-5.1 V Green -5.1 V voltage present On
Instrument Control Board Figure 1-29 shows the instrument control board (P/N 205 4221). The
instrument control board is located in a housing next to the internal
computer. It is connected to the LTQ Orbitrap Discovery main power.
The instrument control board is used to interface the LTQ XL control

electronics to the Orbitrap control electronics. Three signal lines are
passed from the LTQ XL: a digital, parallel (DAC) bus, a serial SPI bus,
and a Link Port Signal line. The instrument control board contains a
micro controller, digital and analog converters, and serial port
connectors.
On the instrument control board, analog signals from vacuum gauges

are converted to digital signals and passed to the data system as well as to
the power distribution board. (See page 1-38.) Turbopumps (Refer to
the topic “Vacuum System” on page 1-19.) are attached to a serial port
connector and this is connected via the signal lines to the linear ion trap.

Diagnostic LEDs Status LEDs
Figure 1-29. Instrument Control board
The diagnostic LEDs listed in Table 1-7 show the status of applied
voltages to the board. The position of the diagnostic LEDs on the board
is indicated by a white rectangle in Figure 1-29.
Table 1-7. Diagnostic LEDs of the Instrument Control board

No. Name Color Description Normal
Operating Condition
LD1 2.5 V Green 2.55 V Input voltage present On
LD2 3.3 V Green 3.3 V Input voltage present On
LD3 5V Green 5 V Input voltage present On
LD4 -15 V Green -15 V Input voltage present On
LD5 +15 V Green +15 V Input voltage present On
Additionally, the board has four green LEDs that are directly connected
to the micro controller. They indicate the state of the micro controller
and possible error bits and can be used for software debugging. See
Table 1-8 on page 1-38. The position of the status LEDs on the board is
indicated by a white oval in Figure 1-29 on page 1-37.

Table 1-8. Software status LEDs of the Instrument Control board

No. Description Normal Operating Condition
6.1 Micro controller is working properly Permanent flashing of LED
6.2 CAN bus connection to power distribution On
board enabled
6.3 Connection to internal computer and LTQ XL On
SPI bus enabled
6.4 Orbitrap SPI bus enabled On
Flashing on error
Power Distribution Board Figure 1-30 on page 1-38 shows the power distribution board
(P/N 210 1320)1. It is located at the bottom of the right side of the
instrument.
Figure 1-30. Power Distribution board
1

The power distribution board controls the vacuum system and the
system power supplies, including the linear ion trap. Depending on the
quality of the vacuum and the status of the turbo molecular pumps, it
switches the vacuum gauges, the pumps, and the 230 V relays. It
controls external relays with 24 V dc connections. In case of a vacuum
failure, it initiates an automatic power down of the instrument. The
board also switches the valve that controls the flow of the HCD collision
gas.
The power distribution board indicates all system states and error
messages by status LEDs (see Table 1-9 on page 1-40) in the middle of
the left side of the board. A green LED indicates that the status is OK.
An orange LED indicates a status that differs from normal. The position
of the LEDs on the board is indicated by a white oval in Figure 1-30 on
page 1-38.
The system status LEDs on the front side of the instrument (See
Figure 1-4 on page 1-6.) are controlled by the power distribution board.
The information partially comes from external boards (for example, the
Communication LED is controlled by the instrument control board).
(Refer to topic “Instrument Control Board” on page 1-36.)
Diagnostic LEDs show the status of voltages applied from the board to
other devices. The positions of the diagnostic LEDs on the board are
indicated by white rectangles in Figure 1-30 on page 1-38.

Table 1-9. Status LEDs of the Power Distribution board

LED green LED orange Information given by orange LED
Vacuum High vacuum failure High vacuum pressure > 10-8 mbar
Comm. No communication with CAN bus problem or
instrument control board instrument control board not
working
System System is not ready FT Electronics switch off or
Vacuum Pumps switch off
Scan Instrument is not scanning
Electr. On Service mode FT Electronics switch off
Vac. Units Ok Vacuum measurement Vacuum gauge defective
failure
Pirani Orbitrap Ok No function, at present
Pirani LT Ok Pirani LTQ XL failure Control signal < 0.5 V
Ion Gauge ON Penning LTQ Orbitrap Forevacuum > 10-2 mbar
Discovery off
Ion Gauge OK Penning LTQ Orbitrap Control signal < 0.5 V
Discovery failure
LT Vacuum Work LTQ XL vacuum failure Vacuum forepump LTQ XL
>10-1 mbar
Vac. <10-3 Forevacuum failure Forevacuum > 10-3 mbar
Vac. <10-5 High vacuum failure High vacuum > 10-5 mbar
Pumps OK Pumps Off Pump down; leakage
Rough P. 1 ON Forepump #1 failure Forepump defective
Turbo P. 1 ON Turbopump #1 failure Turbopump defective/error*
Rotation 1 OK Turbopump #1 failure 80% rotation speed of turbopump
not reached
Turbo P. 2 ON Turbopump #2 failure Turbopump defective/error*
Rotation 2 OK Turbopump #2 failure 80% rotation speed of turbopump
not reached
Heater Off Heater enabled Heater enabled
LAN Conn. Ok LAN connection failure LAN interrupted (Option)
EI ON No function, at present
A System reset System reset has occured
B Micro controller idle
* An error of turbopump 3 is indicated by an LED directly located on the pump controller.

Depending on user actions, the power distribution is switched to various

working modes by the hardware. See Table 1-10.
Table 1-10. Working modes of the Power Distribution board

Action Consequences
a. Main switch off Complete system including linear ion trap and multiple
socket outlets (data system, for example) are without power
b. Vacuum Pumps Everything is switched off
switch off
c. FT Electronics All components are switched off with exception of the
switch off following ones:
• Heater control
• Multiple socket outlets
• Power distribution board
• Pumps
• Vacuum control
• LTQ XL (has a separate Service switch)
Table 1-11 shows the possible operating states of the power distribution.
Table 1-11. Operating states of the Power Distribution board

Action Consequences
1. Main switch on, Vacuum Pumps switch Everything is switched off
off
2. Vacuum Pumps switch on and System starts up: pumps and
FT Electronics switch on electronics switched on
3. Check linear ion trap and LTQ Orbitrap If not ok: switch off system and light
Discovery forevacuum pump: error LED*; power distribution remains
10-0 mbar after 30 s switched on
4. After the system has started, the Pirani Switch on Penning gauge
gauge returns a vacuum < 10-2 mbar
and both turbopumps reach 80%
rotation speed
5. Vacuum and 80% rotation speed of Switch off system (including linear ion
turbopumps not reached after preset trap) and light error LED*; power
time (< 8 min, otherwise the pumps distribution remains switched on
automatically switch off)
6. One or more vacuum gauges defective Light error LED only, otherwise ignore
(control signal < 0.5 V)

Table 1-11. Operating states of the Power Distribution board, continued

Action Consequences
7. After the operating status is reached, System is shut down with exception of
the pressure at one gauge exceeds the power distribution (light error LED).
security threshold for more than the
preset time period:
Rebooting of the system by switching
• Pirani gauge LTQ Orbitrap Discovery off/on of the main switch.
>10-1 mbar
• Penning gauge LTQ Orbitrap
Discovery >10-3 mbar
• Pirani gauge LT forepump >10-1 mbar
8. Rotation speed of a turbopump falls Shut down system (see 7.);
below 80% light LED* of corresponding pump
9. Service switch linear ion trap off Linear ion trap electronics switched off,
pumps keep on running;
LTQ Orbitrap Discovery without data
link, keeps on running
10. FT Electronics switch LTQ Orbitrap LTQ Orbitrap Discovery electronics
Discovery off switched off, pumps keep on running;
LTQ Orbitrap Discovery without data
link, keeps on running
11. Failure of linear ion trap or LTQ Orbitrap If the vacuum in one part deteriorates,
Discovery (e.g. fuse is opened) the complete system is shut down.
12. Mains failure System powers up after the electricity
is available again. All devices reach the
defined state. Linear ion trap and
internal computer must reboot.
* After the shutdown, the LED flashes that represents the reason for the shutdown.
Power Supply 1 Board Figure 1-31 on page 1-43 shows the power supply 1 board
(P/N 205 5810). This board is located next to the power distribution
board. It provides the power for the ion optic supply board (Refer to
topic “Ion Optic Supply Board” on page 1-45.) and the instrument
control board. (Refer to topic “Instrument Control Board” on
page 1-36.)

Figure 1-31. Power Supply 1 board
Warning Parts of the power supply 1 board are at high voltage. ▲
applied to the board. The position of the LEDs on the board is
indicated by the white rectangles in Figure 1-31.
Table 1-12. Diagnostic LEDs of the Power Supply 1 board

Name Color Description Normal Operating
Condition
+285 V Green +285 V Output voltage present On
-285 V Green -285 V Output voltage present On
Over Current +285 V Red LED lit dark red: Iout > 80 mA Off
LED lit bright red: output is
short-circuited
Over Current -285 V Red LED lit dark red: Iout > 80 mA Off
LED lit bright red: output is
short-circuited
+18 V Green +18 V Output voltage present On
-18 V Green -18 V Output voltage present On
+8.5 V Green +8.5 V Output voltage present On

Electronic Boards on the Figure 1-32 shows the left side of the instrument with the panel opened.
Left Side of the Instrument This side of the instrument contains mostly boards that are part of the
Orbitrap control.
Ion Optic Supply board housing
Central Electrode
Pulser board
Temperature
Controller board
CLT RF Main board

RF Off & Feedback
board
Central Electrode
Power Supply board
High Voltage Power
Supply board
Figure 1-32. Electronic boards on the left side of the instrument
The main components on this side are described starting from the top.

Ion Optic Supply Board Figure 1-33 shows the ion optic supply board (P/N 209 9810)1. The
board is located in a housing on top of the left instrument side of the
instrument. This board supplies the voltages and the radio frequency for
the ion guides and interoctapole lenses of the LTQ Orbitrap Discovery.
It has an RF detector for the RF output control. The board also provides
the trap voltage, gate voltage, and reflector dc voltages as well as the
RF voltages to the octapole 1 of the Orbitrap. See topic “Orbitrap
Analyzer” on page 1-13 for further information. Furthermore, the board
provides the voltages for the HCD collision cell.2 See page 1-17.
Figure 1-33. Ion Optic Supply board
The diagnostic LEDs listed in Table 1-13 on page 1-46 show the status
of applied voltages to the board. The position of the LEDs on the board
is indicated by white rectangles in Figure 1-33.
Warning Parts of the board are at high voltage. ▲
1
2HCD

Table 1-13. Diagnostic LEDs of the Ion Optic Supply board

Condition
LD1 +275 V Green +275 V Input voltage On
present
LD2 -275 V Green -275 V Input voltage On
present
LD7 RF1_ON Blue RF1 generator switched on depending on application;
LED flashes during scanning
LD8 RF2_ON Blue RF2 generator switched on depending on application;
LED flashes during scanning
Central Electrode Pulser Board The central electrode pulser board (P/N 207 9640)1 is located in a
housing that is mounted to the flange of the UHV chamber.
Figure 1-34. Central Electrode Pulser board
1

The board switches the injection and measurement voltages for the
central electrode and the detection electrodes of the Orbitrap.
Resistor-capacitor circuits on the board convert the switching pulse into
a smooth transition between the voltages.
applied to the board as well as some operating states. The position of the
LEDs on the board is indicated by the white rectangles in Figure 1-34
on page 1-46.
Table 1-14. Diagnostic LEDs of the Central Electrode Pulser board

Condition
LD1 TRIG Green Trigger signal indicator Flashing when
scanning
LD2 PS Green 24V Power Supply is OK On
Temperature Controller Board The temperature controller board (P/N 207 8930) is located on the top
left side of the instrument, next to the CLT RF main board. See
Figure 1-32 on page 1-44. The temperature controller board keeps the
temperature of the analyzer chamber to a preset value. A Peltier element
that can be used for heating as well as for cooling is used as an actuator.
Activation is done via the serial SPI (Serial Peripheral Interface) bus.
Figure 1-35. Temperature Controller board

applied to the board as well as some operating states. The positions of
the LEDs on the board are indicated by the white rectangles in
Figure 1-35.
Table 1-15. Diagnostic LEDs of the Temperature Controller board

Condition
LD3 TEC >60C Yellow Temperature of cold side Peltier Off
element above 60 ºC
LD4 Unit >60C Yellow Temperature of UNIT heat sink Off
above 60 ºC
LD5 Reg Off Yellow Control switched off Off
LD6 No Term Yellow SPI bus termination board Off
missing
LD7 SDT enable Green Interface has been addressed Flashing on SPI bus
and sends/receives data data transfer
LD8 SEL Green Board has been addressed Flashing on SPI bus
data transfer
LD9 Heating Yellow Peltier element is heating Depending on
system state
LD10 Cooling Yellow Peltier element is cooling Depending on
system state
LD11 UR>0 Yellow Summation voltage controller Off when adjusted
>0 V
LD12 UR<0 Yellow Summation voltage controller Off when adjusted
<0 V
CLT RF Unit The CLT RF unit (P/N 207 9581) comprises the CLT RF main board
and the RF off & feedback board. The unit operates the curved linear
trap (C-Trap) with four phases RF voltage and three pulsed DC voltages
(PUSH, PULL, and OFFSET).
The CLT RF main board (P/N 207 9591) is located in a housing in the
center of the left side of the instrument. See Figure 1-32 on page 1-44.
This board provides an RF voltage (“Main RF”) for the curved linear
trap (C-Trap). It allows switching off the RF and simultaneous pulsing
of each C-Trap electrode. See topic “Orbitrap Analyzer” on page 1-13
for further information. The board communicates with the instrument
control board via an SPI bus.
The RF off & feedback board (P/N 208 2540) is an add-on board to the
CLT RF main board. It is located in the same housing. See Figure 1-36
on page 1-49.

RF off & feedback board
Figure 1-36. CLT RF unit (cover removed)
applied to the board as well as some operating states. The position of the
LEDs on the board is indicated by the white rectangles in Figure 1-36.
Table 1-16. Diagnostic LEDs of the CLT RF Main board

Condition
LD1 NO TERM Yellow SPI bus termination board Off
missing
LD2 SEND Yellow Interface has been addressed and Flashing on SPI-bus
sends/receives data data transfer
LD3 SEL Green Board has been addressed Flashing on SPI-bus
data transfer
LD4 RF ON Green RF voltage on On
LD5 NO LOCK Yellow PLL has been not locked 50% intensity
LD6 OVL Yellow RF Amplifier overload Off
LD7 OVHEAT Red Heatsink temperature > 73 °C Off

Central Electrode The central electrode power supply board (P/N 207 9611)1 is mounted
Power Supply Board in a housing on the bottom left side of the instrument. See Figure 1-37.
Figure 1-37. Central Electrode Power Supply board
The board supplies four dc voltages to the Orbitrap:
• Two central electrode (CE) voltages: CE HIGH and CE LOW
• Two deflector electrode (DE) voltages: DE HIGH and DE LOW.
For positive ions, the CE voltages are negative and the DE voltages are
positive. The maximum CE voltage is 3 kV and the maximum
DE voltage is 1 kV. The board communicates via the SPI bus.
In addition to a ventilator on the bottom right side, a water-cooled

Peltier element on the rear side of the board serves as means of heat
dissipation.
1

The diagnostic LEDs listed in Table 1-17 on page 1-51 show the status
of the voltages applied to the board as well as some operating states. The
position of the LEDs on the board is indicated by the red rectangles in
Figure 1-37.
Table 1-17. Diagnostic LEDs of the Central Electrode Power Supply board
Condition
LD1 OVL DE HI- Yellow Negative side of Deflector High Off when HV is
Supply has been overloaded switched on
LD2 OVL DE HI+ Yellow Positive side of Deflector High Off when HV is
Supply has been overloaded switched on
LD3 No Term Red SPI bus termination board Off
missing
LD4 Send Yellow Interface has been addressed Flashing on SPI-bus
LD5 Sel Green Board has been addressed Flashing on SPI-bus
data transfer
LD6 Polarity Blue Positive/negative ion mode Off (positive mode)
LD7 OVL CE LO+ Yellow Positive side of Central Off when HV is
Electrode Low Supply has been switched on
overloaded
LD8 OVL CE LO- Yellow Negative side of Central Off when HV is
Electrode Low Supply has been switched on
overloaded
LD9 OVL CE HI+ Yellow Positive side of Central Off when HV is
Electrode High Supply has been switched on
overloaded.
LD10 OVL CE HI- Yellow Negative side of Central Off when HV is
Electrode High Supply has been switched on
overloaded
LD11 OVL DE LO+ Yellow Positive side of Deflector Low Off when HV is
Supply has been overloaded. switched on
LD12 OVL DE LO- Yellow Negative side of Deflector Low Off when HV is
Supply has been overloaded. switched on
LD13 HV ON Green High voltage switched on On when HV is
switched on
High Voltage The high voltage power supply board (P/N 207 7991)1 is mounted in a
Power Supply Board housing on the bottom left side of the instrument. See Figure 1-32 on
page 1-44. This board provides five dc voltages for the ion optics of the
LTQ Orbitrap Discovery. Two voltages supply the lenses of the
instrument. Three voltages are applied to the RF CLT main board to be
1

used as focusing potentials for the curved linear trap. See topic
“Orbitrap Analyzer” on page 1-13 for further information. The board
communicates via the SPI bus.
Warning The high voltage power supply board creates voltages up to

3.5 kV! ▲
Figure 1-38. High Voltage Power Supply board (cover removed)
The diagnostic LEDs listed in Table 1-18 on page 1-53 show the
operating states of the board. The position of the LEDs on the board is
indicated by the white rectangles in Figure 1-38.

Table 1-18. Diagnostic LEDs of the High Voltage Power Supply board
Condition
LD1 NO TERM Red SPI bus termination board Off
missing
LD2 SEND Yellow Interface has been addressed Flashing on SPI bus
LD3 SEL Green Board has been addressed Flashing on SPI bus
data transfer
LD4 HV ON Green High voltage is switched on On
LD5 POLARITY Green Positive/negative ion mode Off (positive mode)
SPI Bus Termination Board Various boards communicate via the SPI bus, a serial RS485-based bus
system. The SPI bus termination board reduces unwanted signal
reflections. The boards indicate a missing termination (after
maintenance, for example) by LEDs.
The SPI bus termination board (P/N 208 1480) is located at the bottom
left side of the instrument, below the high voltage power supply board.
See Figure 1-39.
SPI bus termination board
Figure 1-39. High Voltage Power Supply board with SPI Bus Termination
board

Chapter 2 Basic System Operations
Many maintenance procedures for the LTQ Orbitrap Discovery system

require that the MS detector be shut down. In addition, the
LTQ Orbitrap Discovery system can be placed in Standby condition if
the system is not to be used for 12 h or more.
The following topics are discussed in this chapter:
• “Shutting Down the System in an Emergency” on page 2-2
• “Placing the System in Standby Condition” on page 2-4
• “Shutting Down the System” on page 2-5
• “Starting Up the System after a Shutdown” on page 2-7
• “Resetting the System” on page 2-10
• “Resetting the Tune and Calibration Parameters to their Default

Values” on page 2-11

Basic System Operations
Shutting Down the System in an Emergency
Shutting Down the If you need to turn off the MS detector in an emergency, place the main
System in an power switch (located on the power panel at the right side of the
LTQ Orbitrap Discovery) in the Off (O) position. This turns off all
Emergency power to the instrument, including the linear ion trap, multiple socket
outlets for the data system, and the vacuum pumps. The main power
switch must be turned 90° anti-clockwise to switch off the instrument.
See Figure 2-1.
On
Off
Figure 2-1. Main power switch in Off position
The instrument is automatically vented by the vent valve of the linear

ion trap. The vent valve vents the system 30 s after power is switched
off.
Although removing power abruptly will not harm any component

within the system, this is not the recommended shutdown procedure to
follow. Refer to topic “Shutting Down the System” on page 2-5 for the
recommended procedure.
Note To separately turn off the recirculating chiller or computer in an

emergency, use the On/Off switches on the chiller and computer,
respectively. ▲
Behavior of the System in A main power failure has the same consequence as switching off via the
Case of a Main Failure main power switch. If the power is available again, the system is started
up automatically i.e. the pumps are switched on and the vacuum is
created. If the system has been vented during the mains failure, it is
necessary to bakeout the system to obtain the operating vacuum. Refer
to the topic “Baking Out the System” on page 3-4.
It is not possible to check whether the system was vented. The log file of
the data system indicates a reboot of the system. In case of frequent but
short power failures we recommend installing an uninterruptible power

Shutting Down the System in an Emergency
supply (UPS). If main power failures occur frequently while the system
is not attended (e.g. in the night), we recommend installing a power fail
detector.
Note The intentional venting of the system is performed with the vent
valve of the linear ion trap. ▲

Placing the System in Standby Condition
Placing the System in The LTQ Orbitrap Discovery system should not be shut down
Standby Condition completely if you are not going to use it for a short period of time, such
as overnight or over the weekend. When you are not going to operate
the system for 12 hours or more, you can leave the system in Standby
condition.
Use the following procedure to place the LTQ Orbitrap Discovery

system in the Standby condition:
1. Wait until data acquisition, if any, is complete.
2. Turn off the flow of sample solution from the LC (or other sample
introduction device).
Note For instructions on how to operate the LC from the front panel,
refer to the manual that came with the LC. ▲
3. From the Tune Plus window, choose Control > Standby (or click on
the On/Standby button to toggle it to Standby) to put the
instrument in Standby condition. The consequences of this user
action are described in the LTQ XL Hardware Manual. The System
LED on the front panel of the LTQ XL is illuminated yellow when
the system is in Standby condition.
4. Leave the LC power On.
5. Leave the autosampler power On.
6. Leave the data system power On.
7. Leave the LTQ Orbitrap Discovery main power switch in the On

position.

Shutting Down the System
Shutting Down the The LTQ Orbitrap Discovery system does not need to be shut down
System completely if you are not going to use it for a short period of time, such
as overnight or over a weekend. Refer to the topic “Placing the System in
Standby Condition” on page 2-4. This section describes how to shut
down the system for a maintenance or service procedure.
Use the following procedure to shut down the LTQ Orbitrap Discovery
system:
1. Wait until data acquisition, if any, is complete.
2. Turn off the flow of sample solution from the LC (or other sample
introduction device).
Note For instructions on how to operate the LC from the front panel,
refer to the manual that came with the LC. ▲
3. From the Tune Plus window, choose Control > Off to put the
instrument in Off condition. When you choose Control > Off, all
high voltages are shut off, as are the sheath and auxiliary gas.
4. Put the FT Electronics switch to the OFF position. See Figure 1-7
on page 1-9.
5. Put the Vacuum Pumps switch to the OFF position. See Figure 1-7.
When you place the switch in the OFF position, the following
occurs:
a. All power to the instrument, including the turbomolecular

pumps and the rotary-vane pumps, is turned off.
b. After 30 s, power to the vent valve solenoid of the ion trap is
shut off. The vent valve opens and the vacuum manifold is
vented with nitrogen to atmospheric pressure through a filter.
You can hear a hissing sound as the gas passes through the filter.
6. Leave the main power switch of the LTQ Orbitrap Discovery in the
On position.
7. During service or maintenance operations that require opening the

vacuum system of the LTQ XL or LTQ Orbitrap Discovery, always
put the main switch (main circuit breaker) to the OFF position. You

Shutting Down the System
can secure the main switch with a padlock or tie-wrap to prevent

unintended re-powering.
Warning Allow heated components to cool before you service them

(the ion transfer tube at about 300 °C, for example). ▲
Note If you are planning to perform routine or preventive system

maintenance on the LTQ Orbitrap Discovery only, you do not need to
turn off the recirculating chiller, LC, autosampler, or data system. In this
case, the shutdown procedure is completed. However, if you do not plan
to operate your system for an extended period of time, you might want
to turn off the recirculating chiller, LC, autosampler, and data system. ▲

Starting Up the System after a Shutdown
Starting Up the To start up the LTQ Orbitrap Discovery after it has been shut down,
System after a you need to do the following:
Shutdown 1. Start up the instrument
2. Set up conditions for operation
Starting Up the Instrument Note The recirculating chiller and data system must be running before
you start up the instrument. The instrument will not operate until
software is received from the data system. ▲
Use the following procedure to start up the LTQ Orbitrap Discovery:
1. Start up the (optional) LC and autosampler as is described in the

manual that came with the LC and autosampler.
2. Start up the data system and the chiller.
3. Turn on the flows of helium and nitrogen – and argon if present – at

the tanks, if they are off.
4. Make sure that the main power switch of the LTQ XL is in the On
position and the electronics service switch of the LTQ XL is in the
Operating position.
5. Place the main power switch at the right side of the LTQ Orbitrap
Discovery in the On position.
6. Put the Vacuum Pumps switch to the ON position. See Figure 1-7
on page 1-9. The rotary-vane pumps and the turbomolecular pumps
are started.
Note Pumping the system after a complete shut down takes hours and
requires overnight baking of the system. ▲

7. Put the FT Electronics switch to the ON position. See Figure 1-7.

When you place the FT Electronics switch to the ON position, the
following occurs:
a. Power is provided to all electronic boards. (The electron

multiplier, conversion dynode, 8 kV power to the API source,
main RF voltage, and octapole RF voltage remain off.)
b. The internal computer reboots. After several seconds, the
Communication LED on the front panel is illuminated yellow
to indicate that the data system has started to establish a
communication link.
c. After several more seconds, the Communication LED is
illuminated green to indicate that the data system has
established a communication link. Software for the operation of
the instrument is then transferred from the data system to the
instrument.
d. After 3 min, the System LED of the ion trap is illuminated
yellow to indicate that the software transfer from the data system
is complete and that the instrument is in Standby condition.
Note The Vacuum LED on the front panel of the LTQ XL is

illuminated green only if the pressure in the vacuum manifold is below
the maximum allowable pressure (5×10-4 Torr in the analyzer region,
and 2 Torr in the capillary-skimmer region), and the safety interlock
switch on the API source is depressed (that is, the API flange is secured
to the spray shield). ▲
8. Press the Reset button on the LTQ XL to establish the

communication link between LTQ XL and internal computer.
If you have an LC or autosampler, start it as is described in the manual

that came with the LC or autosampler. If you do not have either, go to
the topic “Setting Up Conditions for Operation“ below.
Setting Up Conditions for Set up your LTQ Orbitrap Discovery for operation, as follows:
Operation
1. Before you begin data acquisition with your LTQ Orbitrap
Discovery system, you need to allow the system to pump down for
at least 8 hours. Operation of the system with excessive air and water
in the vacuum manifold can cause reduced sensitivity, tuning
problems, and a reduced lifetime of the electron multiplier.
Note The vacuum in the analyzer system can be improved by an

overnight baking of the system. Refer to the topic “Baking Out the
System” on page 3-4. ▲

2. Ensure that the gas pressures are within the operational limits:
• Helium: 275 ± 70 kPa (2.75 ± 0.7 bar, 40 ±10 psi),
• Nitrogen: 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi).
• Argon if present: 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi)
Note Air in the helium line must be purged or given sufficient time to
be purged for normal performance. ▲
3. Select the Display Status View button in the Tune Plus window.
Check to see whether the pressure measured by the ion gauge is
≤5 × 10-9 mbar, and the pressure measured by the Pirani gauge is
around 1 mbar. Compare the values of the other parameters in the
status panel with values that you recorded previously.
4. Continue to set up for ESI or APCI operation as described in

LTQ Orbitrap Discovery Getting Started manual.

Resetting the System
Resetting the System If communication between the LTQ Orbitrap Discovery and data
system computer is lost, it may be necessary to reset the system using the
Reset button of the LTQ XL.
The procedure given here assumes that the LTQ Orbitrap Discovery
and data system computer are both powered on and are operational. If
the instrument, data system computer, or both are off, refer to topic
“Starting Up the System after a Shutdown” on page 2-7.
To reset the LTQ Orbitrap Discovery, press the Reset button of the
linear ion trap. See the LTQ XL Hardware Manual for the location of the
Reset button. When you press the Reset button, the following occurs:
1. An interrupt on the mainboard of the internal computer causes the

internal computer to reboot. All LEDs on the front panel are off
except the Power LED.
2. After several seconds, the Communication LED is illuminated

yellow to indicate that the data system and the instrument are
starting to establish a communication link.
3. After several more seconds, the Communication LED is illuminated

green to indicate that the data system and the instrument have
established a communication link. Software for the operation of the
instrument is then transferred from the data system to the
instrument.
4. After 3 min, the software transfer is complete. The System LED is

illuminated either green to indicate that the instrument is functional
and the high voltages are on, or yellow to indicate that the
instrument is functional and it is in Standby condition.

Resetting the Tune and Calibration Parameters to their Default Values
Resetting the Tune You can reset the LTQ Orbitrap Discovery system tune and calibration
and Calibration parameters to their default values at any time. This feature may be useful
if you have manually set some parameters that have resulted in less than
Parameters to their optimum performance. To reset the LTQ Orbitrap Discovery tune and
Default Values calibration parameters to their default values, proceed as follows:
In the Tune Plus window,
• Choose File > Restore Factory Calibration to restore the default

calibration parameters, or
• Choose File > Restore Factory Tune Method to restore the default
tune parameters.
Note Make sure that any problems you might be experiencing are not
due to improper API source settings (spray voltage, sheath and auxiliary
gas flow, ion transfer capillary temperature, etc.) before resetting the
system parameters to their default values. ▲

Chapter 3 User Maintenance
This chapter describes routine maintenance procedures that must be

performed to ensure optimum performance of the LTQ Orbitrap
Discovery.
It is the user’s responsibility to maintain the system properly by

performing the system maintenance procedures on a regular basis.
The following topics are described in this chapter:
• ”General Remarks” on page 3-2
• ”Baking Out the System” on page 3-4
• ”Maintaining the Vacuum System” on page 3-6
• ”Maintenance of the Recirculating Chiller” on page 3-7
Note For instructions on maintaining the LTQ XL linear trap, refer to

the LTQ XL Hardware Manual. For instructions on maintaining LCs or
autosamplers, refer to the manual that comes with the LC or
autosampler. ▲

User Maintenance
General Remarks
General Remarks Preventive maintenance must commence with installation, and must
continue during the warranty period to maintain the warranty. Thermo
Fisher Scientific offers maintenance and service contracts. Contact your
local Thermo Fisher Scientific office for more information. Routine and
infrequent maintenance procedures are listed in Table 3-1.
Table 3-1. User maintenance procedures

MS Detector Component Procedure Frequency Procedure Location
Analyzer System bakeout If necessary (e.g. after performing page 3-4
maintenance work on the vacuum system)
Rotary-vane pumps Add oil If oil level is low Manufacturer’s documentation
Change oil Every 3 months or if oil is cloudy or Manufacturer’s documentation
discolored
Turbomolecular pumps Exchange lubricant reservoir Yearly Manufacturer’s documentation
page 3-6
Recirculating chiller Check cooling fluid level See manufacturer’s documentation Manufacturer’s documentation
Check cooling fluid filter page 3-7
Check air inlet filter
To successfully carry out the procedures listed in this chapter, observe

the following:
• Proceed methodically
• Always wear clean, lint-free gloves when handling the components

of the API source, ion optics, mass analyzer, and ion detection
system.
• Always place the components on a clean, lint-free surface.
• Always cover the opening in the top of the vacuum manifold with a
large, lint-free tissue whenever you remove the top cover plate of the
vacuum manifold.
• Never overtighten a screw or use excessive force.
• Dirty tools can contaminate your system. Keep the tools clean and
use them exclusively for maintenance and service work at the
• Never insert a test probe (for example, an oscilloscope probe) into

the sockets of female cable connectors on PCBs.
Returning Parts In order to protect our employees, we ask you for some special
precautions when returning parts for exchange or repair to the factory.
Your signature on the Repair Covering letter confirms that the returned

User Maintenance
General Remarks
parts have been de-contaminated and are free of hazardous materials.

Refer to topic ”Safety Advice for Possible Contamination” on page vii
for further information.
Cleaning the Surface of Clean the outside of the instrument with a dry cloth. For removing
the Instrument stains or fingerprints on the surface of the instrument (panels, for
example), slightly dampen the cloth (preferably made of microfiber)
with distilled water.
Caution Prevent any liquids from entering the inside of the

instrument. ▲

User Maintenance
Baking Out the System
Baking Out the This section provides information and help concerning the system
System bakeout of the LTQ Orbitrap Discovery. The bakeout procedure
removes unwanted gases or molecules (collected or remaining) from the
high vacuum region of the instrument. Ions can collide with those gases
or molecules resulting in lower overall sensitivity. Therefore, we
recommend to bake out the instrument if the high vacuum decreases
noticeable during routine operation.
Bakeout is mandatory after maintenance or service work is performed in

the analyzer region where the system is vented.
Note Pumping down the system after venting takes at least 8 hours, and
usually requires overnight baking of the system. ▲
In case the system has been vented during a power failure, it is necessary
to bake out the system to obtain the operating vacuum. Refer to the
topic ”Behavior of the System in Case of a Main Failure” on page 2-2.
Bakeout Procedure Use the following procedure to perform a system bakeout:
1. Place the system in Standby condition as described in the section

”Placing the System in Standby Condition” on page 2-4.
2. Put the FT Electronics switch at the power control panel into the
ON position.
3. Set the bakeout time by entering the desired time (hh:mm) with the
up/down keys of the bakeout timer. See Figure 3-1.
Elapsed time display

Set time display
Up keys
Down keys
Bakeout Bakeout start button

stop button
Figure 3-1. Bakeout timer

User Maintenance
Baking Out the System
4. Start the bakeout procedure by pressing the green start button on

the right. The LTQ Orbitrap Discovery indicates a running bakeout
procedure by the flashing Vacuum and System LEDs on the front
side of the instrument. See Figure 1-4 on page 1-6.
You can stop a running bakeout procedure by pressing the orange

reset/stop button on the left side. Also press this button after you
have changed the preset bakeout time.
5. The bakeout procedure is terminated because of two reasons:
• The preset duration has expired, or
• The vacuum has risen above a preset value.
The termination of the baking process is indicated by the status LEDs

(System + Vacuum) on the front side that have stopped flashing.

User Maintenance
Maintaining the Vacuum System
Maintaining the The turbopumps1 need maintenance work that is briefly outlined below.
Vacuum System
Note The manuals of the pump manufacturers give detailed advice
regarding safety, operation, maintenance, and installation. Please note
the warnings and precautions contained in these manuals! ▲
Exchanging the Lubricant For all manipulations at the pumps, note the advice, warnings, and
Reservoir of the cautions contained in the pump manuals!
Turbopumps For the turbopumps, we recommend exchanging the lubricant reservoir
in a one-year cycle. At each exchange procedure, the complete lubricant
reservoir must be exchanged!
Note The storage stability of the lubrication oil is limited. The

specification of durability is given by the pump manufacturer. (Refer to
the manuals for the turbopumps.) ▲
Replacements for the turbopump lubricant reservoirs (TMH 071 P:

P/N 017 2350; TMU 262: P/N 105 0160) are available from Thermo
Fisher Scientific.
The disposal of used oil is subject to the relevant regulations.
1For
maintenance of the forepumps, refer to the LTQ XL Hardware Manual or the pump
manufacturer’s manual.

User Maintenance
Maintenance of the Recirculating Chiller
Maintenance of the For the NESLAB ThermoFlex 900 recirculating chiller, the following
Recirculating Chiller checks should be carried out on a regular basis.
Note For further information and maintenance instructions, refer to the

manufacturer’s manual supplied with the instrument. ▲
Reservoir Periodically inspect the fluid inside the reservoir. If cleaning is necessary,
flush the reservoir with a cleaning fluid compatible with the circulating
system and the cooling fluid.
The cooling fluid should be replaced periodically. Replacement

frequency depends on the operating environment and amount of usage.
Warning Before changing the operating fluid make sure it is at safe

handling temperature. ▲
Fluid Bag Filter The ThermoFlex 900 recirculating chiller installed in the cooling circuit
of the instrument is equipped with a fluid bag filter, which needs to be
replaced on a regular basis. Replacement bags are available from Thermo
Fisher Scientific.
Condenser Filter To prevent a loss of cooling capacity and a premature failure of the
cooling system, clean the condenser filter regularly. If necessary, replace
it.

Chapter 4 Replaceable Parts
This chapter contains part numbers for replaceable and consumable

parts for the MS detector, data system, and kits. To ensure proper results
in servicing the LTQ Orbitrap Discovery system, order only the parts
listed or their equivalent.
For information on how to order parts, refer to the topic “Customer

Support” in the LTQ Orbitrap Discovery / LTQ Orbitrap Discovery
Preinstallation Requirements Guide.
Table 4-1. Parts for the LTQ Orbitrap Discovery

Designation Part No.
LTQ Orbitrap Discovery; 50 Hz* 072 3720
LTQ Orbitrap Discovery; 60 Hz 072 3730
Edwards Pumps kit, for LTQ-Hybrid 121 6450
Pumps kit 2, Orbitrap (ILMVAC) 121 4310
ESI probe, for Ion Max source OPTON-20011
Nanospray II Ion Source† OPTON-20050
†
Static Nanospray OPTON-20051
Dynamic Nanospray† OPTON-97017
†
APCI probe OPTON-20012
APPI probe† OPTON-20026
†*
Upgrade kit Orbitrap HCD option 122 4800
* Module, for parts list see below.
† Optional equipment.
Table 4-2. Parts LTQ Orbitrap Discovery; 50 Hz (P/N 072 3720)

Designation Part No.
Basic system Orbitrap-2* 122 4790
LTQ XL Linear trap MS system, with computer LTQ02-10001
Low flow metal needle for API 2 probes OPTON-30004
Dell Laserprinter 1700 106 3385
Software 2.4 Tune LTQ Orbitrap Discovery 122 7040
†
Recirculating chiller Neslab ThermoFlex 900 PD-1 230V/50 Hz 101161010000004
† Some systems are delivered with NESLAB Merlin M33 recirculating chiller.

Replaceable Parts
Parts Basic System
Parts Basic System This section contains parts lists for the mechanical components of the
Table 4-3. Parts basic system Orbitrap-2 (P/N 122 4790)

Pos. No. Qty. Designation Part No.
0010 1 Orbitrap-2 chamber; complete* 122 4780
0020 1 Orbitrap-D30; complete 116 5000
0030 1 CLT and lens system; complete 122 1200
*
0040 1 Pumping system Orbitrap 118 4490
0050 1 Water supply Orbitrap* 117 8460
0060 1 Orbitrap panels 117 2910
0070 1 Mounting devices Orbitrap-2 117 7891
*
0080 1 Gas supply Orbitrap-2 117 7881
0090 1 Orbitrap Installation Kit* 118 8120
*
0100 1 Electronic parts Orbitrap-2 800 1110
Table 4-4. Parts Upgrade kit Orbitrap HCD option (P/N 122 4800)*
0010 1 Collision cell, with mount 122 1320
0020 1 Flange, for options; complete 122 1250
0030 1 Cable kit, Upgrade LTQ Orbitrap Discovery 122 5100
0040 1 Upgrade kit gas supply LTQ Orbitrap XL† 122 4820
0050 1 Cable, power distribution/valve 210 0310
* HCD
is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not
equipped with this option.
†
Module, for parts list see below.
Table 4-5. Parts Orbitrap Installation Kit (P/N 118 8120)

0010 1 Orbitrap Installation Kit Ilmvac 1196990
0020 4 One ear clamp; Ø 17.5 114 4910
0030 6 Ferrule, 1/16”, for GVF/16 067 4800
0040 3.0 m* Tube, 1/8" × 2.1- 1.4301 026 1000
0050 3.0 m* Hose; 4 x 1, Teflon 069 0280
0060 6 Clamping piece 8/16 037 0130
0070 1 Contact wrist strap, with coiled cord 119 3050
0080 1 Ferrule, stainless steel; R. 1/8" 052 0950
0090 1 Ferrule, stainless steel; V. 1/8" 052 2520

Replaceable Parts
Parts Basic System
Table 4-5. Parts Orbitrap Installation Kit (P/N 118 8120), continued
0100 1 Cap nut, stainless steel; 1/8“ 052 0890
0110 1 Connector; C19 to C14 082-2528
0120 10 Miniature fuse; 5 x 20 mm, 8 A 201 1850
*
Specify desired length.
Parts Orbitrap Analyzer Table 4-6. Parts Orbitrap-2 chamber; complete (P/N 122 4780)
0010 1 UHV chamber; complete 116 6110
0020 1 Vacuum chamber, complete 116 6131
0030 1 Octapole Orbitrap, complete 116 6120
0040 4 Washer; 8.4×15×1.5, stainless steel 047 0860
0050 4 Screw; M8X25, silver plated 119 1210
0060 4 Pan head screw; M 2 x 8 DIN 84 A4 045 0720
0070 2 Screw cyl. M 4 x 12 DIN912 045 2800
Parts Pumping System Table 4-7. Parts pumping system Orbitrap (P/N 118 4490)*
Orbitrap Pos. No. Qty. Designation Part No.
0010 1 Turbomolecular pump TMU262; modified 118 4340
0020 2 Turbomolecular pump; TMH 071 P 114 1500
0040 1 Water cooling for TMH 262 114 9140
0050 5 Water cooling for TMH 071 P 079 4742
0080 1 UHV gauge IKR 270; short 118 1380
0130 1 Compact Pirani Gauge TPR280 115 6400
*
For a schematic overview of the vacuum system, refer to Figure 1-15 on page 1-19.
Two kits are available for the pumping system, comprising either
pumps, gauges, and cooling (pump kit Orbitrap: P/N 117 5000) or
hoses, clamps, and gaskets (pump system Orbitrap: P/N 117 5010):
Table 4-8. Parts pump kit Orbitrap (P/N 117 5000)

0010 1 Turbomolecular pump TMU262; modified 118 4340
0020 2 Turbomolecular pump; TMH 071 P 114 1500
0030 1 UHV gauge IKR 270; short 118 1380
0040 1 Compact Pirani Gauge TPR280 115 6400

Replaceable Parts
Parts Basic System
Table 4-8. Parts pump kit Orbitrap (P/N 117 5000), continued
0050 1 Water cooling for TMH 262 114 9140
0060 5 Water cooling for TMH 071 P 079 4742
0070 1 PVC hose, with steel helix; ID=45 mm, L=1.3 m 118 4330
0080 2 Hose nipple, DN 40, ISO-KF-45 115 9230
0090 1 Venting flange; DN 10, KF-G1/8" 118 4400
0100 1 Splinter shield for turbopumps, with DN 100 CF-F 119 8590
flange
0110 2 Centering ring, with integrated splinter shield; 119 8600
DN 63 ISO
Table 4-9. Parts pump system Orbitrap (P/N 117 5010)

0010 2 Gasket; NW 100 CF, copper 055 2440
0020 1 Hose, metal; KF16-KF25 - 250mm 115 4130
0030 1 Gasket; copper, NW 35 055 0480
0040 2 Metal tube, KF NW16×250 052 4260
0050 2 KF Tee piece; NW 16 KF, stainless steel 052 4230
0060 8 Centering ring with o-ring; DN 16, Viton 052 2140
0070 1 Centering ring with o-ring; DN 25, Viton 052 2150
0080 1 Centering ring; NW 16/10, aluminum-Viton 052 2200
0090 6 Clamping ring; NW 10/16, KF 052 1830
0100 1 Clamping ring; NW 20/25, KF 052 1560
0110 1 Reducing cross piece; DN40/DN16 KF 118 4310
0120 1 Metal tube; DN40x500 118 4350
0130 1 Metal tube; DN40x750 118 1290
0140 2 Hose clamp; NW 40 118 1320
0150 4 Centering ring; NW 40 KF, aluminum-Viton 052 2260
0160 4 Tension ring; NW 32/40 KF 118 1250
0170 8 Clamping screw; DN63-100 ISO, aluminum 104 2670
0180 1 Blank flange; NW 16 KF, aluminum 118 1300

Replaceable Parts
Parts Basic System
Parts Gas and Water This topic contains parts lists for the gas and water supply of the
Supply LTQ Orbitrap Discovery. For a schematical overview of the gas supply,
refer to Figure 1-19 on page 1-24.
Table 4-10. Parts gas supply (P/N 117 7881)

0010 2 Bulkhead union; 1/16”, for hose 4 x 1 (for 115 3660
P/N 069 1130)
0020 1 Bulkhead union; 1/8"×1/8" 052 3450
0030 4.5 m* Hose; 4 x 1, Teflon 069 0280
*
0040 3.5 m Hose; 4 x 1, polyurethane, blue 069 1130
0050 0.5 m* Capillary 1/16" ID-SS 060 5470
0060 2 Plug-in T-piece; 3 x 6mm 112 8140
0070 1 Stainless steel reducing union; Swagelok, 117 8070
6 mm-1/16”
0080 1 T-piece; 1/16" (SS-100-3) 052 3550
0090 1 Coupling; 1/16”, SS-100-6 052 4340
0100 3 PEEKSIL capillary; 1/16", 500 × 0.075 mm 118 6970
0110 1 Reducer Swagelok; 1/8" × 1/16", stainless steel 066 2880
0120 2 Support jack; for hose 4 mm 104 9620
0130 6 Ferrule; 1/16" GVF/16 067 4800
0140 1 N2 venting Orbitrap 119 1480
0150 1 Connector 1/8”, for hose OD 4 mm 112 8680
0160 1 Cap nut; 1/16”, stainless steel 052 0880
0170 3.0 m* Hose; 2 x 1, PTFE 109 1650
0180 1 Sleeve; Ø 6 mm 104 7320
*
Specify required length.
Table 4-11. Upgrade kit gas supply LTQ Orbitrap XL (P/N 122 4820)
0050 0.10 m* Capillary 1/16" ID-SS 060 5470
0070 1 Stainless reducing union; Swagelok, 6 mm-1/16” 117 8070
0080 1 T-piece; 1/16" (SS-100-3) 052 3550
0090 1 Coupling; 1/16”, SS-100-6 052 4340
0100 2 PEEKSIL capillary; 1/16", 500 × 0.075 mm 118 6970
0130 6 Ferrule; 1/16" GVF/16 067 4800
0190 2 Capillary; PEEKsil, 1/16", 0.1 × 500 mm 122 3420
0200 1 Valve, with angle 122 4070
* Specify required length.

Replaceable Parts
Parts Basic System
Table 4-12. Parts water supply (P/N 117 8460) *

0010 2 Quick coupling insert; 9.6 mm 114 1640
0020 2 Quick coupling body; 9.6 mm 113 8960
0030 10 m† Hose; 9 x 3, black, PVC 104 9540
0040 4 Hose clamp; 1-ear, 14.6–16.8 mm 114 4910
0050 1.5 m† Hose; 4 x 1, Teflon 069 0280
0060 2 Quick coupling insert; Delrin Acetal, NW 6.4 118 5030
0070 2 Quick coupling body; Delrin Acetal, NW 6.4 118 5020
0080 16 Clamping piece 8/16 037 0130
0090 2 Adaptor hose nipple; male, 1/2 x 10 118 5840
0100 1 Flow control sensor 119 1740
* For a schematic overview of the cooling water circuit, refer to Figure 1-22 on page 1-27.
† Specify required length.
Table 4-13. Kit gas-water assembly (P/N 208 7351)

0010 1 Bulkhead union; 1/16”, for hose 4 x 1 (for 115 3660
P/N 069 1130)
0020 1 Bulkhead union; 1/8"×1/8" 052 3450
*
0030 5.0 m Hose; 4 x 1, Teflon 069 0280
0040 3.5 m* Hose; 4 x 1, polyurethane, blue 069 1130
*
0050 3.5 m Capillary 1/16" ID-SS 060 5470
0060 1 Stainless steel reducer, 1/16" OD - 1/8" ID 066 2880
0070 2 Quick coupling insert; 9.6 mm 114 1640
0080 2 Quick coupling body; 9.6 mm 113 8960
*
0090 6.0 m Hose; 9 x 3, black, PVC 104 9540
0100 2 Hose clamp; 1-ear, 14.6–16.8 mm 114 4910
*
Specify required length.

Replaceable Parts
Electronic Parts
Electronic Parts This section contains parts list for the electronic components of the
Table 4-14. Electronic parts Orbitrap-2 (P/N 800 1110)

0050 1 Orbitrap-2 Electronics; right panel* 208 1010
*
0060 1 Orbitrap-2 Electronics; left panel 208 1020
0070 1 Electronics analyzer Orbitrap-2* 210 0160
*
0080 1 Electronics main supply Orbitrap 208 1040
0090 1 Electronics rear panel assembly Orbitrap-2 208 1050
0100 1 Cable kit Orbitrap-2 208 1060
0140 1 Kit gas-water assembly† 208 7351
0150 1 CLT-II adapter board 209 9500
† Module, see Table 4-13 on page 4-6.
Electronics - Right Panel The following replaceable parts are available for the electronics at the
right panel of the LTQ Orbitrap Discovery.
Table 4-15. Parts Orbitrap-2 electronics; right panel (P/N 208 1010)
0010 1 Power supply 1 205 5810
0020 1 Power supply 29V/2A 206 4040
0030 1 Power distribution 206 2130*
0040 1 Unit PS 24V/20A 208 1130
0050 1 Unit PS +/-15V/2.75A 208 1140
0060 1 KIT E_RIGHT PANEL ASSEMBLY 206 9790
0070 1 Unit data acquisition† 206 4132
0080 1 Instrument control board 205 4221
0085 1 CLT RF TRIGGER board 208 5880
0090 1 LT ANALOG INTERFACE board Orbitrap-2 208 1940
0100 1 LT DIGITAL INTERFACE board 208 7180
0110 1 UNIT PS-BASIC LOAD 208 5900
* This item is replaced by P/N 210 1320.
† Module, for parts list see below.

Replaceable Parts
Electronic Parts
Table 4-16. Parts Unit data acquisition (P/N 206 4132)

0010 1 Housing PC2 FTMS / ORBITRAP 115 5320
0020 1 Network interface card LCS 8038 TXR 208 2140
0030 1 MATRIX-STL FRONTEND-PC LTQ-FT 207 6470
0040 1 UNIT_PC POWER SUPPLY PS_ON 209 5950
0050 1 LP DAQ DIGITAL PCI BOARD 206 0501
0060 1 IDC/26POL/1.1M 203 0340
0070 1 DAQ ANALOG FRONT END 206 4150
0080 3 SMB BU-90ø/ST-0ø/0.7M 205 9630
0090 1 IDC/14POL/0.12M 206 3790
0100 2 IDC/40POL/0.10M 205 2190
0110 1 PS2/DAQ ANALOG 205 9710
0120 1 POWER SUPPLY 2 206 1440
0130 1 Load resistor 4R7 206 5230
0140 1 Angle bracket, for PC 121 8680
Electronics - Left Panel The following replaceable parts are available for the electronics at the left
panel of the LTQ Orbitrap Discovery.
Table 4-17. Parts Orbitrap-2 electronics; left panel (P/N 208 1020)
0010 1 UNIT HIGH VOLTAGE PS 207 7991
0020 1 UNIT CENTRAL ELECTRODE PS 207 9611
0030 1 LP SPI-BUS-TERMINATION 208 1480
Electronics Analyzer The following replaceable parts are available for the analyzer electronics
of the LTQ Orbitrap Discovery.
Table 4-18. Parts electronics analyzer Orbitrap-2 (P/N 210 0160)

0010 1 UNIT CLT RF SUPPLY 207 9581
0020 1 UNIT CENTRAL ELECTRODE PULSER 207 9640
0030 1 UNIT TEMPERATUR CONTROLLER 207 8930
0040 1 UNIT PRE AMPLIFIER 207 8900
0060 1 UNIT ION OPTIC SUPPLY, Orbitrap-2 209 9810

Replaceable Parts
Electronic Parts
Electronics Main Supply The following replaceable parts are available for the electronics main
supply of the LTQ Orbitrap Discovery.
Table 4-19. Parts electronics main supply Orbitrap (P/N 208 1040)
0010 1 UNIT SWITCH PANEL 208 1120
0020 1 Mains cable; IEC-CONNECTOR-16A 209 6110
0030 1 Mains cable; MAIN INPUT/LINE FILTER 208 1420
0040 1 KIT BAKEOUT-SWITCHES 207 9040
0050 1 Cable loom, mains supply 208 1110
0070 1 Mains cable; LINE FILTER/MAIN SWITCH 208 1280
0080 1 Mains cable; terminal/LTQ-relay 208 1290
0090 1 Mains cable; POWER DIS./SWITCH PANEL 1 208 1300
0100 1 Mains cable; POWER DIS./SWITCH PANEL 2 208 1310
0110 1 Cable; power distribution/LTQ-relay 208 1320
0120 1 Cable loom, power distribution/bakeout timer 207 9010
0130 1 Unit bakeout timer Orbitrap 208 0960
0140 1 KIT MAINS SUP.ASSEMBLY MAT. 208 1100
0150 1 Cable; BAKEOUT-TIMER/POWER DIS. 208 1470
0160 1 Mains cable; POWER DIS./SOCKET R-PUMP 208 1350
0170 1 Mains cable; LTQ-relay/LTQ-filter 208 9230

Glossary
This section lists and defines terms used in this CRM consecutive reaction monitoring
manual. It also includes acronyms, metric prefixes,
symbols, and abbreviations. C-Trap curved linear trap
A ampere <Ctrl> control key on the terminal keyboard
ac alternating current d depth
ADC analog-to-digital converter Da dalton
AGC™ Automatic Gain Control DAC digital-to-analog converter
AP acquisition processor dc direct current
APCI atmospheric pressure chemical ionization DS data system
API atmospheric pressure ionization DSP digital signal processor
ASCII American Standard Code for Information EI electron ionization

Interchange
EMBL European Molecular Biology Laboratory
b bit
<Enter> Enter key on the terminal keyboard
B byte (8 b)
ESD electrostatic discharge
°C degrees Celsius
ESI electrospray ionization
CAN Controller Area Network
eV electron volt
cfm cubic feet per minute
f femto (10-15)
CI chemical ionization
°F degrees Fahrenheit
CID collision-induced dissociation
.fasta file extension of a SEQUEST™ search
CLT curved linear trap database file
cm centimeter ft foot
cm3 cubic centimeter FFT Fast Fourier transformation
CPU central processing unit (of a computer) FT Fourier Transformation
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual G-1

Glossary: FTMS
FTMS Fourier Transformation Mass Spectroscopy KEGG Kyoto Encyclopedia of Genes and
Genomes
FTP file transfer protocol
kg kilogram
FWHM Full Width at Half Maximum
l length
g gram
L liter
9
G Gauss; giga (10 )
LAN local area network
GC gas chromatograph; gas chromatography
lb pound
GC/MS gas chromatograph / mass spectrometer
LC liquid chromatograph; liquid chromatography
GUI graphical user interface
LC/MS liquid chromatograph / mass spectrometer
h hour
LED light-emitting diode
h height
μ micro (10-6)
HCD Higher Energy Collision Induced
Dissociation m meter
HPLC high-performance liquid chromatograph m milli (10-3)
HV high voltage M mega (106)
Hz hertz (cycles per second) M+ molecular ion
ICIS™ Interactive Chemical Information System MB Megabyte (1048576 bytes)
ICL™ Instrument Control Language™

MH+ protonated molecular ion
ID inside diameter
min minute
IEC International Electrotechnical Commission
mL milliliter
IEEE Institute of Electrical and Electronics
mm millimeter
Engineers
MS mass spectrometer; mass spectrometry
in inch
MS MSn power: where n = 1
I/O input/output
MS/MS MSn power: where n = 2
k kilo (103, 1000)
K kilo (210, 1024) MSn MSn power: where n = 1 through 10
m/z mass-to-charge ratio
G-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Glossary: n
n nano (10-9) ROM read-only memory
NCBI National Center for Biotechnology RS-232 industry standard for serial
Information (USA) communications
NIST National Institute of Standards and s second

Technology (USA)
SIM selected ion monitoring
OD outside diameter
SPI Serial Peripheral Interface
Ω ohm
SRM selected reaction monitoring
-12
p pico (10 )
TCP/IP transmission control protocol / Internet
Pa pascal protocol
PCB printed circuit board TIC total ion current
PE protective earth Torr torr
PID proportional / integral / differential u atomic mass unit
P/N part number UHV ultra high vacuum
P/P peak-to-peak voltage V volt
ppm parts per million V ac volts alternating current
psig pounds per square inch, gauge V dc volts direct current
RAM random access memory vol volume
RF radio frequency w width
RMS root mean square W watt
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual G-3

Index
Numerics axial ion ejection 1-12
axial oscillations 1-13
017 2350 3-6
frequency 1-16
105 0160 3-6
117 5000 4-3
117 5010 4-3–4-4
118 4490 4-3 B
205 4221 1-36 bakeout 3-4
205 5810 1-42 control buttons 1-8
206 0501 1-34 controls 1-7
206 1440 1-36 start button 3-4
206 4132 1-33 stop button 3-4
timer 1-7–1-8, 3-4
206 4150 1-35
bakeout procedure
207 6470 1-33
indication 1-8
207 7991 1-51
starting 1-7, 3-5
207 8900 1-32
stopping 1-7, 3-5
207 8930 1-47
basic system operations 2-1
207 9581 1-48 bath gas 1-13, 1-24
207 9591 1-48
buttons
207 9611 1-50 Display Status View 2-9
207 9640 1-46 On/Standby 2-4
208 1480 1-53 system bakeout 1-7
208 2540 1-48
209 9810 1-45
210 1320 1-38
C
cable tie 1-10
calibration parameters 2-11
A CAN bus 1-40
Active Pirani gauge 1-22 central electrode 1-13
active temperature control 1-17 voltages 1-15, 1-50
AGC central electrode power supply board 1-17, 1-44, 1-50
See Automatic Gain Control diagnostic LEDs 1-51
air flow 1-4 location 1-50
air, in helium line 2-9 central electrode pulser board 1-44, 1-46
analog signals 1-36 diagnostic LEDs 1-47
analyzer location 1-46
chamber temperature 1-47 changing, the operating fluid 3-7
system 2-8 circuit breakers 1-7–1-8
temperature 1-27 cleaning, the instrument surface 3-3
analyzing, hazardous materials 1-21 CLT compartment 1-19
anti-aliasing filters 1-35 CLT RF main board 1-14, 1-25, 1-44, 1-49
API source diagnostic LEDs 1-49, 1-51
safety interlock switch 2-8 housing 1-25
settings 2-11 location 1-48
API source settings 2-11 CLT RF unit 1-48
Automatic Gain Control 1-12 CLT RF voltage 1-14
autosampler 2-6–2-7 Cold Ion Gauge 1-20, 1-22–1-23, 1-30, 1-32
auxiliary gas 1-24 collision gas
C-Trap 1-13, 1-24
Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual I-1

Index: D
HCD 1-10, 1-24–1-26, 1-39 instrument control 1-36

inlet 1-11 ion optic supply 1-45
linear trap 1-25 left side 1-44
valve 1-24 power distribution 1-38
Communication LED 1-39 preamplifier 1-32
communication link 1-6 right side 1-31
computer housing 1-31, 1-33 electronic connections, of linear trap 1-30
condenser filter, of recirculating chiller 3-7 emergency 2-2
control elements 1-6 error indication 1-41
control panel 1-7 error messages 1-23, 1-39
control unit, for turbopumps 1-21 Ethernet 1-10
cooling water 1-10 ports 1-11
circuit 1-17, 1-27–1-28 evacuating, after a complete shut down 3-4
flow control sensor 1-27 exchanging, the lubricant reservoir of the turbopumps 3-6
inlet port 1-11 exhaust
outlet port 1-11 hose 1-10
properties 1-28 system 1-10, 1-21
temperature 1-27 external calibration 1-5
cooling water supply, for Peltier element 1-20, 1-32 external connections 1-11
cover lid, for bakeout controls 1-7–1-8 extracting voltage 1-14
C-Trap extraction, of ion packets 1-14
See curved linear trap
curved linear trap 1-3, 1-13, 1-17
F
fingerprints, removing 3-3
D flow rates
data acquisition analog board 1-33–1-35 cooling water 1-27
diagnostic LEDs 1-36 nitrogen 1-25
location 1-33, 1-35 fluid bag filter 3-7
data acquisition digital PCI board 1-33–1-34 focusing potentials 1-52
diagnostic LEDs 1-35 forepumps 1-21
location 1-33–1-34 cabinet 1-7, 1-21
data acquisition unit 1-33 effluent 1-21
data communication 1-30 linear trap 1-19, 1-21
data system 1-6, 1-10, 1-23, 1-34, 1-36, 2-6–2-7, 2-10 location 1-7, 1-12, 1-21
log file 2-2 oil level 1-22
default values, of tune and calibration parameters 2-11 oil mist filters 1-21, 3-6
deflector electrode voltages 1-50 power supply 1-22
diagnostic LEDs, of instrument control board 1-37 switches 1-22
diagnostics, in Tune Plus 1-29 front panel 1-4
disconnecting, cooling water hoses 1-28 front side, LEDs 1-6
Display Status View button 2-9 FT Electronics switch 1-6, 1-9, 1-41, 3-4
distilled water 3-3 fuse 1-42
down keys 3-4
dynamic range 1-5
G
gas ballast 1-22
E gas flow divider 1-25–1-26
elapsed time display 3-4 gas pressures 2-9
electric power, for recirculating chiller 1-28 gas supply 1-24
electrodynamic squeezing 1-15 HCD collision gas 1-10
helium 1-10
electronic boards
data acquisition analog 1-35 nitrogen 1-10
schematics 1-24
data acquisition digital PCI 1-34
I-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Index: H
gate voltage 1-45 location 1-33

gloves 3-2 rebooting 2-10
ground wires 1-31 timer 1-34
side panel 1-31 ion dephasing 1-16
ion detection 1-15
ion optic supply board 1-14, 1-18, 1-45
diagnostic LEDs 1-46
H housing 1-44
harmonic oscillations 1-13 location 1-44–1-45
hazardous materials 1-21 ion oscillation 1-15
HCD ion packets 1-15
collision cell 1-3, 1-17, 1-24, 1-45 shape 1-16
collision gas 1-24–1-25 ion trajectory 1-13
collision gas supply 1-10
ionization techniques 1-12
collision octapole 1-14
ions
fragment spectra 1-18
detection 1-15
housing 1-20
electrodynamic squeezing 1-15
status, of collision gas valve 1-39
image current 1-15
valve for collision gas 1-26
packet shape 1-16
heated components 2-6
heater control 1-41
helium
gas capillary 1-25 L
inlet 1-11 laboratory
purging the line 2-9 exhaust system 1-21
supply 1-10 gas supply 1-25
high voltage 1-29 LC 2-7
high voltage power supply board 1-14, 1-44, 1-52–1-53 operating 2-4–2-5
diagnostic LEDs 1-53 LEDs
location 1-51 power control 1-8
system status 1-6, 1-8
vacuum 1-6
I left side panel, of instrument 1-4
lens stack 1-3
image current 1-13, 1-15, 1-32
lens voltages 1-51
detection 1-15
line power 1-10
inlet, for nitrogen gas 1-11
linear trap 1-2, 1-12, 1-19, 1-36
instrument
collision gas 1-25
controls 1-7
Communication LED 2-8, 2-10
diagnostics 1-29
electronics 1-30
forevacuum measurement 1-22
forepumps 1-19, 1-21
front view 1-2
LEDs 1-6
high vacuum measurement 1-22
maintenance 3-1
parts 4-1
Power LED 2-8, 2-10
rear side 1-7
power panel 1-7, 1-21
right side 1-10
Reset button 2-10
shutdown 1-39
System LED 2-8, 2-10
switching off 1-10, 2-2
system status LEDs 1-7
instrument control board 1-33, 1-36–1-37
turbopump 1-21
Vacuum LED 2-8
housing 1-31
vacuum measurement 1-22
location 1-31, 1-33, 1-36
vent valve 1-23, 1-25–1-26, 2-2–2-3
software status LEDs 1-38
Link Port Signal line 1-36
internal calibration 1-5
liquids, entering the instrument 3-3
internal computer 1-31, 1-33
locations
add-ons 1-34–1-35
data acquisition analog board 1-33
data communication 1-30

Index: M
nitrogen pressure regulator 1-26 electrodes 1-13

log file 2-2 ion extraction 1-14
lubricant reservoir, of turbopumps 3-6 ion trajectories 1-16
layout 1-14
lenses 1-14
measuring principle 1-13
M system status LEDs 1-7
main circuit breaker 2-5 voltages 1-14, 1-16
main power switch 1-6–1-7, 1-10, 2-2 output current 1-32
Off position 2-2
securing 1-10
main power switch, securing 1-10
P
main RF supply 1-48
padlock 1-10
main switch 1-41
parameters
mains failure 1-42, 2-2, 3-4
calibration 2-11
maintenance 1-12
resetting to default values 2-11
API source 1-12
part numbers 4-1
linear trap 3-1
procedures 3-2 Peltier element 1-17, 1-32, 1-47–1-48, 1-50
recirculating chiller 3-7 water supply 1-20
vacuum system 3-6 Penning gauge 1-41
mass accuracy 1-5 peripherals
mass range 1-5 power outlet 1-11
turning off 2-6
micro controller 1-36–1-37
Pirani gauge 1-20, 1-23, 1-41
multiple socket outlets 1-8, 1-41, 2-2
power
connector 1-7, 1-11
connector for linear trap 1-12
N control LEDs 1-9
nitrogen 1-24 control panel 1-8–1-9
flow rates 1-25 panel 1-7
gas flow 1-25 power distribution
inlet 1-11 operating states 1-41
pressure 1-25 resetting 1-23
pressure regulator 1-25–1-26 working modes 1-41
supply 1-10 power distribution board 1-6, 1-8–1-9, 1-27, 1-31, 1-36, 1-38, 1-
tubing 1-25–1-26 41
location 1-31, 1-38
status LEDs 1-40
O power fail detector 2-3
octapole RF voltages 1-45 Power LED 1-6
offset, between the C-Trap and HCD 1-18 power outlet, for peripheral devices 1-11
oil power panel, of linear trap 1-7
level 1-22
power supply 1 board 1-31, 1-42–1-43
mist filters 1-21, 3-6
On/Standby button 2-4 location 1-42
open split interface 1-18, 1-25 power supply 2 board 1-33, 1-36
operating vacuum 1-6 diagnostic LEDs 1-36
options, power supply 1-31 location 1-33
Orbitrap power supply, for linear trap 1-12
applied voltages 1-14 preamplifier 1-20, 1-31–1-32
central electrode 1-47 diagnostic LEDs 1-33
chamber 1-19 location 1-31–1-32
control LEDs 1-7 pressure regulator
detection electrodes 1-47 location 1-26
differential pumping 1-14

Index: Q
nitrogen 1-25–1-26 serial port connector 1-36

preventive maintenance 2-6, 3-2 service switch, of linear trap 1-9
rules 3-2 set time display 3-4
printed circuit boards 1-29 setting up, conditions for operation 2-8
pumping, the system 2-7, 3-4 sheath gas 1-24
pumps shutdown 1-42, 2-5, 2-7
exhaust 1-10 signal communication 1-30
forevacuum 1-21 software 1-27, 1-29, 2-7
manuals 3-6 debugging 1-37
oil mist filters 1-21 status LEDs of the instrument control board 1-38
purging, helium line 2-9 Tune Plus window 2-4
spacers, at rear instrument side 1-4
specifications, of instrument 1-5
Q spectrum 1-16
quality, of vacuum 1-39 SPI bus 1-30, 1-47–1-48, 1-50, 1-52
location of termination board 1-53
termination board 1-48–1-49, 1-51, 1-53
stains, removing 3-3
R standby condition 2-4
rear panel, of instrument 1-4 starting up, instrument 2-7
rebooting, of instrument 2-2 starting up, the instrument 2-7
recirculating chiller 1-4, 1-28 status LEDs
condenser filter 3-7 instrument control board 1-37
fluid bag filter 3-7 power distribution board 1-40
maintenance 3-7 storage stability, of lubrication oil 3-6
reflector DC voltages 1-45 sweep gas 1-24
removing switches
gases 2-8, 3-4 forepumps 1-22
stains 3-3 FT Electronics 1-9, 3-4
repair covering letter 3-2 linear trap 1-9
replaceable parts 4-1 main power 1-10
electronics (left panel) 4-8 Vacuum Pumps 1-9
electronics (right panel) 4-7 switching on, the vacuum system 1-23
electronics analyzer Orbitrap 4-8 system
electronics main supply 4-9 bakeout 1-6–1-7, 1-23, 2-7, 3-4
pumping system Orbitrap 4-3 bakeout timer 1-7
replacements, for turbopump lubricant reservoirs 3-6 buttons for bakeout 1-7
reservoir, of recirculating chiller 3-7 heating 1-23
resetting pump down time 2-8
instrument 2-10 rebooting 2-2
system parameters 2-11 resetting 2-10
tune and calibration parameters 2-11 shutdown 2-2, 2-5
resolution 1-5 standby 2-4
RF CLT main board 1-51 starting up 2-7
RF off & feedback board 1-44, 1-48–1-49 status LEDs 1-6, 1-39
timing 1-34
RF output control 1-45
venting 1-26, 2-2
RF voltage supply 1-48
system status LEDs
right side panel, of instrument 1-4
linear trap 1-7
routine maintenance 2-6
LTQ Orbitrap Discovery 1-7
S T
safety interlock switch 2-8
temperature
SEM detector 1-12 analyzer chamber 1-47

Index: U
control 1-17 V
differential 1-17
vacuum
temperature controller board 1-17, 1-25, 1-44, 1-47
analyzer system 2-8
chamber 1-19–1-20
location 1-47
compartments 1-19
temperature, of chiller operating fluid 3-7 deterioration 1-23
thermoelectric elements 1-17 failure 1-23, 1-39
TMP 1 1-19–1-20 gauges 1-22, 1-36
TMP 2 1-19–1-20 quality 1-39
TMP 3 1-19–1-21 safety threshold 1-22–1-23
tools 3-2 system 1-10, 1-19
top lid, of instrument 1-4 vacuum components
transfer chamber 1-12 left instrument side 1-20
trap voltage 1-45 UHV chamber 1-20
tune parameters 2-11 Vacuum LED
Tune Plus window 1-29, 2-5, 2-9, 2-11 linear trap 2-8
buttons 2-4, 2-9 LTQ Orbitrap Discovery 1-6
turbopumps 1-20, 1-36 Vacuum Pumps switch 1-6, 1-9, 1-41
controller 1-21–1-22 vacuum system
error 1-40 controls 1-22
exchanging the lubricant reservoir 3-6 heating 1-23
linear trap 1-21 maintenance 3-6
maintenance intervals 3-6 moisture 1-23
TMP 2 1-20 valve, for HCD collision gas 1-26, 1-39
TMP 1 1-20 vent valve 1-26, 2-2–2-3, 2-5
TMP 3 1-20 linear trap 1-25, 2-3
vent valves 1-23 venting pressure 1-26
turning off, the peripherals 2-2, 2-6 venting, the system 2-3
U W
UHV chamber 1-17, 1-19–1-20 water 1-10
temperature control 1-17 chiller 1-4
uninterruptible power supply 2-2 hoses 1-28
up keys 3-4 ports 1-11
upper control panel 1-7–1-8 temperature 1-28
UPS wheels, of instrument 1-4
See uninterruptible power supply working modes, of the power distribution 1-41
user maintenance 3-1–3-2 working principle, of the Orbitrap analyzer 1-3
procedures 3-2
X
Xcalibur 1-29

Thermo Fisher Scientific Inc.
81 Wyman Street
P.O. Box 9046
Waltham, Massachussetts 02454-9046
United States
www.thermo.com
Part of Thermo Fisher Scientific

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LTQ Orbitrap Discovery™

Revision A - 122 5850

For Research Use Only

Part of Thermo Fisher Scientiﬁc

Revision A - 122 5850

For Research Use Only

Notice on the Proper Use of

In compliance with international regulations: If this instrument is used in a manner not

Notice on the Susceptibility

Your instrument is designed to work in a controlled electromagnetic environment. Do not use

Thermo Fisher Scientific hat Vereinbarungen getroffen mit Verwertungs-/Entsorgungsanlagen in

This manual includes the following chapters:

• Chapter 1: “Functional Description” describes the principal

• Chapter 2: “Basic System Operations” provides procedures for

• Chapter 3: “User Maintenance” outlines the maintenance

• Chapter 4: “Replaceable Parts” lists the replaceable parts for the

Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual i

You are encouraged to report errors or omissions in the text or index.

ii LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Typographical Typographical conventions have been established for Thermo Fisher

• Messages displayed on the screen are represented by capitalizing the

• Input that you enter by keyboard is identified by quotation marks:

• Any command enclosed in angle brackets < > represents a single

• Any command that requires pressing two or more keys

Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual iii

Admonitions can be of the following types:

• Note – information that can affect the quality of your data. In

• Caution – information necessary to protect your instrument from

• Warning – hazards to human beings. Each Warning is accompanied

The following headings appear in the left column of each page:

Second Level Topics

Third Level Topics

Fourth Level Topics

iv LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Designed, manufactured and tested in an ISO9001 registered facility,

Caution This instrument must be used as described in this manual. Any

Table i. Warning Symbols

The source of danger is described in the accompanying text. ▲

Hot Surface / Heat Allow heated components to cool down before

1. Before plugging in any of the instrument modules or turning on the

Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual v

4. Do not change the external or internal grounding connections.

Caution The instrument is properly grounded in accordance with

6. Do not turn the instrument on if you suspect that it has incurred

7. Damage can also result if the instrument is stored for prolonged

8. Always disconnect the power cord before attempting any type of

9. Capacitors inside the instrument may still be charged even if the

vi LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

In order to protect our employees, we ask you to adhere to special

If hazardous materials have contaminated mass spectrometer parts,

Your signature on the Repair-Covering letter confirms that the

The Repair-Covering letter can be ordered from your service engineer or

Parts contaminated by radioisotopes are not subject to return to Thermo

Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual vii

Chapter 2 Basic System Operations ........................................................2-1

Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual ix

Chapter 3 User Maintenance.................................................................... 3-1

Chapter 4 Replaceable Parts .................................................................... 4-1

Glossary .................................................................................... G-1

Index ............................................................................................ I-1