LTQ Orbitrap XL ETD Hardware Manual

LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
LTQ Orbitrap XL ETD™
Hardware Manual
Revision A - 1245510
For Research Use Only
Not for use in Diagnostic Procedures
Part of Thermo Fisher Scientific
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The contents of this document are subject to change without notice. All technical information in this document
is for reference purposes only. System configurations and specifications in this document supersede all previous
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Printing History: Revision A printed in October 2008.
Place Declaration of Conformity here
Regulatory Compliance
Thermo Electron San Jose performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc..
EN 61000-3-2
1995, A1;
1998, A2;
1998, A14;
2000
EN 61000-4-4
IEC 61000-4-4
1995, A1; 2001,
A2; 2001;
A2-1995
EN 61000-3-3
1998
EN 61000-4-5
1995, A1; 2001
IEC 61000-4-5
2005
EN 61000-4-6
1996, A1; 2001
IEC 61000-4-6
2004
1994, A1; 2001
EN 61326-1
1998, A3
EN 61000-4-2
2000
EN 61000-4-11
IEC 61000-4-2
2001
IEC 61000-4-11 2001-03
FCC Class A,
CFR 47 Part 15
2005
CISPR 11
1999, A1; 1999,
A2; 2002
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Electron. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Electron or one
of its authorized representatives.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 18 OF THE FCC RULES.
WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic
Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling/disposal companies in each EU
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Read This First
Welcome to the Thermo Scientific LTQ Orbitrap XL ETD™ system!
The LTQ Orbitrap XL ETD is a member of the family of LTQ™ mass
spectrometer (MS) hybrid instruments.
About This Guide
This LTQ Orbitrap XL ETD Hardware Manual contains a description of
the modes of operation and principle hardware components of your
LTQ Orbitrap XL ETD instrument. In addition, this manual provides
step-by-step instructions for cleaning and maintaining your instrument.
Who Uses This Guide
This LTQ Orbitrap XL ETD 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 manual includes the following chapters:
Thermo Fisher Scientific
•
Chapter 1: “Functional Description” describes the principal
components of the LTQ Orbitrap XL ETD.
•
Chapter 2: “Basic System Operations” provides procedures for
shutting down and starting up the LTQ Orbitrap XL ETD.
•
Chapter 3: “User Maintenance” outlines the maintenance
procedures that you should perform on a regular basis to maintain
optimum instrument performance.
•
Chapter 4: “Replaceable Parts” lists the replaceable parts for the
MS detector and data system.
•
Appendix A: “Fluoranthene” describes properties of the reagent that
is used in the ETD Module portion of the LTQ Orbitrap XL ETD.
LTQ Orbitrap XL ETD Hardware Manual
i
Read This First
Related Documentation
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the
following documents for LTQ Orbitrap XL ETD:
•
LTQ Orbitrap XL / LTQ Orbitrap Discovery Preinstallation
Requirements Guide
•
LTQ Orbitrap XL Getting Started Guide
•
LTQ XL manual set
The software also provides Help.
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LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Read This First
Contacting Us
Contacting Us
There are several ways to contact Thermo Fisher Scientific.
Assistance
For technical support and ordering information, visit us on the Web:
www.thermo.com/advancedms
Customer Information Service
cis.thermo-bremen.com is the Customer Information Service site aimed
at providing instant access to
•
latest software updates
•
manuals, application reports, and brochures.
Note Thermo Fisher Scientific recommends that you register with the
site as early as possible. ▲
To register, visit register.thermo-bremen.com/form/cis and fill in the
registration form. Once your registration has been finalized, you will
receive confirmation by e-mail.
Changes to the Manual
To suggest changes to this manual, please send your comments (in
German or English) to:
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.
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
iii
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Typographical Conventions
Typographical Conventions
This section describes typographical conventions that have been
established for Thermo Fisher Scientific manuals.
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”.
Topic Headings
The following headings are used to show the organization of topics
within a chapter:
Chapter 1
Chapter Name
Second Level Topics
Third Level Topics
Fourth Level Topics
iv
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Read This First
Safety and EMC Information
Safety and EMC Information
In accordance with our commitment to customer service and safety, this
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. ▲
Notice on Lifting and Handling of Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the
physical handling of this Thermo Scientific instrument requires a team
effort for lifting and/or moving the instrument. This instrument is too
heavy and/or bulky for one person alone to handle safely.
Notice on the Proper Use of Thermo Scientific Instruments
In compliance with international regulations: If this instrument is used
in a manner not specified by Thermo Fisher Scientific, the protection
provided by the instrument could be impaired.
Notice on the Susceptibility to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic
environment. Do not use radio frequency transmitters, such as mobile
phones, in close proximity to the instrument.
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
v
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Safety and EMC Information
Safety and Special Notices
Note Read and understand the various precautionary notes, signs, and
symbols contained inside this manual pertaining to the safe use and
operation of this product before using the device. ▲
Make sure you follow the precautionary statements presented in this
guide. The safety and other special notices appear different from the
main flow of text. Safety and special notices include the following:
Warning Warnings highlight hazards to human beings. Each Warning is
accompanied by a Warning symbol. ▲
Caution Cautions highlight information necessary to protect your
instrument from damage. ▲
Note Notes highlight information that can affect the quality of your
data. In addition, notes often contain information that you might need
if you are having trouble. ▲
vi
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
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Safety and EMC Information
Identifying Safety Information
The LTQ Orbitrap XL ETD Hardware Manual contains precautionary
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. The most common warning symbols are:
Warning This general symbol indicates that a hazard is present that
could result in injuries if it is not avoided.
The source of danger is described in the accompanying text. ▲
Warning 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 is performed. Do not operate the
instrument with the top cover off. Do not remove protective covers from
PCBs. ▲
Warning Treat heated zones with respect. Parts of the instrument might
be very hot and might cause severe burns if touched. Allow hot
components to cool before servicing them. ▲
Warning Wear gloves when handling toxic, carcinogenic, mutagenic, or
corrosive/irritant chemicals. Use approved containers and procedures for
disposal of waste solution. ▲
In addition to the above described, every instrument has specific
hazards. So, be sure to read and comply with the precautions described
in the subsequent chapters of this guide. They will help ensure the safe,
long-term use of your system.
General Safety Precautions
Observe the following safety precautions when you operate or perform
service on your instrument:
Thermo Fisher Scientific
•
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.
•
Only use fuses of the type and current rating specified. Do not use
repaired fuses and do not short-circuit the fuse holder.
LTQ Orbitrap XL ETD Hardware Manual
vii
Read This First
Safety and EMC Information
•
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.
•
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. ▲
viii
LTQ Orbitrap XL ETD Hardware Manual
•
Never run the system without the housing on. Permanent damage
can occur.
•
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.)
•
Damage can also result if the instrument is stored for prolonged
periods under unfavorable conditions (e.g., subjected to heat, water,
etc.).
•
Always disconnect the power cord before attempting any type of
maintenance.
•
Capacitors inside the instrument may still be charged even if the
instrument is turned off.
•
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.
Thermo Fisher Scientific
Read This First
Safety and EMC Information
Safety Advice for Possible Contamination
Hazardous Material Might Contaminate Certain Parts of Your
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 XL ETD Hardware Manual
ix
Contents
Thermo Fisher Scientific
Chapter 1
Functional Description.............................................................1-1
General Description .......................................................... 1-2
Mechanical Characteristics ............................................. 1-4
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........................................................ 1-18
ETD System ................................................................... 1-19
Principle of Operation ................................................. 1-19
ETD Module ............................................................... 1-19
Vacuum System .............................................................. 1-28
Turbopumps ................................................................ 1-29
Forevacuum Pumps of the Linear Trap ........................ 1-31
Forevacuum Pump of the ETD Module....................... 1-32
Vacuum System Controls............................................. 1-33
Vacuum System Heating during a System Bakeout ...... 1-35
Gas Supply...................................................................... 1-36
Gas Supply for the Mass Analyzers ............................... 1-36
Gas Supply of the Reagent Ion Source ......................... 1-39
Cooling Water Circuit .................................................... 1-40
Recirculating Chiller .................................................... 1-41
Properties of Cooling Water......................................... 1-41
Printed Circuit Boards .................................................... 1-42
Linear Ion Trap Electronics.......................................... 1-43
Electronic Boards at the Right Side of the Instrument.. 1-44
Electronic Boards on the Left Side of the Instrument ... 1-58
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 LTQ Orbitrap XL ETD in Standby
Condition ......................................................................... 2-4
Placing the ETD Module in Standby Condition............ 2-4
Placing the MS in Standby Condition............................ 2-6
LTQ Orbitrap XL ETD Hardware Manual
xi
Contents
Shutting Down the LTQ Orbitrap XL ETD Completely.. 2-7
Shutting Down the Instrument ...................................... 2-7
Starting Up the System after a Shutdown.......................... 2-9
Starting Up the Instrument............................................ 2-9
Setting Up Conditions for Operation........................... 2-10
Starting the ETD Module After a Complete Shutdown 2-11
Resetting the System ....................................................... 2-12
Resetting the Tune and Calibration Parameters to their
Default Values ................................................................ 2-13
Turning Off the Reagent Ion Source: What to Expect .... 2-14
Chapter 3
User Maintenance.................................................................... 3-1
General Remarks............................................................... 3-2
Returning Parts .............................................................. 3-3
Cleaning the Surface of the Instrument .......................... 3-3
Maintenance of the Vacuum System ................................. 3-4
Baking Out the System .................................................. 3-4
Maintenance of the Forepumps...................................... 3-5
Maintenance of the Turbopumps................................. 3-12
Maintenance of the ETD Module ................................... 3-13
Requirements for Handling and Cleaning Reagent Ion
Source Parts ................................................................. 3-14
Maintenance of the Reagent Ion Source ....................... 3-18
Changing the Reagent Vials ......................................... 3-48
Cleaning the Fan Filters of the ETD Module............... 3-60
Maintenance of the Recirculating Chiller ........................ 3-61
Reservoir ...................................................................... 3-61
Fluid Bag Filter ............................................................ 3-61
Condenser Filter .......................................................... 3-61
Chapter 4
Replaceable Parts.................................................................... 4-1
Parts List for the Mass Analyzer......................................... 4-2
Parts Basic System.......................................................... 4-2
Electronic Parts .............................................................. 4-7
Parts Lists for the ETD System ....................................... 4-11
Mechanical Parts for ETD System ............................... 4-12
Electronic Parts of ETD System ................................... 4-14
Parts Lists for the ETD Module ................................... 4-15
Appendix A Fluoranthene ............................................................................ A-1
Glossary .................................................................................... G-1
Index ............................................................................................I-1
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LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Figures
LTQ Orbitrap XL ETD front view ....................................................... 1-2
Schematical view of the LTQ Orbitrap XL ETD .................................. 1-3
Top lid of MS portion opened .............................................................. 1-4
System status LEDs ............................................................................... 1-6
Right side of the LTQ Orbitrap XL ETD ............................................. 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 XL ETD .......................... 1-11
Schematical 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
LTQ Orbitrap XL ETD, rear side ....................................................... 1-20
Rear view of the ETD Module, with major component locations ........ 1-20
ETD Module functional block diagram .............................................. 1-21
ETD Power Module panel .................................................................. 1-22
Reagent Ion Source dialog box ............................................................ 1-24
Reagent ion source schematics ............................................................. 1-26
Schematical view of Orbitrap vacuum system (CLT compartment and
Orbitrap chamber not shown) ............................................................. 1-28
Vacuum components on the left instrument side ................................ 1-29
Vacuum components on the right instrument side .............................. 1-30
ETD mechanics .................................................................................. 1-30
Forepumps cabinet .............................................................................. 1-31
Forepump for ETD Module ............................................................... 1-33
Schematical view of the gas supply ...................................................... 1-36
Valve for HCD collision gas ................................................................ 1-37
Nitrogen pressure regulator and gas flow dividers ................................ 1-38
UHP nitrogen port at the ETD Module ............................................. 1-39
Schematical view of cooling water circuit ............................................ 1-40
Electronic connections to linear trap (covers removed) ........................ 1-43
Electronic boards on the right side of the instrument .......................... 1-44
ETD Ion Optic Supply board ............................................................. 1-45
Preamplifier board ............................................................................... 1-46
Data Acquisition unit .......................................................................... 1-47
Data Acquisition Digital PCI board .................................................... 1-48
Data Acquisition Analog board ........................................................... 1-49
Instrument Control board ................................................................... 1-51
Power Distribution board ................................................................... 1-52
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LTQ Orbitrap XL ETD Hardware Manual
xiii
Figures
Power Supply 1 board ......................................................................... 1-57
Electronic boards on the left side of the instrument ............................. 1-58
Ion Optic Supply board ...................................................................... 1-59
Central Electrode Pulser board ............................................................ 1-60
Temperature Controller board ............................................................ 1-61
CLT RF unit (cover removed) ............................................................. 1-63
Central Electrode Power Supply board ................................................ 1-64
High Voltage Power Supply board (cover removed) ............................ 1-66
High Voltage Power Supply board with SPI Bus Termination board .. 1-67
Main power switch in Off position ....................................................... 2-2
Tune Plus window, toolbar ................................................................... 2-4
Reagent Ion Source dialog box with Reagent Ion Source On box and Actual
condition circled ................................................................................... 2-5
Placing the reagent ion source in Standby condition ........................... 2-14
Bakeout timer ....................................................................................... 3-4
Schematic of ETD forepump ................................................................ 3-6
Accessing the ETD Forepump: Removing the panel ............................. 3-7
Hooks (left) and top side of detached bottom panel (right) ................... 3-7
Lugs for fixing the bottom panel ........................................................... 3-8
Gas Ballast Control Positions .............................................................. 3-10
Routine maintenance sequence for ETD system .................................. 3-13
Ion source components (left view) ....................................................... 3-19
Tune Plus window .............................................................................. 3-20
Ion volume tool components ............................................................... 3-21
Guide bar being inserted into guide bar opening ................................. 3-21
Guide bar insertion complete .............................................................. 3-22
Rear view of the ETD Module, showing the inlet valve ....................... 3-23
Ion volume tool handle in the unlock position .................................... 3-23
Ion volume tool guide bar first stop ..................................................... 3-24
Reagent Ion Source dialog box, Open Probe Interlock button. ............ 3-25
Instrument Message box: The Ball Valve can now be opened .............. 3-25
Ion volume tool inserted into the inlet valve ........................................ 3-26
Detail of ion volume tool fully inserted into the inlet valve ................. 3-26
Ion volume tool handle in the locked position .................................... 3-27
Ion volume assembly ........................................................................... 3-28
Placing the ion volume on the ion volume tool ................................... 3-28
Ion volume tool handle in the unlock position .................................... 3-30
Ion volume tool handle in the locked position .................................... 3-30
Rear view of the ETD Module ............................................................ 3-32
Inlet valve components (ion volume tool not shown) .......................... 3-35
Valve shield (1) covering the vacuum manifold probe plate ................. 3-36
Removing the foreline hose from its connection .................................. 3-36
Unscrewing the vacuum manifold probe plate ..................................... 3-37
Removing the vacuum manifold probe plate ....................................... 3-37
Interior of vacuum manifold ............................................................... 3-38
Removing the ion source assembly from the vacuum manifold ........... 3-39
Ion source assembly ............................................................................. 3-39
Ion source assembly exploded view ...................................................... 3-40
Ion source, exploded view ................................................................... 3-42
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LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Figures
Ion source lens assembly and ion source .............................................. 3-43
Filament wire as seen from the bottom of the filament through the electron
lens hole .............................................................................................. 3-45
Inlet valve ............................................................................................ 3-46
Inlet valve components (ion volume tool not shown) .......................... 3-47
Inlet valve seal removal tool (P/N 119283-0001) ................................ 3-47
Reagent Ion Source dialog box ............................................................ 3-50
Schematical rear view of the ETD Module .......................................... 3-52
ETD Module with back panel removed .............................................. 3-54
Reagent vials with holders ................................................................... 3-55
ETD Module with vial heater cover removed ...................................... 3-56
Reagent inlet assembly ........................................................................ 3-58
ETD Module, top panel ...................................................................... 3-60
ETD Reagent (fluoranthene radical anion) generation from
fluoranthene ..........................................................................................A-1
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LTQ Orbitrap XL ETD Hardware Manual
xv
Tables
System status LEDs of the LTQ Orbitrap XL ETD .............................. 1-6
Circuit breakers of the LTQ Orbitrap XL ETD .................................... 1-8
Typical pressure readings in the ETD Module .................................... 1-34
Diagnostic LEDs on the ETD Ion Optic Supply board ....................... 1-45
Diagnostic LEDs on the Preamplifier board ........................................ 1-47
Diagnostic LEDs of the Data Acquisition Digital PCI board .............. 1-49
Diagnostic LEDs of the Data Acquisition Analog board ...................... 1-50
Diagnostic LEDs of the Power Supply 2 board ................................... 1-50
Diagnostic LEDs of the Instrument Control board ............................. 1-51
Software status LEDs of the Instrument Control board ....................... 1-52
Status LEDs of the Power Distribution board ..................................... 1-54
Working modes of the Power Distribution board ................................ 1-55
Operating states of the Power Distribution board ............................... 1-55
Diagnostic LEDs of the Power Supply 1 board ................................... 1-57
Diagnostic LEDs of the Ion Optic Supply board ................................. 1-60
Diagnostic LEDs of the Central Electrode Pulser board ...................... 1-61
Diagnostic LEDs of the Temperature Controller board ....................... 1-62
Diagnostic LEDs of the CLT RF Main board ..................................... 1-63
Diagnostic LEDs of the Central Electrode Power Supply board .......... 1-65
Diagnostic LEDs of the High Voltage Power Supply board ................ 1-67
User maintenance procedures ................................................................ 3-2
Parts for the LTQ Orbitrap XL ............................................................. 4-2
Parts LTQ Orbitrap XL; 50 Hz (P/N 072 3852) .................................. 4-2
Parts basic system Orbitrap-2 (P/N 122 4790) ...................................... 4-2
Parts Upgrade kit Orbitrap HCD option (P/N 122 4800) .................... 4-3
Parts Orbitrap Installation Kit (P/N 118 8120) .................................... 4-3
Parts Orbitrap-2 chamber; complete (P/N 122 4780) ........................... 4-4
Parts pumping system Orbitrap (P/N 118 4490) .................................. 4-4
Parts pump kit Orbitrap (P/N 117 5000) ............................................. 4-4
Parts pump system Orbitrap (P/N 117 5010) ....................................... 4-5
Parts gas supply (P/N 117 7881) ........................................................... 4-5
Parts water supply (P/N 117 8460) ...................................................... 4-6
Upgrade kit gas supply LTQ Orbitrap XL (P/N 122 4820) .................. 4-6
Kit gas-water assembly (P/N 208 7351) ................................................ 4-7
Electronic parts Orbitrap-2 (P/N 800 1110) ......................................... 4-7
Parts Orbitrap-2 electronics; right panel (P/N 210 1480) ...................... 4-8
Parts Unit data acquisition (P/N 206 4132) .......................................... 4-8
Parts Orbitrap-2 electronics; left panel (P/N 208 1020) ........................ 4-9
Parts electronics analyzer Orbitrap-2 (P/N 210 0160) ........................... 4-9
Parts electronics main supply Orbitrap (P/N 208 1040) ...................... 4-10
Parts ETD Option for Orbitrap XL (P/N 072 3890) .......................... 4-11
Parts ETD Upgrade kit for Orbitrap XL (P/N 124 1480) ................... 4-11
Parts Upgrade kit Orbitrap XL to ETD (P/N 124 4690) .................... 4-11
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Tables
ETD unit mechanics (P/N 123 9920) ................................................. 4-12
Parts for transfer tube with flatapole for ETD (P/N 121 7000) ........... 4-12
Parts Housing HCD/ETD (P/N 123 1780) ........................................ 4-12
Mounting parts ETD (P/N 123 9300) ................................................ 4-13
Pfeiffer - Kit for ETD (P/N 124 1510) ............................................... 4-13
ILMVAC - Kit for ETD (P/N 124 1520) ........................................... 4-13
Springer - Kit for ETD (P/N 124 1530) ............................................. 4-14
Mounting parts - Kit for ETD (P/N 124 1540) .................................. 4-14
Parts KIT_ETD-ELECTRONICS (P/N 210 8880) ........................... 4-14
ETD upgrade from LTQ XL (P/N OPTON-97103) .......................... 4-15
Parts Kit, Mechanical Pump, ETD (P/N 98000-0005) ....................... 4-16
Parts Installation Kit Reagent Inlet Module (P/N 98000-62006) ........ 4-16
Parts Inlet Valve Seal Kit (P/N 119265-0003) .................................... 4-16
Parts Filament Assembly DSQ II (P/N 120320-0030) ........................ 4-16
ETD Reagent Kit (P/N 98000-62008) ............................................... 4-17
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Chapter 1
Functional Description
This chapter provides an overview of the functional elements of the
LTQ Orbitrap XL ETD. It contains the following topics:
Thermo Fisher Scientific
•
“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
•
“ETD System” on page 1-19
•
“Vacuum System” on page 1-28
•
“Gas Supply” on page 1-36
•
“Cooling Water Circuit” on page 1-40
•
“Printed Circuit Boards” on page 1-42
LTQ Orbitrap XL ETD Hardware Manual
1-1
Functional Description
General Description
General Description
LTQ Orbitrap XL ETD is a hybrid mass spectrometer incorporating the
LTQ XL™ linear trap, the Orbitrap™ analyzer, and the ETD Module.
Figure 1-1 shows a front view of the instrument.
System status LEDs of linear trap
System status LEDs of LTQ Orbitrap XL ETD
ETD Module
Orbitrap
Analyzer
Linear Trap
Forepumps cabinet
Figure 1-1.
LTQ Orbitrap XL ETD front view
The LTQ Orbitrap XL ETD consists of five main components (See
Figure 1-2 on page 1-3.), which are described in the following topics:
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LTQ Orbitrap XL ETD Hardware Manual
•
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 higher energy CID experiments.
•
A reagent ion source for enabling post-translational modification
analyses of peptides by Electron Transfer Dissociation.
Thermo Fisher Scientific
LTQ XL
API Ion Source
Orbitrap
Linear Ion Trap
Quadrupole
Mass Filter
C-Trap
HCD Collision Cell
ETD Module
Transfer Multipole
Reagent Ion Source
Orbitrap Mass Analyzer
Figure 1-2.
Schematical view of the LTQ Orbitrap XL ETD
Note The ETD system is also available as an upgrade on new and existing LTQ Orbitrap (only after upgrade to
LTQ Orbitrap XL) and LTQ Orbitrap XL systems. The ETD system is not available for LTQ Orbitrap Discovery
systems. ▲
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1-3
Functional Description
General Description
Mechanical Characteristics
Wheels at the bottom side of the instrument facilitate positioning the
LTQ Orbitrap XL ETD at the intended place in the laboratory.
The mains inlet as well as a power outlet for peripheral devices are
located at the right side of the instrument. The rotary pumps for the
vacuum system of the linear trap and the Orbitrap are hidden under the
linear trap and accessible from the front. The rotary pump for the
ETD Module is accessible after removing the bottom panel of the rear
side. The left side panel and the front panel of the MS portion are
mounted on hinges and the right side panel is removable. The top lid of
the MS portion opens upwards to allow easy access for Field Engineers
from the top. See Figure 1-3. After removing the cables, the top lid of
the ETD Module is also removable to allow accessing its electronic
components.
Figure 1-3.
Top lid of MS portion opened
A stand-alone recirculating water chiller is delivered with the
instrument. It is connected to the right side of the instrument.
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Functional Description
General Description
Specifications
The LTQ Orbitrap XL ETD has the following measuring specifications:
60000 (FWHM) @ m/z 400
with a scan repetition rate of 1 second
Minimum resolution 7500,
maximum resolution 100000 @ m/z 400
Cycle Time
1 scan at 60000 resolution @ m/z 400 per second
Mass Range
m/z 50–2000; m/z 200–4000
Mass Accuracy <3 ppm RMS for 2 h period with external calibration
using defined conditions,
<2 ppm RMS with internal calibration
Dynamic Range >10000 between mass spectra,
>4000 between highest and lowest detectable ion
signal in one spectrum
MS/MS
MS/MS and MSn scan functions
Resolution
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Functional Description
Control Elements
Control Elements
The LTQ Orbitrap XL ETD 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.) The Power LED is directly controlled by the
3 × 230 V input and all other LEDs are controlled by the power
distribution board (Refer to topic “Power Distribution Board” on
page 1-52). 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 XL ETD
LED
Status
Information
Power
Green
Main switch on
Off
Main switch off
Green
Operating vacuum reached
Yellow
Insufficient vacuum or Vacuum Pumps switch off
Green
Communication link between instrument and data system
established
Yellow
Communication link starting up or Vacuum Pumps switch off
Green
System ready
Yellow
FT Electronics switch off or Vacuum Pumps switch off
Blue
Orbitrapis scanning
Off
Orbitrap is not scanning
*
Vacuum
Communication
System*
Detect
* These LEDs are flashing when a system bakeout is performed. See topic “Baking Out the System” on
page 3-4.
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Functional Description
Control Elements
Control Panels
Figure 1-5 shows the right side of the LTQ Orbitrap XL ETD. Located
here are the control panels, switches, and the ports for the external
connections (mains supply, gases, Ethernet communication, and cooling
water). The ETD Module power panel is also accessible from this side.
Power panel of linear trap
Bakeout timer
Cover lid for
bakeout controls
Switches and
control LEDs
ETD Module
power panel
See page 1-22
Main power
switch
Forepumps cabinet
Power connector
Figure 1-5.
Right side of the LTQ Orbitrap XL ETD
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
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Functional Description
Control Elements
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.
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 XL ETD 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.
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LTQ Orbitrap XL ETD Hardware Manual
Circuit breakers of the LTQ Orbitrap XL ETD
Circuit breaker
Ampere
LED
Instrument parts
F1
10
L1
Power Distribution
F2
16
L2
Linear ion trap
F3
10
L3
Multiple socket outlets (Peripherals, LC, heater,
etc.)
Thermo Fisher Scientific
Functional Description
Control Elements
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 XL ETD 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.)
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:
Thermo Fisher Scientific
•
Fans
•
Heater control
•
Power distribution (Refer to the topic “Power Distribution Board”
on page 1-52)
•
Pumps (Refer to the topic “Vacuum System” on page 1-28)
LTQ Orbitrap XL ETD Hardware Manual
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Functional Description
Control Elements
•
Temperature controller (Refer to the topic “Temperature Controller
Board” on page 1-61)
•
Vacuum control
The linear ion trap also remains on because it has a separate Service
switch.
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 XL ETD, the linear ion trap, the vacuum pumps, and
the ETD Module.
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 1-40.) A Teflon® hose connects
the instrument to the nitrogen gas supply. An analogous port is used for
the HCD collision gas supply. Metal tubing connects the instrument
with the helium gas supply. (See also topic “Gas Supply” on page 1-36.)
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Functional Description
Control Elements
Located at the top are two ports for Ethernet cables for connecting the
LTQ Orbitrap XL ETD 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.
Ethernet ports
Power outlet for
peripheral devices
Power connector
Helium gas inlet
Cooling water inlet port
Collision gas inlet
Inlet for nitrogen gas
Figure 1-9.
Cooling water outlet port
External connections to the LTQ Orbitrap XL ETD
The power outlet for peripheral devices is located above the mains
supply port. The outlet provides the mains supply for the ETD Module.
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Functional Description
Linear Ion Trap
Linear Ion Trap
The LTQ Orbitrap XL ETD 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 application of a supplementary RF voltage on the end lenses of the
linear trap allows ions of opposite polarity to be trapped in the same
space at the same time (charge-sign independent trapping – CSIT). This
allows performing ion-ion reactions of previously isolated precursor
cations with ETD reagent anions.
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 1-24 on page 1-31. The LTQ Orbitrap XL ETD
provides power for the linear ion trap – and for the ETD Module.
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.
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Functional Description
Orbitrap Analyzer
Orbitrap Analyzer
This section describes the basic principle of the Orbitrap™ mass
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. Schematical view of the Orbitrap cell and example of a stable
ion trajectory
Measuring Principle
In the mass analyzer shown in Figure 1-10, ions rotate on stable
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 ions’ mass-to-charge ratios m/q and
the instrumental constant k:
w =
q
--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-only quadrupole 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
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LTQ Orbitrap XL ETD Hardware Manual
1-13
Functional Description
Orbitrap Analyzer
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.
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 1-62.) Trap and gate dc voltages are
provided by the ion optic supply board. (See page 1-59.) The
RF voltages to the quadrupole mass filter are supplied by the linear trap.
High voltages to the lenses are provided by the high voltage power
supply board. (See page 1-65.)
Quadrupole
Gate
CLT Trap
Collision Cell
Squeezing in CLT
Pulsing from LTQ
Static
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 C-Trap and the
subsequent lenses, the ion beam converges on the entrance into the
Orbitrap. The lenses form also differential pumping slots and cause
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Functional Description
Orbitrap Analyzer
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.
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-to-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
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Functional Description
Orbitrap Analyzer
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.
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, whereas 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
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Functional Description
Orbitrap Analyzer
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.
Active Temperature Control
Active temperature control is achieved by monitoring temperature
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 1-61.
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 1-41 on page 1-58.
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 XL ETD.
See topic “Cooling Water Circuit” on page 1-40 for further
information.
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Functional Description
HCD Collision Cell
HCD Collision Cell
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. 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 1-36 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 1-59.)
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 XL Getting
Started manual for more information.
To reduce damping of ions by the collision gas (collisional damping), a
potential gradient is applied to the collision cell, such that it transmits
ions at a reliable rate. The direction of the gradient (and the voltage
offset of the cell) can be switched to allow alternation between positive
ion HCD mode, negative ion HCD mode, ETD mode, or auxiliary ion
source mode.
Note ETD reagent anions can efficiently pass through the high pressure
region of the HCD cell. This is an important prerequisite to allow for a
fast switching (i.e. scan to scan) between HCD and
ETD fragmentation, thus making comparative measurements possible.
When compared with the standard LTQ Orbitrap XL,
HCD performance is not in any way compromised by the addition of
the ETD Module. ▲
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Functional Description
ETD System
ETD System
Protein or peptide analyte ions may also be fragmented in the linear trap
by negatively charged reagent ions (fluoranthene radical anions) from
the reagent ion source (ETD Module). These negatively charged ions
deliver electrons to protein or peptide analyte ions and cause them to
fragment at their peptide bonds to produce c and z type fragments
(versus the y and b type fragments produced by CID). The resulting
analyte fragment ions provide another way of analyzing these molecules
as compared to CID and PQD. Electron Transfer Dissociation (ETD)
improves the identification of important post-translational modification
(PTM) for characterization.
Principle of Operation
During a typical ETD MS/MS scan, analyte cations are injected into the
linear trap for subsequent precursor cation isolation. Then,
ETD reagent anions are generated in the CI ion source and are
transferred into the linear trap via RF-only ion guides (transfer
multipoles), the gas-filled HCD collision cell, and the C-Trap. (See
Figure 1-2 on page 1-3.)
The reagent ions pass a quadrupole mass filter1 between C-Trap and
linear trap. This ion guide works as a low pass mass filter to remove the
adduct of the fluoranthene radical and molecular nitrogen at m/z 216.
This adduct favors proton transfer reactions instead of electron transfer.
The application of a supplementary RF voltage on the end lenses of the
linear trap allows ions of opposite polarity to be trapped in the same
space at the same time (charge-sign independent trapping – CSIT).
During ion-ion reactions in the linear trap, electrons are transferred
from the reagent anions to the precursor cations. The resulting product
ions are mass-to-charge (m/z) analyzed in either the linear trap (if speed
and sensitivity are important) or the Orbitrap (if mass resolution and
accuracy are important).
ETD Module
Figure 1-14 on page 1-20 shows the rear side of the ETD Module. It is
mounted to the rear side of the instrument. It consists of the reagent ion
source, ETD Module electronics, ETD Module power supply, ETD
Module forepump, and the hardware that connects the ETD Module to
the mass detectors.
1
The linear trap provides the voltages for the quadrupole mass filter.
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Functional Description
ETD System
Fan filter
Control elements
of inlet valve
Inlet port for
UHP nitrogen
Cabinet for ETD
forepump
Figure 1-14. LTQ Orbitrap XL ETD, rear side
15 14
Labeled components: 1=power module, 2=connector to Interface Board
(Interface Board is behind the ETD Control PCB, item #4), 3=DC HV Supply
PCB, 4=ETD Control PCB, 5=Heater Control PCB, 6=ion gauge,7=inlet valve
solenoid, 8=inlet valve lever in closed (down) position, 9=reagent heater 1,
10=reagent heater 2, 11=ion volume tool handle, 12=guide bar,
13=turbopump, 14=Convectron gauge, 15=vacuum manifold (contains ion
source and ion volume)
Figure 1-15. Rear view of the ETD Module, with major component locations
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Functional Description
ETD System
ETD Ion Optic
Supply Board
Peripherals
Power Outlet
Orbitrap Vacuum System,
see Figure 1-20 on page 1-28
Orbitrap Instrument
Control Board
Heater Control PCB
Interface
Board
Ion Gauge
Power Module
Reagent
Heaters
ETD Control PCB
Ion Source
ETD
Turbopump
Flow
Control
DC HV Supply PCB
ETD Forepump
UHP Nitrogen
Convectron Gauge
3 = Transfer line
4 = Ion volume
Figure 1-16. ETD Module functional block diagram
The following sections describe the major ETD Module components
that are shown in Figure 1-15 on page 1-20 and Figure 1-16.
ETD Power Module
The ETD power module (item #1 in Figure 1-15) receives 220 V, 10 A,
from the peripherals power outlet. See Figure 1-9 on page 1-11. It
distributes appropriate voltages and currents to the ETD components. It
also contains DC power supplies.
ETD Module Power Panel
The external receptacles and switches for the power module are located
on the ETD power module panel at the right side of the ETD Module.
See Figure 1-5 on page 1-7 and Figure 1-17. Power In is connected to
the peripherals power outlet. See Figure 1-9 on page 1-11. Forepump is
a receptacle to power the ETD forepump (220 V AC, 5 A).
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LTQ Orbitrap XL ETD Hardware Manual
1-21
Functional Description
ETD System
ETD Module Service switch
ETD Module Power switch
ETD Module Forepump receptacle
ETD Module Power receptacle
ETD Module Power Panel
Figure 1-17. ETD Power Module panel
The ETD power module panel contains the main breaker and the
service switch for the ETD Module. Use the main breaker to turn on or
off all power to the ETD Module. The service switch turns On or Off
power to all ETD Module components except the turbopump and
forepump. During normal operation the ETD Power switch is left On
and the service switch is left in the Operating Mode position.
ETD Module Interface Board
The ETD Module Interface board (item #2 in Figure 1-15) provides an
electronic interface between the ETD Module and the MS. This board
also allows the power to both the MS and the ETD Module to be
controlled by the MS power control panel switches:
•
The MS Main Power switch controls the power supply to all
components in both the MS and the ETD Module.
•
The MS FT Electronics switch controls the power supply to all mass
spectrometer and ETD Module components except the pumps that
are connected to the MS and the ETD Module.
Note The ability to control the power to both components of the
LTQ Orbitrap XL ETD at one point (the power control panel switches
of the MS) is a safety feature. ▲
ETD Control PCB
The ETD Control PCB (item #4 in Figure 1-15) controls most of the
ETD Module functions. The ETD Control PCB consists of circuits that
control:
•
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LTQ Orbitrap XL ETD Hardware Manual
ETD Module operating logic
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Functional Description
ETD System
•
Ion source (filament, ion source heater, lenses)
•
Heater temperature and readback logic (for reagent heaters, transfer
line heater, and the restrictor oven heater)
•
Reagent gas flow
•
Oven cooling gas control
•
Ion gauge
•
Convectron gauge
The DC HV Supply PCB (item #3 in Figure 1-15) is plugged in to the
ETD Control PCB.
ETD Heater Control PCB
The ETD Module Heater Control PCB (item #6 in Figure 1-15)
contains the power source and temperature sensing circuitry for the four
heaters in the reagent ion source. The heaters are H1 and H2 (the two
reagent heaters, Figure 1-16 on page 1-21, and items #9 and #10 in
Figure 1-15), transfer line heater (#3 in Figure 1-15), and the restrictor
oven heater (not shown in Figure 1-15). The Heater Control PCB
reports temperature information to the heater temperature and readback
logic on the ETD Control PCB. The heater temperature and readback
logic controls how the Heater Control PCB applies power to the
ETD Module heaters.
Nitrogen Flow Control for ETD
The reagent ion source in the ETD Module requires UHP nitrogen.
The UHP nitrogen supply in the laboratory is connected to the
UHP nitrogen port at rear side of the ETD Module. See Figure 1-29 on
page 1-39. The ETD Module contains a digital flow control for
UHP nitrogen (Figure 1-15 on page 1-20). This flow control is
controlled by the ETD Control PCB (item #4 in Figure 1-15).
UHP nitrogen serves two functions in the ETD Module:
•
Thermo Fisher Scientific
As a carrier gas, the nitrogen sweeps the reagent (fluoranthene) from
the vial to the ion source where the reagent radical anions are
formed.
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Functional Description
ETD System
•
As a chemical ionization (CI) vehicle, the nitrogen undergoes
collisions with 70 eV electrons from the filament in the ion volume.
These 70 eV electrons from the filament knock electrons off of the
nitrogen molecules (nitrogen ions are created). The secondary
electrons resulting from these collisions have near thermal kinetic
energies. These thermal electrons are captured by the fluoranthene
to form reagent radical anions that react with the analyte.
Note High-purity nitrogen is used to cool the reagent vials when the
reagent ion source is turned off. ▲
Reagent Heaters
The reagent heaters (items #9 and #10 in Figure 1-15 on page 1-20, H1
andH2 in Figure 1-16 on page 1-21, ) heat the reagent to obtain a
sufficient amount of reagent vapor in the carrier gas. The reagent heaters
are powered by the Heater Control PCB which, in turn, is controlled by
the ETD Control PCB.
The reagent heaters are turned on by selecting the Reagent Ion Source
On check box in the Reagent Ion Source dialog box (Figure 1-18).
Figure 1-18. Reagent Ion Source dialog box
When you deselect the Reagent Ion Source On check box, the reagent
heaters and filament to immediately turn off and the reagent ion source
goes into Standby mode.
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Functional Description
ETD System
Note When the reagent ion source is placed in Off mode, cooling
nitrogen (high-purity nitrogen) will turn on. This is confirmed by an
audible rush (hissing noise) of nitrogen from the reagent ion source area
in the back of the ETD Module. This is normal operation. See also
topic “Turning Off the Reagent Ion Source: What to Expect” on
page 2-14. ▲
Warning When the reagent ion source is in Off mode, the restrictor
oven, the transfer line, and the ion source remain at 160 °C. ▲
The nitrogen cooling gas turns off when the reagent heaters reach 70 °C.
If it is necessary to install or replace the reagent vials, follow the
procedure in topic “Changing the Reagent Vials” on page 3-48.
Note The rushing or hissing noise of the nitrogen coming from the back
of the ETD Module will stop when the cooling nitrogen turns off. ▲
Warning Do not attempt to handle the vials or vial holders when the
cooling nitrogen stops. They are still too hot to handle when the cooling
nitrogen stops at a vial temperature of 70 °C. Follow the procedures in
topic “Changing the Reagent Vials” on page 3-48 if it is necessary to
install or replace the reagent vials. ▲
When the reagent heaters are in Standby mode, they are immediately
turned on by selecting the Reagent Ion Source On check box
(Figure 1-18). When starting from room temperature, it takes up to ten
minutes for the reagent heaters and vials to stabilize at 108 °C and
reagent to delivered to the ion source.
Note When you switch on a cold reagent ion source, the Tune Plus
software warns you that the vial temperature is not sufficient. The
filament is automatically switched on after the temperature has
stabilized. ▲
On
Thermo Fisher Scientific
Off
Standby
When you click the Standby button in the Tune Plus window (shown
in the left margin), you initiate a Standby process. It delays turning off
the reagent heaters and the start of nitrogen cooling for one hour after
the system is placed in Standby. This method of placing the system in
Standby permits a quick return to operation after a break (lasting one
hour or less) rather than waiting up to ten minutes for the heaters to
return to temperature and reagent delivery to be fully restored.
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Functional Description
ETD System
In summary:
•
The reagent heaters turn off immediately when the Reagent Ion
Source On check box is deselected in the Reagent Ion Source dialog
box. (See Figure 1-18 on page 1-24.)
•
The reagent heaters turn off one hour after the system is placed in
Standby by clicking the Standby button in the Tune Plus window.
Reagent Ion Source
The ion source (Figure 1-15 on page 1-20 and inside of the vacuum
manifold, see item #14 in Figure 1-15) is where the reagent ions are
formed. The ion source contains the filament, the reagent ion volume,
and the ion source heater. The filament is the source of electrons that
react with the reagent to form reagent ions. The reagent ion volume is
the space where this reaction takes place. See Figure 1-19. The ion
source heater is controlled by the ETD Control PCB.
Filament
Changeable Ion Volume
Heated Transfer Line
Fused Silica
Heated Dual Restrictor
Enclosure
Figure 1-19. Reagent ion source schematics
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Functional Description
ETD System
The reagent ion source contains two reagent vials, CI/carrier gas
(nitrogen) handling hardware and flow restrictors, the ion volume and
filament, ion optics, and heaters for these components. The flow
restrictors keep the internal pressure of the reagent vials below
atmospheric pressure. This prevents the contents of the reagent vials
from being expelled to the laboratory atmosphere.
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LTQ Orbitrap XL ETD Hardware Manual
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Functional Description
Vacuum System
Vacuum System
Figure 1-20 shows a schematical overview of the Orbitrap vacuum
system.
HCD Housing
UHV Chamber
Vacuum Chamber
LTQ XL
ETD Module
Vacuum System,
see Figure 1-16 on page 1-21
Turbopump TMH 071
(TMP 4)
Cold Ion Gauge
Pirani Gauge
Turbopump TMH 071 Turbopump TMU 262 Turbopump TMH 071
(TMP 2)
(TMP 3)
(TMP 1)
Forepump
Forepump
Figure 1-20. Schematical view of Orbitrap vacuum system (CLT compartment and Orbitrap chamber not shown)*
* For an abridged version of the parts list, see Table 4-7 on page 4-4.
The LTQ Orbitrap XL ETD has the following vacuum compartments:
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LTQ Orbitrap XL ETD Hardware Manual
•
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)
Thermo Fisher Scientific
Functional Description
Vacuum System
•
Orbitrap chamber (pumped by a 210 L/s – for N2 – water-cooled
turbopump TMU 262, TMP 3, manufacturer: Pfeiffer)
•
HCD housing (pumped by a water-cooled 60 L/s turbopump
TMH 071, TMP 4, manufacturer: Pfeiffer)
The forepumps of the linear trap provide the forevacuum for the
turbopumps TMP 1 to TMP 4.
Turbopumps
All parts of the system except for the Orbitrap analyzer are mounted in a
aluminum vacuum chamber that is evacuated by a 60 L/s turbopump
(TMP 1, see Figure 1-21). 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 1-21. 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 1-22 on page 1-30).
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 1-22). All turbopumps are equipped with TC 100
control units (manufacturer: Pfeiffer).
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1-29
Functional Description
Vacuum System
Preamplifier
HCD housing
Cooling water
supply for Peltier
element
Cold ion
gauge
Turbopump
TMU 262
(TMP 3)
Turbopump TMH 071
(TMP 2)
Figure 1-22. Vacuum components on the right instrument side
A tube, which contains the transfer multipole (flatapole), connects the
HCD housing to the ETD Module. This part of the instrument is
evacuated by a 60 L/s UHV turbopump (TMP 4, see Figure 1-23) at
the bottom of the HCD housing.
ETD tube
HCD housing
CLT RF Unit housing
Turbopump TMP 4
Figure 1-23. ETD mechanics
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Functional Description
Vacuum System
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.
ETD Module Turbopump
A separate turbopump (Edwards EXT70H) provides the high vacuum
for the ETD reagent ion source. See Figure 1-15 on page 1-20. It is
backed up by a dedicated rotary vane pump at the bottom of the
ETD Module. See Figure 1-25 on page 1-33. This turbopump contains
no user-serviceable parts.
Forevacuum Pumps of the Linear Trap
The rotary vane pumps from the linear trap serve as forepumps for the
three smaller turbopumps (TMP 1, TMP 2, and TMP 4). 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 1-24.
Oil mist filters
Forepumps
Figure 1-24. 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 3-12 on
instructions about returning the collected oil to the forepumps.
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Functional Description
Vacuum System
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! ▲
Leave the 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.
Forevacuum Pump of the ETD Module
A rotary vane pump (BOC Edwards RV 3) provides the forevacuum for
the ETD turbopump. It is located in a cabinet at the bottom of the
ETD Module. The forepump is equipped with an oil mist filter and
stands on a drip pan. See Figure 1-25 on page 1-33.
An exhaust hose connects the forepump to the exhaust system in the
laboratory. A forevacuum tube connects the ETD forepump to the
ETD turbopump. The forepump electrical cord is plugged into the
Forepump receptacle on the ETD Module power panel. See Figure 1-17
on page 1-22.
For maintenance instructions for the ETD forepump, see topic
“Maintenance of the ETD Forepump” on page 3-5 and the manual that
came with the forepump.
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Functional Description
Vacuum System
Exhaust hose
Forevacuum tube
Oil mist filter
Drip pan
Forepump electrical cord
Figure 1-25. Forepump for ETD Module
Vacuum System Controls
The power distribution board controls all turbopumps via voltage levels.
Refer to topic “Power Distribution Board” on page 1-52. 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 1-50.) The turbopump of the linear ion trap
and the ETD turbopump have individual controllers.
Vacuum Gauges
The vacuum is monitored by several vacuum gauges:
•
Thermo Fisher Scientific
The forevacuum of the LTQ Orbitrap XL ETD is monitored by an
Active Pirani gauge (TPR 280, manufacturer: Pfeiffer) connected to
the LTQ Orbitrap XL ETD forevacuum line. See Figure 1-21 on
page 1-29.
LTQ Orbitrap XL ETD Hardware Manual
1-33
Functional Description
Vacuum System
•
The high vacuum of the LTQ Orbitrap XL ETD is monitored by a
Cold Ion Gauge (IKR 270, manufacturer: Pfeiffer) connected to the
UHV chamber. See Figure 1-22 on page 1-30. Because the gauge
would be contaminated at higher pressures, it is turned on only
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.
•
Two dedicated vacuum gauges monitor the vacuum in the
ETD Module. A Convectron gauge (see Figure 1-15 on page 1-20
and Figure 1-16 on page 1-21) ) monitors the pressure in the ETD
forevacuum line and an ion gauge (see Figure 1-15) monitors the
pressure in the reagent ion source. Table 1-3 shows typical pressure
readings in the ETD Module.
Table 1-3.
Typical pressure readings in the ETD Module
Conditions
Convection Gauge Reading
(foreline, capillary skimmer region)
Ion Gauge Reading
(analyzer region)
CI gas pressure set
to 20 psi
0.1–0.01 Torr
20–35×10-5 Torr
The vacuum gauges of the LTQ Orbitrap XL ETD are connected to the
power distribution board that directly responds to the pressure values.
(Refer to the topic “Power Distribution Board” on page 1-52.) The
analog values are digitized by the instrument control board. (Refer to
the topic “Instrument Control Board” on page 1-50.) 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 Pumps & Electronics switch is switched On, the pumps of
the linear ion trap and the LTQ Orbitrap XL ETD are run up. The
Pirani gauge (see above) controls the LTQ Orbitrap XL ETD 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).
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Functional Description
Vacuum System
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 XL ETD 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 1-52.) 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 1-38.)
Vacuum System Heating during a System Bakeout
After the system has been open to the atmosphere (e.g. for maintenance
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.
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LTQ Orbitrap XL ETD Hardware Manual
1-35
Functional Description
Gas Supply
Gas Supply
This section describes the gas supplies for the mass analyzers and the
reagent ion source of the LTQ Orbitrap XL ETD.
Gas Supply for the Mass Analyzers
Figure 1-26 shows a schematical view of the gas supply for the
instrument.
UHP Nitrogen (N2) for
Reagent Ion Source
Nitrogen (N2) for CLT
HCD collision gas (N2/Argon)
Helium (He)
ETD Module
Connection to Power
Distribution Board
Gas flow
dividers
Linear Trap
Three way valve
Port 3: blind
Port 2: OUT
Port 1: IN
Analyzer
Turbopump TMH 071
Turbopump TMU 262
CLT
Turbopump TMH 071
Capillaries
Cooling Gas
N2 venting
Turbopump TMH 071
Collision Cell
Vent valve
Figure 1-26. Schematical view of the gas supply*
* For parts lists of the gas supply, refer to Table 4-10 on page 4-5 and to Table 4-30 on page 4-14.
The mass analyzers use at least two gases for operation:
•
The linear trap requires high-purity (99%) nitrogen for the
API sheath gas and auxiliary/sweep gas. The Orbitrap uses
high-purity nitrogen as collision gas (bath gas) for the curved linear
trap and the HCD collision octapole. The ETD system uses
high-purity nitrogen for cooling the reagent vials when the reagent
ion source is turned off.
Note In addition to high-purity nitrogen, the LTQ Orbitrap XL ETD
requires ultra-high purity nitrogen. See topic “Gas Supply of the
Reagent Ion Source” on page 1-39 for details. ▲
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Functional Description
Gas Supply
•
The linear trap requires ultra-high purity (99.999%) helium for the
collision gas.
•
In case 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. High purity nitrogen gas
and HCD collision gas are both led via Teflon tubing to the right side of
the LTQ Orbitrap XL ETD.
Part of the high purity 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 is also directed through Teflon tubing to the ETD Module to
be used for cooling the reagent vials when the reagent ion source is
turned off.
CLT RF Main board housing
Temperature controller board
Figure 1-27. Valve for HCD collision gas
Nitrogen gas pressure to the C-Trap is kept constant by using an
“open-split” interface (gas flow divider, see Figure 1-28 on page 1-38). It
contains a capillary line from the nitrogen line of the instrument to
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LTQ Orbitrap XL ETD Hardware Manual
1-37
Functional Description
Gas Supply
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” PEEK tubing).
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” PEEK tubing).
The HCD collision gas valve is located at the left instrument side next
to the temperature controller board. See Figure 1-27 on page 1-37. It is
switched by the software via the power distribution board. (See
page 1-52.)
Vent Valve of the Linear Ion Trap
If the system and pumps are switched off, the system is vented. The vent
valve is controlled by the linear ion trap. The LTQ XL Hardware Manual
contains further information about the vent valve.
Nitrogen pressure regulator
Gas flow dividers
Figure 1-28. Nitrogen pressure regulator and gas flow dividers
1
The third port of the valve is closed.
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Functional Description
Gas Supply
The instrument is vented with high purity nitrogen from the same
tubing that supplies the LTQ XL sheath gas. See Figure 1-26 on
page 1-36. 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 XL ETD. See
Figure 1-28.
Gas Supply of the Reagent Ion Source
In addition to high purity nitrogen for cooling, the reagent ion source of
the LTQ Orbitrap XL ETD uses ultra high purity (UHP, 99.995%)
nitrogen gas as carrier gas and chemical ionization (CI) vehicle. The
UHP nitrogen supply of the laboratory is connected to the inlet port at
the rear side of the instrument. See Figure 1-29.
Figure 1-29. UHP nitrogen port at the ETD Module
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LTQ Orbitrap XL ETD Hardware Manual
1-39
Functional Description
Cooling Water Circuit
Cooling Water Circuit
Figure 1-30 on page 1-40 shows a schematical view of the cooling water
circuit in the LTQ Orbitrap XL ETD. 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 4 → TMP 2. Then it
passes through the heating element (Peltier element) that maintains
(±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.
Input
Output
Recirculating
chiller
Power Distribution Board
Linear Trap
Heating element
(Peltier element)
Turbopump
TMU 262
Analyzer
Flow control sensor
Turbopump
TMH 071
Peltier element Central Electrode Turbopump TMH 071 Turbopump Water cooler for
Power Supply Box (ETD/HCD housing) TMH 071 TMH 071 (2x)
Figure 1-30. 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.
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Functional Description
Cooling Water Circuit
Recirculating Chiller
A recirculating chiller (NESLAB ThermoFlex™ 900) is delivered with
the instrument, making the LTQ Orbitrap XL ETD 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 3-61. See also the
manufacturer’s manual for the chiller.
Properties of Cooling Water
The water temperature is not critical, but should be in the range of 20 to
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:
Resistivity:
Total dissolved solids:
pH:
<0.05 ppm
1–3 MΩ/cm
<10 ppm
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! ▲
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Functional Description
Printed Circuit Boards
Printed Circuit Boards
The LTQ Orbitrap XL ETD 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 electronic boards in
the MS portion of the LTQ Orbitrap XL ETD. For each board, its
respective location and function are given. If applicable, the diagnostic
LEDs on the board are described. For a description of the printed circuit
boards in the ETD Module, see topic “ETD Module” on page 1-19.
The electronics of the LTQ Orbitrap XL ETD 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 XL ETD diagnostics, which is accessible from the Tune
Plus window. ▲
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Functional Description
Printed Circuit Boards
Linear Ion Trap Electronics
The linear ion trap is connected to the LTQ Orbitrap XL ETD main
power switch. The linear ion trap has a sheet metal back cover.
Figure 1-31 shows the electronic connections at the rear side of the
linear trap.
Cold Ion Gauge
Figure 1-31. Electronic connections to linear trap (covers removed)
The linear ion trap electronics has two connections with the
LTQ Orbitrap XL ETD electronics:
•
Data communication with the internal computer of the
LTQ Orbitrap XL ETD. Refer to the topic “Electronic Boards at the
Right Side of the Instrument” on page 1-44.
•
Signal communication (SPI bus) with supply information for the
instrument control board. Refer to the topic “Instrument Control
Board” on page 1-50.
For further information about the linear ion trap electronics, refer to the
LTQ XL Hardware Manual.
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LTQ Orbitrap XL ETD Hardware Manual
1-43
Functional Description
Printed Circuit Boards
Electronic Boards at the Right Side of the Instrument
Figure 1-32 shows the parts of the instrument when the right side panel
is opened. A transparent cover protects the lower part.
ETD Ion Optic Supply
board housing
Preamplifier
Computer housing
(data acquisition
unit)
Instrument Control
board housing
Power Supply 1
board
Power Distribution
board
Ground wire for
side panel
Figure 1-32. 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 1-32. 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!
ETD Ion Optic Supply Board
The ETD Ion Optic Supply board (P/N 210 8920)1 is mounted on top
of the data acquisition unit. See Figure 1-33. It supplies the RF voltage
and the dc voltages for the ETD Module: an RF voltage with dc offset,
three dc voltages with ±250 V, and a dc voltage with ±12 V.
1
Part number of complete unit.
1-44
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Figure 1-33. ETD Ion Optic Supply board
The diagnostic LEDs on the ETD ion optic supply board are listed in
Table 1-4 on page 1-45. The positions of the diagnostic LEDs on the
board are indicated by white rectangles in Figure 1-34.
Table 1-4.
Thermo Fisher Scientific
Diagnostic LEDs on the ETD Ion Optic Supply board
No.
Name
Color
Description
Normal Operating
Condition
LD1
+275 V
Green
+275 V input voltage present
On
LD2
-275 V
Green
-275 V input voltage present
On
LD3
RF Supply
Green
RF input voltage (22 V) present
On
LD4
+24 V
Green
+24 V input voltage present
On
LD5
+15 V
Green
+15 V input voltage present
On
LD6
-15 V
Green
-15 V input voltage present
On
LD7
RF1_ON
Blue
RF-generator switched on
On/Off, depending on
active application
LTQ Orbitrap XL ETD Hardware Manual
1-45
Functional Description
Printed Circuit Boards
Preamplifier
Figure 1-34 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 1-34. 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 1-5 on
page 1-47. The positions of the diagnostic LEDs on the board are
indicated by white rectangles in Figure 1-34.
1
Part number of complete unit.
1-46
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Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Table 1-5.
Diagnostic LEDs on the Preamplifier board
No.
Name
Color
Description
Normal Operating
Condition
LD1
Overload
Yellow
RF output is overloaded
Off
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
Yellow
RF inputs are shortened
(protection)
On, off during
Detect
Internal Computer
Figure 1-35 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.
ETD Ion Optic Supply
board housing
Computer housing with
Data Acquisition Analog
board, Data Acquisition
Digital PCI board, and
Power Supply 2 board
Instrument Control board housing
Figure 1-35. Data Acquisition unit
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.
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LTQ Orbitrap XL ETD Hardware Manual
1-47
Functional Description
Printed Circuit Boards
Data Acquisition Digital PCI Board
Figure 1-36 shows the data acquisition digital PCI board
(P/N 206 0501). It is an add-on board to the internal computer. (See
Figure 1-35 on page 1-47.)
Figure 1-36. 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.
Precision timing is derived from the data acquisition analog board and
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 XL ETD 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 1-6 on page 1-49 show the status of
the board. The position of the LEDs on the board is indicated by a
white rectangle in Figure 1-36.
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Functional Description
Printed Circuit Boards
Table 1-6.
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
+2.5 V
Green
+2.5 V voltage present
On
Data Acquisition Analog Board
Figure 1-37 shows the data acquisition analog board (P/N 206 4150).
Figure 1-37. Data Acquisition Analog board
This board is an add-on board to the mainboard of the internal
computer. See Figure 1-35 on page 1-47. 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 1-7 on page 1-50 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 1-37.
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LTQ Orbitrap XL ETD Hardware Manual
1-49
Functional Description
Printed Circuit Boards
Table 1-7.
Diagnostic LEDs of the Data Acquisition Analog board
Name
Color
Description
Normal Operating Condition
+5 V
Green
+5 V voltage present
On
-5 V
Green
-5 V voltage present
On
+3.3 V
Green
+3.3 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 1-35 on page 1-47.
The diagnostic LEDs listed in Table 1-8 show the status of the voltages
applied to the board.
Table 1-8.
Diagnostic LEDs of the Power Supply 2 board
Name
Color
Description
Normal Operating Condition
+5.1 V
Green
+5.1 V voltage present
On
-5.1 V
Green
-5.1 V voltage present
On
+3.3 V
Green
+3.3 V voltage present
On
Instrument Control Board
Figure 1-38 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 XL ETD 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 1-52.) Turbopumps (Refer to
the topic “Vacuum System” on page 1-28.) are attached to a serial port
connector and this is connected via the signal lines to the linear ion trap.
1-50
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Diagnostic LEDs
Status LEDs
Figure 1-38. Instrument Control board
The diagnostic LEDs listed in Table 1-9 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 1-38.
Table 1-9.
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 1-10 on page 1-52. The position of the status LEDs on the board
is indicated by a white oval in Figure 1-38 on page 1-51.
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Functional Description
Printed Circuit Boards
Table 1-10. 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
board enabled
On
6.3
Connection to internal computer and LTQ XL
SPI bus enabled
On
6.4
Orbitrap SPI bus enabled
On
Flashing on error
Power Distribution Board
Figure 1-39 on page 1-52 shows the power distribution board
(P/N 206 2130)1. It is located at the bottom of the right side of the
instrument.
Figure 1-39. Power Distribution board
1
Part number of complete unit.
1-52
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
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 1-11 on page 1-54) 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 1-39 on
page 1-52.
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 1-50.)
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 1-39 on page 1-52.
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LTQ Orbitrap XL ETD Hardware Manual
1-53
Functional Description
Printed Circuit Boards
Table 1-11. 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
instrument control board
CAN bus problem or
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
failure
Vacuum gauge defective
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 XL ETD Off
Forevacuum > 10-2 mbar
Ion Gauge OK
Penning
LTQ Orbitrap XL ETD failure
Control signal < 0.5 V
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
B
System reset has occured
Micro controller idle
* An
error of turbopump 3 is indicated by an LED directly located on the pump controller. An error of
turbopump 4 is indicated in the software.
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Functional Description
Printed Circuit Boards
Depending on user actions, the power distribution is switched to various
working modes by the hardware. See Table 1-12.
Table 1-12. Working modes of the Power Distribution board
Action
Consequences
a.
Main switch off
Complete system including linear ion trap and multiple
socket outlets (ETD Module, for example) are without
power
b.
Vacuum Pumps
switch off
Everything is switched off
c.
FT Electronics
switch off
All components are switched off with exception of the
following ones:
• Heater control
• Multiple socket outlets
• Power distribution board
• Pumps
• Vacuum control
• LTQ XL (has a separate Service switch)
Table 1-13 shows the possible operating states of the power distribution.
Table 1-13. Operating states of the Power Distribution board
Action
Consequences
1.
Main switch on, Vacuum Pumps switch
off
Everything is switched off
2.
Vacuum Pumps switch on and FT
Electronics switch on
System starts up: pumps and
electronics switched on
3.
Check linear ion trap and
LTQ Orbitrap XL ETD forevacuum pumps:
If not ok: switch off system and light
error LED*; power distribution remains
switched on
10-0 mbar after 30 s.
Thermo Fisher Scientific
4.
After the system has started, the Pirani
gauge returns a vacuum < 10-2 mbar and
both turbopumps reach 80% rotation
speed
Switch on Penning gauge
5.
Vacuum and 80% rotation speed of
turbopumps not reached after preset
time (< 8 min, otherwise the pumps
automatically switch off).
Switch off system (including linear ion
trap) and light error LED*; power
distribution remains switched on
6.
One or more vacuum gauges defective
(control signal < 0.5 V).
Light error LED only, otherwise ignore
LTQ Orbitrap XL ETD Hardware Manual
1-55
Functional Description
Printed Circuit Boards
Table 1-13. Operating states of the Power Distribution board, continued
7.
Action
Consequences
After the operating status is reached,
the pressure at one gauge exceeds the
security threshold for more than the
preset time period:
System is shut down with exception of
power distribution (light error LED).
• Pirani gauge LTQ Orbitrap XL ETD
>10-1 mbar
Rebooting of the system by switching
off/on of the main switch.
• Penning gauge LTQ Orbitrap XL ETD
>10-3 mbar
• Pirani gauge LT forepump >10-1 mbar
8.
9.
Rotation speed of a turbopump falls
below 80%
Shut down system (see 7.);
Service switch linear ion trap off
Linear ion trap electronics switched
off, pumps keep on running;
light LED* of corresponding pump.
LTQ Orbitrap XL ETD without data link,
keeps on running
10.
FT Electronics switch
LTQ Orbitrap XL ETD off
LTQ Orbitrap XL ETD electronics
switched off, pumps keep on running;
LTQ Orbitrap XL ETD without data link,
keeps on running
11.
Failure of linear ion trap or
LTQ Orbitrap XL ETD (e.g. fuse is
opened).
If the vacuum in one part deteriorates,
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 1-40 on page 1-57 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 1-59.) and the instrument
control board. (Refer to topic “Instrument Control Board” on
page 1-50.)
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Functional Description
Printed Circuit Boards
Figure 1-40. Power Supply 1 board
Warning Parts of the power supply 1 board are at high voltage. ▲
The diagnostic LEDs listed in Table 1-14 show the status of the voltages
applied to the board. The position of the LEDs on the board is
indicated by the white rectangles in Figure 1-40.
Table 1-14. 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
Thermo Fisher Scientific
+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
LTQ Orbitrap XL ETD Hardware Manual
1-57
Functional Description
Printed Circuit Boards
Electronic Boards on the Left Side of the Instrument
Figure 1-41 shows the left side of the instrument with the panel opened.
This side of the instrument contains mostly boards that are part of the
Orbitrap control.
Ion Optic Supply board housing
Central Electrode Pulser
board housing
CLT RF Main board housing
with RF Off & Feedback board
and CLT Offset Connector
Temperature
Controller board
High Voltage Power Supply
board housing
Central Electrode
Power Supply board
housing
Figure 1-41. Electronic boards on the left side of the instrument
The main components on this side are described starting from the top.
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Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Ion Optic Supply Board
Figure 1-42 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 XL ETD.
It has an RF detector for the RF output control. The board also provides
the trap voltage, the gate voltage, and the reflector dc voltages. See topic
“Orbitrap Analyzer” on page 1-13 for further information.
Furthermore, the board provides the voltages for the HCD collision cell.
See page 1-18.
Figure 1-42. Ion Optic Supply board
The diagnostic LEDs listed in Table 1-15 on page 1-60 show the status
of applied voltages to the board. The position of the LEDs on the board
is indicated by white rectangles in Figure 1-42.
Warning Parts of the board are at high voltage. ▲
1
Part number of complete unit.
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LTQ Orbitrap XL ETD Hardware Manual
1-59
Functional Description
Printed Circuit Boards
Table 1-15. Diagnostic LEDs of the Ion Optic Supply board
No.
Name
Color
Description
Normal Operating
Condition
LD1
+275 V
Green
+275 V Input voltage
present
On
LD2
-275 V
Green
-275 V Input voltage
present
On
LD3
+29 V
Green
+29 V Input voltage present
On
LD5
+15 V
Green
+15 V Input voltage present
On
LD6
-15 V
Green
-15 V Input voltage present
On
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 1-43. Central Electrode Pulser board
1
Part number of complete unit.
1-60
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
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.
The diagnostic LEDs listed in Table 1-16 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 white rectangles in Figure 1-43
on page 1-60.
Table 1-16. Diagnostic LEDs of the Central Electrode Pulser board
No.
Name
Color
Description
Normal Operating 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 1-41 on page 1-58. 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 1-44. Temperature Controller board
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LTQ Orbitrap XL ETD Hardware Manual
1-61
Functional Description
Printed Circuit Boards
The diagnostic LEDs listed in Table 1-17 show the status of the voltages
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 1-44.
Table 1-17. Diagnostic LEDs of the Temperature Controller board
No.
Name
Color
Description
Normal Operating
Condition
LD1
+15 V
Green
+15 V Input voltage present
On
LD2
-15 V
Green
-15 V Input voltage present
On
LD3
TEC >60C
Yellow
Temperature of cold side Peltier
element above 60 ºC
Off
LD4
Unit >60C
Yellow
Temperature of UNIT heat sink
above 60 ºC
Off
LD5
Reg Off
Yellow
Control switched off
Off
LD6
No Term
Yellow
SPI bus termination board
missing
Off
LD7
SDT enable
Green
Interface has been addressed
and sends/receives data
Flashing on SPI bus
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
>0 V
Off when adjusted
LD12
UR<0
Yellow
Summation voltage controller
<0 V
Off when adjusted
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 (CLT) 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 1-41 on page 1-58.
This board provides an RF voltage (“Main RF”) for the curved linear
trap. It allows switching off the RF and simultaneous pulsing of each
CLT electrode. See topic “Orbitrap Analyzer” on page 1-13 for further
information. The board communicates with the instrument control
board via an SPI bus.
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Functional Description
Printed Circuit Boards
CLT Offset Connector
RF Off & Feedback board
Figure 1-45. CLT RF unit (cover removed)
The diagnostic LEDs listed in Table 1-18 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 white rectangles in Figure 1-45.
Table 1-18. Diagnostic LEDs of the CLT RF Main board
No.
Name
Color
Description
Normal Operating
Condition
LD1
NO TERM
Yellow
SPI bus termination board
missing
Off
LD2
SEND
Yellow
Interface has been addressed and
sends/receives data
Flashing on SPI-bus
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
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 1-45
on page 1-63.
The CLT Offset connector (P/N 211 0470), which removes interfering
signals from the circuit, is also mounted in the housing.
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LTQ Orbitrap XL ETD Hardware Manual
1-63
Functional Description
Printed Circuit Boards
Central Electrode Power Supply Board
The central electrode power supply board (P/N 207 9611)1 is mounted
in a housing on the bottom left side of the instrument. See Figure 1-46.
Figure 1-46. 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
Part number of complete unit.
1-64
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Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
The diagnostic LEDs listed in Table 1-19 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 1-46.
Table 1-19. Diagnostic LEDs of the Central Electrode Power Supply board
No.
Name
Color
Description
Normal Operating
Condition
LD1
OVL DE HI-
Yellow
Negative side of Deflector High
Supply has been overloaded
Off when HV is
switched on
LD2
OVL DE HI+
Yellow
Positive side of Deflector High
Supply has been overloaded
Off when HV is
switched on
LD3
No Term
Red
SPI bus termination board
missing
Off
LD4
Send
Yellow
Interface has been addressed
and sends/receives data
Flashing on SPI bus
data transfer
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
Electrode Low Supply has been
overloaded
Off when HV is
switched on
LD8
OVL CE LO-
Yellow
Negative side of Central
Electrode Low Supply has been
overloaded
Off when HV is
switched on
LD9
OVL CE HI+
Yellow
Positive side of Central
Electrode High Supply has been
overloaded
Off when HV is
switched on
LD10
OVL CE HI-
Yellow
Negative side of Central
Electrode High Supply has been
overloaded
Off when HV is
switched on
LD11
OVL DE LO+
Yellow
Positive side of Deflector Low
Supply has been overloaded
Off when HV is
switched on
LD12
OVL DE LO-
Yellow
Negative side of Deflector Low
Supply has been overloaded
Off when HV is
switched on
LD13
HV ON
Green
High voltage switched on
On when HV is
switched on
High Voltage Power Supply Board
The high voltage power supply board (P/N 207 7991)1 is mounted in a
housing on the bottom left side of the instrument. See Figure 1-41 on
page 1-58. This board provides five dc voltages for the ion optics of the
LTQ Orbitrap XL ETD. Two voltages supply the lenses of the
instrument. Three voltages are applied to the RF CLT main board to be
1
Part number of complete unit.
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1-65
Functional Description
Printed Circuit Boards
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 1-47. High Voltage Power Supply board (cover removed)
The diagnostic LEDs listed in Table 1-20 on page 1-67 show the
operating states of the board. The position of the LEDs on the board is
indicated by the white rectangles in Figure 1-47.
1-66
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Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Table 1-20. Diagnostic LEDs of the High Voltage Power Supply board
No.
Name
Color
Description
Normal Operating
Condition
LD1
NO TERM
Red
SPI bus termination board
missing
Off
LD2
SEND
Yellow
Interface has been addressed
and sends/receives data
Flashing on SPI bus
data transfer
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 1-48.
SPI bus termination board
Figure 1-48. High Voltage Power Supply board with SPI Bus Termination
board
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LTQ Orbitrap XL ETD Hardware Manual
1-67
Chapter 2
Basic System Operations
Many maintenance procedures for the LTQ Orbitrap XL ETD system
require that the MS detector be shut down. In addition, the
LTQ Orbitrap XL ETD 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:
Thermo Fisher Scientific
•
“Shutting Down the System in an Emergency” on page 2-2
•
“Placing the LTQ Orbitrap XL ETD in Standby Condition” on
page 2-4
•
“Shutting Down the LTQ Orbitrap XL ETD Completely” on
page 2-7
•
“Starting Up the System after a Shutdown” on page 2-9
•
“Resetting the System” on page 2-12
•
“Resetting the Tune and Calibration Parameters to their Default
Values” on page 2-13
•
“Turning Off the Reagent Ion Source: What to Expect” on
page 2-14
LTQ Orbitrap XL ETD Hardware Manual
2-1
Basic System Operations
Shutting Down the System in an Emergency
Shutting Down the System in an Emergency
If you need to turn off the MS detector in an emergency, place the main
power switch (located on the power panel at the right side of the
LTQ Orbitrap XL ETD) in the Off (0) position. This turns off all
power to the instrument, including the linear ion trap, multiple socket
outlets, 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 Instrument” on page 2-7 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 Case of a Main Failure
A main power failure has the same consequence as switching off via the
main power switch. If the power is available again, the system starts up
automatically: the pumps are switched on and the instrument is
pumped down. If the system has been vented during the mains failure, it
is necessary to bake out the system to obtain the operating vacuum.
Refer to the topic “Baking Out the System” on page 3-4.
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Thermo Fisher Scientific
Basic System Operations
Shutting Down the System in an Emergency
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
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. ▲
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LTQ Orbitrap XL ETD Hardware Manual
2-3
Basic System Operations
Placing the LTQ Orbitrap XL ETD in Standby Condition
Placing the LTQ Orbitrap XL ETD in Standby Condition
The LTQ Orbitrap XL ETD system should not be shut down
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.
First place the ETD Module in Standby condition and then place the
mass spectrometer in Standby condition according to the procedures
that follow.
Placing the ETD Module in Standby Condition
To place the ETD Module in Standby condition, do the following:
1. If the Tune Plus window is not already open, choose Start >
Programs > Thermo Instruments > LTQ > LTQ Tune from the
taskbar. The Tune Plus window will open.
On/Standby button
Figure 2-2.
Reagent Ion Source instrument control icon
Tune Plus window, toolbar
On
Off
Standby
You can determine the state of the MS detector by observing the
state of the On/Off/Standby button on the Control/Scan Mode
toolbar. See Figure 2-2. The three different states of the On/Standby
button are shown at the left.
2. Click the Reagent Ion Source portion of the instrument control
graphic at the top of the Tune Plus window. (See Figure 2-2.) The
Reagent Ion Source dialog box appears. (See Figure 2-3.)
3. In the Reagent Ion Source dialog box, deselect the Reagent Ion
Source On box to place the Reagent Ion Source in Standby
condition. See Figure 2-3 on page 2-5. This places the Reagent Ion
Source in Standby condition as indicated by the Actual condition
shown to the right of the Reagent Ion Source On box.
2-4
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Basic System Operations
Placing the LTQ Orbitrap XL ETD in Standby Condition
Figure 2-3.
Reagent Ion Source dialog box with Reagent Ion Source On
box and Actual condition circled
When the reagent ion source is placed in Standby condition, the
filament and vial heaters turn off. Simultaneously, a valve opens to
allow the nitrogen gas to cool the reagent vials. This cooling
nitrogen runs until the reagent vials reach 70 °C. The audible rush
(hissing noise) of nitrogen from the reagent ion source area in the
back of the ETD Module is normal operation.
Warning Install or exchange the reagent vials by following the
procedure in topic “Changing the Reagent Vials” on page 3-48. The
reagent vials will be too hot to touch after the cooling nitrogen turns off
at 70°C. Verify that the reagent vials are cool to the touch before
handling them. ▲
More information about turning on and off the reagent heaters is
given in topic “Reagent Heaters” on page 1-24.
Warning The restrictor, the transfer line, and the ion source heater
operate at 160 °C. Do not attempt to touch them unless the
LTQ Orbitrap XL ETD is shut down (See topic “Shutting Down the
LTQ Orbitrap XL ETD Completely” on page 2-7.) and these heaters
have had sufficient time to cool down to room temperature. ▲
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LTQ Orbitrap XL ETD Hardware Manual
2-5
Basic System Operations
Placing the LTQ Orbitrap XL ETD in Standby Condition
Placing the MS in Standby Condition
Use the following procedure to place the LTQ Orbitrap XL ETD system
in Standby condition:
1. Wait until data acquisition, if any, is complete.
2. Turn off the flow of solvent 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. ▲
On
Off
Standby
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 XL ETD main power switch in the On
position.
2-6
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Thermo Fisher Scientific
Basic System Operations
Shutting Down the LTQ Orbitrap XL ETD Completely
Shutting Down the LTQ Orbitrap XL ETD Completely
The LTQ Orbitrap XL ETD does not need to be shut down completely
if you are not going to use it for a short period of time, such as overnight
or over weekends. Shut down ETD Module and MS system completely
only if you do not want to use them for an extended period or if you
want to perform a maintenance or service procedure.
To shut down the instrument completely, do the following:
1. Place the ETD Module in Standby condition as described in topic
“Placing the ETD Module in Standby Condition” on page 2-4.
2. Shut down the instrument as described in topic “Shutting Down the
Instrument“ below. This also shuts down the ETD Module because
the its power controls are linked to the LTQ Orbitrap XL ETD
power controls through the ETD Module Interface board. See topic
“ETD Module Interface Board” on page 1-22.
Shutting Down the Instrument
Use the following procedure to shut down the LTQ Orbitrap XL ETD
system:
1. Wait until data acquisition, if any, is complete.
2. Turn off the flow of solvent 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 flows of the sheath gas and the
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:
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LTQ Orbitrap XL ETD Hardware Manual
2-7
Basic System Operations
Shutting Down the LTQ Orbitrap XL ETD Completely
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 XL ETD in the
On position.
7. During service or maintenance operations that require opening the
vacuum system of the LTQ XL or LTQ Orbitrap XL ETD, always
put the main switch (main circuit breaker) to the Off position. You
can secure the main switch with a padlock or tie-wrap to prevent
unintended re-powering.
Warning Allow heated components to cool down before you service
them (the ion transfer tube is operated at about 300 °C, for example). ▲
Note If you are planning to perform routine or preventive system
maintenance on the LTQ Orbitrap XL ETD 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. ▲
2-8
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Thermo Fisher Scientific
Basic System Operations
Starting Up the System after a Shutdown
Starting Up the System after a Shutdown
To start up the LTQ Orbitrap XL ETD after it has been shut down, you
need to do the following:
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 it has
established a communication link to the data system. ▲
Use the following procedure to start up the LTQ Orbitrap XL ETD:
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, nitrogen, and argon 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 XL ETD 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. ▲
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LTQ Orbitrap XL ETD Hardware Manual
2-9
Basic System Operations
Starting Up the System after a Shutdown
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 quadrupole 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 three minutes, 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 pressed down (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. Then, proceed to topic “Setting
Up Conditions for Operation“ below. If you do not have either, go to
the topic directly.
Setting Up Conditions for Operation
Set up your LTQ Orbitrap XL ETD for operation, as follows:
1. Before you begin data acquisition with your LTQ Orbitrap XL ETD
system, you need to allow the system to pump down for at least
eight 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.
2-10
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Basic System Operations
Starting Up the System after a Shutdown
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: 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. Click the Display Status View button in the Tune Plus window.
Check 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 XL Getting Started manual.
Starting the ETD Module After a Complete Shutdown
To start up the ETD Module after a complete shutdown, do the
following:
1. Start the LTQ Orbitrap XL ETD according to the start up
procedures given in topic “Starting Up the System after a
Shutdown“ above. This also turns on the ETD Module as the
ETD Module power controls are linked to the MS power controls
(see topic “ETD Module Interface Board” on page 1-22).
2. If the Tune Plus window is not already open, choose Start >
Programs > Thermo Instruments> LTQ> LTQ Tune from the
taskbar. The Tune plus window will open.
On
Thermo Fisher Scientific
Off
Standby
You can determine the state of the MS detector by observing the
state of the On/Off/Standby button on the Control/Scan Mode
toolbar. (See Figure 2-2 on page 2-4.) The three different states of
the On/Standby button are shown at the left.
LTQ Orbitrap XL ETD Hardware Manual
2-11
Basic System Operations
Resetting the System
Resetting the System
If the communication link between LTQ Orbitrap XL ETD 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 XL ETD 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 2-9.
To reset the LTQ Orbitrap XL ETD, press the Reset button of the
LTQ XL. 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 three 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.
2-12
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Thermo Fisher Scientific
Basic System Operations
Resetting the Tune and Calibration Parameters to their Default Values
Resetting the Tune and Calibration Parameters to their Default Values
You can reset the LTQ Orbitrap XL ETD system tune 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
optimum performance. To reset the LTQ Orbitrap XL ETD tune and
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. ▲
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LTQ Orbitrap XL ETD Hardware Manual
2-13
Basic System Operations
Turning Off the Reagent Ion Source: What to Expect
Turning Off the Reagent Ion Source: What to Expect
The reagent ion source controls can be accessed as described in topic
“Placing the ETD Module in Standby Condition” on page 2-4. When
you deselect the Reagent Ion Source On check box in the Reagent Ion
Source dialog box (See Figure 2-4.), the ETD source and reagent heaters
are placed in Standby condition.
Figure 2-4.
Placing the reagent ion source in Standby condition
When the ETD Module is placed in Standby condition, the filament
and vial heaters are turned off. Simultaneously a valve opens to allow
nitrogen gas to cool the reagent vials. This cooling nitrogen runs until
the vials reach 70 °C. The audible rush (hissing noise) of nitrogen from
the reagent ion source area in the back of the ETD Module is normal
operation.
Warning The reagent vials are too hot to handle after the cooling
nitrogen turns off at a vial temperature of 70 °C. Verify that the reagent
vials have cooled down to a safe temperature before handling them. This
can take up to 90 minutes after the cooling nitrogen has turned off. ▲
Other conditions that will cause the ETD Module to remain in
Standby:
•
2-14
LTQ Orbitrap XL ETD Hardware Manual
Attempting to turn on the reagent ion source when the restrictor
heater, transfer line heater, and the source heater are not at their
target temperatures.
Thermo Fisher Scientific
Basic System Operations
Turning Off the Reagent Ion Source: What to Expect
•
Whenever either the mass spectrometer or the ETD Module goes
into Standby mode. Reagent vial nitrogen cooling will turn on if the
vials are at an elevated temperature.
Exception: If the LTQ Orbitrap XL ETD is placed in Standby by
clicking the Standby button in Tune Plus (see Standby icon in the
margin), there is an hour delay before the cooling nitrogen turns
on. ▲
Thermo Fisher Scientific
•
Whenever the pressure in the mass spectrometer or the
ETD Module exceeds its protection limit. Reagent vial nitrogen
cooling will turn on if the vials are at an elevated temperature.
•
Whenever the abundance of reagent ions becomes insufficient as
determined by the AGC setting. When this occurs, the
LTQ Orbitrap XL ETD completes the Xcalibur Sequence step in
progress before going into Standby mode.
LTQ Orbitrap XL ETD Hardware Manual
2-15
Chapter 3
User Maintenance
This chapter describes routine maintenance procedures that must be
performed to ensure optimum performance of the
LTQ Orbitrap XL ETD.
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
•
“Maintenance of the Vacuum System” on page 3-4
•
“Maintenance of the ETD Module” on page 3-13
•
“Maintenance of the Recirculating Chiller” on page 3-61
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. ▲
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LTQ Orbitrap XL ETD Hardware Manual
3-1
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
maintenance work on the vacuum system)
page 3-4
Rotary-vane pumps
Add oil
If oil level is low
Manufacturer’s documentation
Change oil
Every three months or if oil is cloudy or
discolored
Manufacturer’s documentation
Exchange lubricant reservoir
Once a year
Manufacturer’s documentation
Turbomolecular pumps
page 3-12
Recirculating chiller
Check cooling fluid level
See manufacturer’s documentation
Check cooling fluid filter
Manufacturer’s documentation
page 3-61
Check air inlet filter
ETD Module
Clean the ion volume
As needed*
page 3-19
Replace the inlet valve
components
As needed*
page 3-46
Clean the ion source lenses
As needed*
page 3-34
Clean the ion source
As needed*
page 3-41
*
page 3-43
Replace the ion source
filament
As needed
Check the rotary-vane pump
oil and add when needed
Every month
page 3-8
Change the rotary-vane
pump oil
Every 4 months
page 3-10
Clean the rear cooling fans
Every four months
page 3-60
* As needed depends on how close the component is to the electron transfer reagent introduction point. For example, the ion volume is closer to the fluoranthene
introduction point than any other component and requires the most frequent cleaning.
To successfully carry out the procedures listed in this chapter, observe
the following rules:
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LTQ Orbitrap XL ETD Hardware Manual
•
Proceed methodically.
•
Always wear clean, lint-free, and powder-free gloves when handling
the components of the API source, ion optics, mass analyzer, and
ion detection system.
Thermo Fisher Scientific
User Maintenance
General Remarks
•
Always place the components on a clean, lint-free, and powder-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
LTQ Orbitrap XL ETD.
•
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
parts have been de-contaminated and are free of hazardous materials.
Refer to topic ”Safety Advice for Possible Contamination” on page ix for
further information.
Cleaning the Surface of the Instrument
Clean the outside of the instrument with a dry cloth. For removing
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. ▲
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User Maintenance
Maintenance of the Vacuum System
Maintenance of the Vacuum System
This sections contains instructions for performing a system bakeout and
for performing pumps maintenance.
Baking Out the System
Collected or remaining gases and molecules as well as moisture can lead
to an increased number of collisions with sample ions in the high
vacuum region of the instrument. The bakeout procedure removes these
contaminations. 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 eight 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 topic “Placing
the LTQ Orbitrap XL ETD in Standby Condition” on page 2-4.
2. Put the FT Electronics switch at the power control panel into the
On position.
Elapsed time display
Set time display
Up keys
Down keys
Bakeout
stop button
Figure 3-1.
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Bakeout start button
Bakeout timer
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User Maintenance
Maintenance of the Vacuum System
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 on page 3-4.
4. Start the bakeout procedure by pressing the green start button on
the right. The LTQ Orbitrap XL ETD 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 and Vacuum) on the front side that have stopped flashing.
Maintenance of the Forepumps
Rotary-vane pumps require minimal maintenance. All that is required to
maintain the rotary-vane pump is to inspect, add, purge, and change the
pump oil.
For maintenance of the forepumps of the MS portion, refer to the
LTQ XL Hardware Manual or the pump manufacturer’s manual.
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! ▲
Maintenance of the ETD Forepump
Rotary-vane pump oil (P/N A0301-15101) is a translucent light amber
color and it should be checked often. During normal operation, oil must
always be visible in the oil level sight glass between the MIN and MAX
marks. If the oil level is below the MIN mark, add oil. If the oil is cloudy
or discolored, purge the oil to decontaminate dissolved solvents. If the
pump oil is still discolored, change it. You should change the pump oil
every 3000 hours (about four months) of operation.
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User Maintenance
Maintenance of the Vacuum System
The rotary-vane pump major components are shown in Figure 3-2.
1
2
33
4
14
5
6
7
13
8
12
11
10
9
Labeled components: 1=Foreline Vacuum Hose, 2=Electrical Inlet Connector,
3=Voltage Indicator, 4=Inlet Port, 5=Gas Ballast Control, 6=Oil Filler Plugs,
7=Outlet Port, 8=MAX Marks, 9=Oil Drain Plug, 10=MIN Marks, 11=Oil Level
Sight Glass, 12=Mode Selector, 13= On/Off Switch, 14=Lifting Handle
Figure 3-2.
Schematic of ETD forepump
Note During normal operation, the mode selector switch is set to
high-vacuum mode (turned fully clockwise) and the gas-ballast control
is closed (0). ▲
Accessing the ETD Forepump
As described in topic “Forevacuum Pump of the ETD Module” on
page 1-32, the ETD forepump is located in a cabinet at the bottom of
the ETD Module. To access the ETD forepump you have to remove the
lower panel as indicated in Figure 3-3.
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Maintenance of the Vacuum System
Pull to remove panel
Loosen screws on both sides
Figure 3-3.
Accessing the ETD Forepump: Removing the panel
Two pairs of hooks under the top panel hold the bottom panel. They
mount into corresponding openings at the top side of the bottom panel.
Figure 3-4 shows the details for the right side of the instrument.
Figure 3-4.
Hooks (left) and top side of detached bottom panel (right)
On the bottom of the rear side of the MS portion, two Allen screws fix
the panel to the instrument frame by means of fork-like extensions
(lugs). See Figure 3-5.
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Maintenance of the Vacuum System
Figure 3-5.
Lugs for fixing the bottom panel
To remove the panel, do the following:
1. Use a 6 mm Allen wrench to loosen the screws that fix the bottom
panel. Take care not to loosen the screws completely.
2. Pull the panel horizontally away from the instrument until it comes
clear from the hooks.
3. Remove the panel from the instrument and store it at a safe place.
To reattach the panel, proceed in the reverse order.
Adding Oil to the ETD Forepump
The pump oil level must be between the MIN and MAX marks on the
oil level sight glass for the pump to operate properly. Pump oil
(P/N A0301-15101) is added as needed when the oil level is below the
MIN mark on the oil level sight glass.
You can check the oil level by looking at the oil level sight glass, which is
shown in Figure 3-2. If the ETD forepump oil level is low, follow these
steps to add more oil.
To add oil to the ETD forepump, do the following:
1. Shut down and vent the LTQ Orbitrap XL ETD.
Caution Shut down and unplug the instrument before adding oil. ▲
2. Remove the lower panel at the rear side of the ETD Module as
described on page 3-8.
3. Remove one of the oil filler plugs from the rotary-vane pump.
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User Maintenance
Maintenance of the Vacuum System
Caution To maintain optimal performance and prevent damage to the
ETD forepump, only use factory-approved rotary-vane pump oil. ▲
4. Add fresh oil to the reservoir until the oil is half way between the
MIN and MAX level marks. If the oil level goes above the MAX
level mark, remove the drain plug and drain the excess oil into a
suitable container.
5. Insert the oil filler plug back into the rotary-vane pump.
6. Reattach the lower panel at the rear side of the ETD Module.
7. Plug in the instrument.
8. Restart the system.
Purging the Rotary-Vane Pump Oil
When the rotary-vane pump oil becomes cloudy or discolored, purge
the oil. Purging (or decontaminating) the oil removes dissolved gases
and low boiling-point liquids. You can purge the oil without
interrupting system operation, but do not purge it during an acquisition
or while the electron multiplier or filament is powered on.
To purge the rotary-vane pump oil, do the following:
1. Remove the lower panel at the rear side of the ETD Module as
described on page 3-8.
2. Set the gas ballast control (See Figure 3-2.) to Low Flow (I).
3. Operate the pump for 10 minutes or until the oil is clear. If the oil
remains cloudy or discolored after 10 minutes, replace the oil.
4. Set the gas ballast control to Closed (O), as shown in Figure 3-6.
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1
2
3
Labeled components: 1=High Flow (Position II), 2=Low Flow (Position I),
3=Closed (Position O)
Figure 3-6.
Gas Ballast Control Positions
5. Reattach the lower panel at the rear side of the ETD Module.
Changing the Rotary-Vane Pump Oil
You should change the ETD forepump oil every four months (about
3000 hours of operation).
Supplies needed for changing the ETD forepump oil:
•
Rotary-vane pump oil (P/N A0301-15101)
•
Suitable container for removing spent or excess oil
Note For best results, change the oil while the ETD forepump is still
warm after operation. Be careful, however, as the oil can still be very hot
at this time. ▲
Warning Danger of Burns. Handle hot pump oil carefully to avoid
being burned or injured. ▲
To change the ETD forepump oil, do the following:
1. Shut down and vent the LTQ Orbitrap XL ETD.
Caution Shut down and unplug the instrument before adding oil. ▲
2. Remove the lower panel at the rear side of the ETD Module as
described on page 3-8.
3. Disassemble the rotary-vane pump.
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Maintenance of the Vacuum System
a. Disconnect the foreline vacuum hose. (See Figure 3-2.)
b. Disconnect the exhaust vacuum hose.
c. Place the rotary-vane pump on a bench.
Warning Lifting Hazard. Use the proper lifting technique to lift the
ETD forepump. It weighs approximately 50 pounds (22.7 kg). ▲
4. Drain the spent oil.
a. Remove one of the oil filler plugs.
b. Remove the oil drain plug and allow the oil to drain into a
suitable container.
c. Dispose of the spent oil according to local environmental
regulations.
d. Replace the oil drain plug.
5. Add fresh oil.
a. Add oil into oil filler reservoir half way between the MIN and
MAX level marks.
b. If the oil level goes above the MAX level mark, remove the drain
plug and drain the excess oil from the pump.
6. Reassemble the rotary-vane pump.
a. Replace the oil filler plug.
b. Return the rotary-vane pump to the floor.
c. Reconnect the foreline vacuum hose to the rotary-vane pump.
d. Reconnect the exhaust vacuum hose to the rotary-vane pump.
e. Plug in the rotary-vane pump.
7. Reattach the lower panel at the rear side of the ETD Module.
8. Plug in the instrument.
9. Restart the system.
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Maintenance of the Vacuum System
Maintenance of the Turbopumps
The turbopumps in the MS portion of the LTQ Orbitrap XL ETD
need maintenance work that is briefly outlined below. In contrast, the
turbopump in the ETD Module contains no user-serviceable parts.
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 Reservoir of the Turbopumps
Note For all manipulations at the pumps, note the advice, warnings, and
cautions contained in the pump manuals! ▲
For the turbopumps, we recommend exchanging the lubricant reservoir
once per year. 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.
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User Maintenance
Maintenance of the ETD Module
Maintenance of the ETD Module
This section describes routine ETD Module maintenance procedures
that must be carried out to ensure optimum performance of the system.
Some of the procedures describe how to clean components of the
ETD Module. Others involve replacing components or replenishing the
electron transfer reagent.
Figure 3-7 illustrates the sequence in which to perform routine
maintenance on the ETD System.
Figure 3-7.
Thermo Fisher Scientific
Routine maintenance sequence for ETD system
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Requirements for Handling and Cleaning Reagent Ion Source Parts
A large part of maintaining your reagent ion source consists of making
sure that all the components are clean. Use the cleaning procedures
listed in this section to clean stainless steel and non-stainless steel parts.
However, use caution when doing so, because some components can be
damaged by exposure to liquids.
How often you clean the reagent ion source depends on the amount of
reagent introduced into the system. In general, the closer a component
is to where the reagent ion is introduced, the more rapidly it becomes
dirty (see the footnote in Table 3-1 on page 3-2). For example, the ion
volume needs to be cleaned more often than other parts.
Many parts can be removed and disassembled by hand. Make sure you
have all the necessary tools before carrying out a procedure. See below
for a list of the tools and supplies generally needed for maintenance of
the reagent ion source. Tools should be used only for the maintenance of
the reagent ion source and be free of grease or other residues. Handle
parts in a manner that maintains their cleanliness.
Note It is crucial that the cleanliness of the parts be maintained when
they are handled. Wear gloves and place the parts on surfaces that are
clean if the parts are not returned directly to the instrument. If clean
surfaces are not available, place the parts on fresh lint free wipes or
cloths or aluminum foil that has not been used for any other purpose. ▲
The following tools and supplies are needed for reagent ion source
maintenance:
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•
Clean, dry gas (air or nitrogen)
•
Gloves, clean, lint- and powder-free
•
Gloves, nitrile
•
Lint-free cloth or paper
•
Nut driver, 5.5 mm
•
Protective eyewear
•
Screwdriver, Phillips #2
•
Screwdriver, flat blade
•
Wrench, adjustable
Thermo Fisher Scientific
User Maintenance
Maintenance of the ETD Module
•
Wrench, Allen, 2 mm, 2.5 mm, 3 mm, 4 mm, 5/32-in., 5/64-in.,
1/16-in.
•
Wrench, open-ended, 1/4-in., 5/16-in., 7/16-in. (2), 1/2-in.,
9/16-in.
•
Wrench, socket, 1/2-in.
Cleaning Stainless Steel Parts
The reagent ion source, ion volume assembly, ion source block, and
lenses are made from stainless steel. These parts are cleaned by following
the procedure described in this topic. Use this procedure with caution
because some components can be damaged when exposed to liquids.
The following tools and supplies are needed for cleaning stainless steel
parts in the reagent ion source:
Thermo Fisher Scientific
•
Acetone, analytical grade (or other suitable solvent)
•
Aluminum oxide abrasive, number 600 (P/N 32000-60340)
•
Applicators, cotton-tipped (P/N A0301-02000)
•
Beaker, 450 mL
•
Clean, dry gas
•
De-ionized water
•
Detergent (Alconox, Micro, or equivalent)
•
Dremel rotary tool or equivalent (recommended)
•
Foil, aluminum
•
Forceps
•
Gloves, clean, lint- and powder-free
•
Gloves, nitrile
•
Glycerol, reagent grade
•
Lint-free cloth
•
Protective eyewear
•
Tap water
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Maintenance of the ETD Module
•
Toothbrush, soft
•
Ultrasonic cleaner
Caution Do not use this procedure to clean ceramic, aluminum, or gold
plated parts. See page 3-17 for the method for cleaning ceramic,
aluminum, or gold plated parts. ▲
Caution Follow the subsequent instructions precisely. If done wrong, the
cleaning procedure could damage the ion source lenses. ▲
Warning Wear impermeable laboratory gloves and eye protection when
performing these cleaning procedures. ▲
To clean reagent ion source stainless steel parts, do the following:
1. Remove contamination from the surfaces being cleaned.
a. Use a slurry of number 600 aluminum oxide in glycerol and a
cleaning brush or cotton-tipped applicator. Contamination
appears as dark or discolored areas, but may not be visible. The
heaviest contamination is usually found around the apertures,
such as the electron entrance hole on the ion volume.
b. Clean each part thoroughly, even if no contamination is visible.
c. Use the wooden end of an applicator that is cut at an angle to
clean the inside corners.
d. Use a Dremel® tool with the polishing swab at its lowest speed.
This will increase the cleaning efficiency and decrease the time
required to clean the part.
Warning To prevent personal injury, be sure to keep the Dremel tool
away from possible hazards, such as standing water or flammable
solvents. ▲
2. Rinse the parts with clean water. Use a clean applicator or
toothbrush to remove the aluminum oxide slurry. Do not let the
slurry dry on the metal because dried aluminum oxide is difficult to
remove.
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3. Place the parts in a warm detergent solution in an ultrasonic bath
and sonicate them.
a. Using forceps, place the parts in a beaker containing warm
detergent solution.
b. Place the beaker and contents in an ultrasonic bath for five
minutes.
c. Rinse the parts with tap water to remove the detergent.
4. Sonicate the parts in deionized water.
a. Using forceps, place the parts in a beaker containing deionized
water.
b. Place the beaker and contents in an ultrasonic bath for five
minutes.
c. If the water is cloudy after sonicating, pour off the water, add
fresh water, and place the beaker and its contents in a ultrasonic
bath again for five minutes. Repeat until the water is clear.
5. Sonicate the parts in acetone.
a. Using forceps, place the parts in a beaker containing fresh
acetone.
b. Place the beaker and contents in an ultrasonic bath again for five
minutes.
6. Blow-dry the parts immediately. Use clean, dry gas (air or nitrogen)
to blow the acetone off the parts.
Cleaning Non-Stainless Steel or Hybrid Parts
To clean the stainless-steel portion of hybrid parts, follow step 1 and
step 2 of the instructions on page 3-16. Perform these steps only on the
stainless-steel surfaces of hybrid parts. Do not allow the aluminum oxide
slurry to contact the aluminum, ceramic, or gold plated portions of
these parts.
Warning Wear impermeable laboratory gloves and eye protection when
performing the following cleaning procedures. ▲
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The reagent ion source heater ring, filament spacer, lens holder, and
spacers are non-stainless steel parts that are made from aluminum,
ceramic, or are gold plated. To clean the non-stainless-steel portions of
hybrid parts, do the following:
1. Scrub all of the parts with a warm detergent solution.
a. Scrub the parts with a toothbrush or clean applicator. Do not
soak or sonicate the parts in detergent.
b. Using forceps, rinse the parts thoroughly with tap water to
remove the detergent.
Caution Do not leave aluminum parts, such as the heater ring, in the
detergent. Basic solutions, like detergent, damage the surface of
aluminum. ▲
2. Rinse the parts in deionized water. Using forceps, dip the parts in a
beaker of deionized water. Change the water if it becomes cloudy.
Do not soak or sonicate the parts.
3. Rinse the parts with acetone. Using forceps, dip the parts in a beaker
of acetone. Change the acetone if it becomes cloudy. Do not soak or
sonicate the parts.
4. Blow-dry the parts immediately. Use clean, dry gas (air or nitrogen)
to blow the acetone off the parts.
Maintenance of the Reagent Ion Source
The reagent ion source consists of an ion volume, filament, and ion
source lenses. Because the ion volume is exposed directly to samples
introduced into the reagent ion source, it requires the most frequent
cleaning. You can access the ion volume assembly with or without an
inlet valve.
To restore system performance, always clean the ion volume first, then
the ion source lenses. If cleaning either of these components does not
restore system performance, try cleaning the entire reagent ion source.
This section contains these maintenance procedures:
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•
“Cleaning the Ion Volume With an Inlet Valve” on page 3-19
•
“Cleaning the Ion Source Lens Assembly” on page 3-34
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User Maintenance
Maintenance of the ETD Module
•
“Cleaning the Ion Source” on page 3-41
•
“Replacing the Ion Source Filament” on page 3-43
•
“Replacing Inlet Valve Components” on page 3-46
The ion source, the ion trap, and their components are shown in
Figure 3-8.
2
3
4
1
6
5
Labeled components: 1=ion source lenses, 2=filament assembly, 3=ion
source block, 4=magnet support, 5=magnets, 6=ion volume (inside the ion
source block, 3)
Figure 3-8.
Ion source components (left view)
Cleaning the Ion Volume With an Inlet Valve
The ion volume is where molecules interact with energetic electrons to
form ions. Because the ion volume is exposed directly to reagents
introduced into the reagent ion source, you will have to clean it more
frequently than other parts. How often you have to clean the ion volume
assembly will depend on the types and amounts of reagents used.
For cleaning the ion volume with an inlet valve, the following tools and
supplies are needed:
Thermo Fisher Scientific
•
Cleaning supplies for stainless steel parts (See topic “Cleaning
Stainless Steel Parts” on page 3-15.)
•
Gloves (clean, lint-free, and powder-free)
•
Ion volume tool and guide bar
•
Lint-free cloth
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Using the ion volume tool allows you to access the ion volume by
entering the vacuum manifold through the inlet valve without venting
the instrument.
To clean the ion volume with an inlet valve, do the following:
1. Click the On/Standby button in the Tune Plus window to place the
LTQ Orbitrap XL ETD in Standby mode. See Figure 3-9.
On
Off
Standby
On/Standby button
Reagent Ion Source instrument control icon
Status View
Figure 3-9.
Tune Plus window
2. Open the Reagent Ion Source dialog box (Figure 3-16 on page 3-25)
in Tune Plus by clicking the Reagent Ion Source instrument control
icon.
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1
2
3
4
5
12
11
10
9
8
13
7
6
Labeled components: 1=alignment line, 2=lock position, 3=unlock position,
4=ion volume tool, 5=bayonet lock, 6=second stop, 7=guide ball track, 8=first
stop, 9=guide bar, 10=guide ball hole, 11=guide ball, 12=ion volume tool
handle, 13=guide bar handle
Figure 3-10. Ion volume tool components
3. Place the guide bar handle (item 13 in Figure 3-10 on page 3-21) to
the 3 o’clock position (Figure 3-11 on page 3-21).
4. Insert the guide bar (item 9 in Figure 3-10) into the guide bar
opening in the back of the ETD Module (Figure 3-11).
Inlet valve lever in
down (closed) position
Guide bar handle
Guide bar opening
Figure 3-11. Guide bar being inserted into guide bar opening*
* Guide bar handle is facing to the right. The inlet valve is closed when the inlet valve lever is in the down
position and open when it is in the up position.
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5. Push the guide bar in as far as it will go, then rotate it 90° clockwise
to lock in the guide bar (Figure 3-12). The guide bar handle faces
the floor at the completion of this step.
Inlet valve lever in
down (closed) position
Guide bar handle
Figure 3-12. Guide bar insertion complete*
* Guide bar handle is facing the floor. The inlet valve is closed when the inlet valve lever is in the down
position and open when it is in the up position.
6. Prepare the inlet valve and ion volume tool for insertion.
Make sure the inlet valve is closed (inlet valve lever is down, as
shown in Figure 3-12) and remove the inlet valve plug (item 2 in
Figure 3-13). Do this by rotating (loosening) the inlet valve knob
(item 1 in Figure 3-13 on page 3-23) until the inlet valve plug (item
2 in Figure 3-13) will slide out easily. The inlet valve plug prevents
air from entering the vacuum manifold in case the inlet valve is
inadvertently opened.
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1
2
3
4
5
Labeled components: 1=inlet valve knob, 2=inlet valve plug, 3=inlet valve
lever (down is closed, up is open), 4= guide bar opening, 5=main access panel
Figure 3-13. Rear view of the ETD Module, showing the inlet valve
7. Turn the ion volume tool handle to the unlock position, which
indicates that the ion volume tool is in position to accept the ion
volume. See Figure 3-14.
Figure 3-14. Ion volume tool handle in the unlock position
8. Insert the ion volume tool and evacuate the inlet valve:
a. Insert the guide ball into the guide ball hole.
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b. Slide the ion volume tool forward in the guide bar track until
the guide ball is at the guide bar’s first stop, which is shown in
Figure 3-10 on page 3-21 and Figure 3-15.
1
7
2
5
6
4
3
Labeled components: 1=ion volume tool entry housing, 2=inlet valve opening,
3=first stop, 4=guide bar, 5=ion volume tool, 6=inlet valve lever, 7=inlet valve
knob
Figure 3-15. Ion volume tool guide bar first stop
c. Slide the ion volume tool so the guide ball is in the groove at the
first stop (Figure 3-10 on page 3-21 and Figure 3-15). This
prevents the probe from being pulled forward when the inlet
valve is evacuated.
d. Tighten the inlet valve knob (Figure 3-15) to ensure that a
leak-tight seal is made.
e. Click Open Probe Interlock in the Reagent Ion Source dialog
box (Figure 3-16). A message box appears stating that the probe
interlock is being pumped down. The target pressure is
<0.1 mTorr. If a pressure of 0.1 mTorr or less is not obtained,
replace the inlet valve seal as described in topic “Replacing Inlet
Valve Components” on page 3-46. When the target pressure is
achieved, a message appears stating that the ball valve can be
opened (Figure 3-17).
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Open Probe Interlock
Figure 3-16. Reagent Ion Source dialog box, Open Probe Interlock button.
Figure 3-17. Instrument Message box: The Ball Valve can now be opened
f. Once evacuation is complete, push up the inlet valve lever to
open the inlet valve (Figure 3-18).
9. Remove the ion volume:
a. Slide the ion volume tool into the vacuum manifold until the tip
of the ion volume tool is fully inserted into the ion volume
holder, as shown in Figure 3-18.
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5
1
6
2
4
3
Labeled components: 1=ion volume tool, 2=inlet valve opening, 3=guide bar,
4=second stop, 5=inlet valve lever in open (up) position, 6=inlet valve knob
Figure 3-18. Ion volume tool inserted into the inlet valve
You will know that the ion volume tool is fully inserted into the
ion volume holder because the guide ball (item #11, Figure 3-10
on page 3-21) will be just past the first mark on the guide bar as
shown in Figure 3-19.
second mark
second stop
first mark
Guide Ball
Figure 3-19. Detail of ion volume tool fully inserted into the inlet valve
b. Turn the ion volume tool handle counterclockwise to the lock
position, See Figure 3-20. Listen for a click indicating that the
handle is fully engaged in the lock position and is holding the
ion volume.
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Figure 3-20. Ion volume tool handle in the locked position
c. Withdraw the ion volume tool (the ion volume is attached) until
the guide ball reaches the first stop (see Figure 3-10 on
page 3-21 and Figure 3-15 on page 3-24 for the first stop
position).
d. Close the inlet valve by pushing the lever down.
Caution Do not withdraw the ion volume tool beyond the point where
the guide ball reaches the first stop in the guide bar. Close the inlet valve
before withdrawing the ion volume tool past the first stop. Otherwise,
the system will vent to the atmosphere and cleaning the components
under vacuum will be required. ▲
e. Loosen the inlet valve knob (Figure 3-18).
f. Continue withdrawing the ion volume tool completely from the
inlet valve by sliding the ion volume tool through the guide ball
track in the guide bar.
Warning The ion volume will be too hot to touch. Let it cool to room
temperature before handling it. ▲
10. Clean the ion volume:
a. Turn the ion volume tool handle to the unlock position
(Figure 3-14 on page 3-23). The ion volume tool handle unlock
position icon is shown at the left.
b. Remove the ion volume from the ion volume tool. Using clean
gloves, press the ion volume into the tip of the ion volume tool
and rotate it to disconnect the bayonet pins from the pin guides.
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Pull the ion volume out of the ion volume tool, as illustrated in
Figure 3-21.
Labeled components: 1=bayonet pin, 2=bayonet pin guide, 3=ion volume
holder, 4=spring washer, 5=ion volume
Figure 3-21. Ion volume assembly
c. Clean the ion volume and ion volume holder according to the
instructions in topic “Cleaning Stainless Steel Parts” on
page 3-15.
11. Place the clean ion volume on the ion volume tool:
a. Place the ion volume into the bayonet lock located on the ion
volume tool. Make sure that the alignment arrows on the ion
volume and ion volume tool are facing each other. See
Figure 3-22.
Labeled components: 1=ion volume alignment arrow, 2=bayonet pin,
3=bayonet lock, 4=ion volume tool alignment arrow, 5=bayonet guide, 6=ion
volume tool, 7=ion volume
Figure 3-22. Placing the ion volume on the ion volume tool
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Note Wear clean, lint-free, and powder-free gloves when you handle
parts inside the vacuum manifold. ▲
b. Slide the ion volume tool handle to the lock position. (See
Figure 3-20 on page 3-27.)
Caution The arrows on the ion volume tool and ion volume must be
aligned to avoid damage to the ion source.
12. Insert the ion volume tool and evacuate the inlet valve:
a. Insert the guide ball into the guide ball hole and slide the ion
volume tool forward in the guide bar track until the guide ball is
at the guide bar’s first stop (see Figure 3-10 on page 3-21 and
Figure 3-15 on page 3-24).
b. Turn the ion volume tool so that the guide ball is in the groove
at the first stop (Figure 3-15 on page 3-24). This prevents the
probe from being pulled forward when the inlet valve is
evacuated.
c. Tighten the inlet valve knob to ensure a leak-tight seal
(Figure 3-18 on page 3-26).
d. Click Open Probe Interlock in the Reagent Ion Source dialog
box (Figure 3-16 on page 3-25). A message box will appear
stating that the probe interlock is being pumped down. The
target pressure is <0.1 mTorr. If a pressure of 0.1 mTorr or less is
not obtained, the inlet valve seal must be replaced as described
in topic “Replacing Inlet Valve Components” on page 3-46.
When the target pressure is achieved, a message will appear
stating that the ball valve can be opened. See Figure 3-17 on
page 3-25.
e. Once evacuation is complete, push the inlet valve lever up to
open the inlet valve. See Figure 3-18 on page 3-26.
13. Reinsert the ion volume:
a. Slide the ion volume tool into the vacuum manifold, as
illustrated in Figure 3-18.
b. Listen for a click indicating that the ion volume has connected
with the ion source block. The guide ball will be slightly beyond
the second stop on the guide bar. See Figure 3-19 on page 3-26.
c. Turn the ion volume tool handle to the unlock position. See
Figure 3-23.
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Figure 3-23. Ion volume tool handle in the unlock position
i. Withdraw the ion volume tool away from the ion volume
about 2.5 cm (1 in) and turn the ion volume tool handle to
the lock position. See Figure 3-24 on page 3-30.
ii. Slide the ion volume tool back into the vacuum manifold
until the end of the ion volume tool just touches the ion
volume.
iii. If the ion volume tool does not go into the inlet valve
completely, the ion volume is not seated properly.
d. Withdraw the ion volume tool until the guide ball reaches the
first stop (see Figure 3-10 on page 3-21 and Figure 3-15 on
page 3-24).
Figure 3-24. Ion volume tool handle in the locked position
e. Close the inlet valve by pushing down on the inlet valve lever
(Figure 3-13 on page 3-23).
Caution Do not withdraw the ion volume tool beyond the point where
the guide ball reaches the first stop in the guide bar. Close the inlet valve
before withdrawing the ion volume tool past the first stop. Otherwise,
the system vents to the atmosphere. ▲
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f. Loosen the inlet valve knob (item 6 in Figure 3-18 on
page 3-26).
g. Continue withdrawing the ion volume tool completely from the
inlet valve by sliding the ion volume tool through the guide ball
track in the guide bar.
14. Remove the ion volume tool and guide bar from the vacuum
manifold:
a. Remove the guide bar by rotating it 90º counter-clockwise and
sliding it out of the entry housing.
b. Replace the inlet valve plug and tighten the inlet valve knob
(item 6 in Figure 3-18 on page 3-26).
c. Click Close in the message stating that the ball valve can be
opened. (See Figure 3-17 on page 3-25.)
Note Tune Plus provides an evaluation procedure for CI gas pressure
under Diagnostics > Diagnostics > Tools > System evaluation >
Reagent CI gas pressure evaluation. Thermo Fisher Scientific
recommends performing this procedure after replacing the filament
and/or the ion volume. ▲
Removing the ETD Main Access Panel
During some ETD Module maintenance activities it is necessary to
remove either the ETD main access panel or side access panel or both
(see Figure 3-25). Follow the subsequent procedures to remove these
panels.
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7
8
6
5
9
4
3
2
1
Labeled components: 1=ETD main access panel, 2=side access panel, 3=inlet
valve knob, 4=inlet valve lever (down is closed, up is open), 5=inlet valve
plug, 6, 7, 8, 9=panel fasteners.
Figure 3-25. Rear view of the ETD Module
To remove the ETD main access panel, do the following:
1. Place the ETD Module to Service mode as directed in topic “Place
the Instrument in Off Condition and Service Mode” on page 3-49.
Note In Service mode, all power to the LTQ Orbitrap XL ETD
electronics is turned off. There are no user accessible components that
carry a voltage in this mode. However, the vacuum pumps continue to
operate. ▲
Warning The reagent vial heaters can be 108 °C (or set point); the
transfer line, the restrictor, and the ion source can be at 160 °C. These
components may be too hot to touch. Verify that all of these
components are safe to touch before handling them. ▲
Note The ETD main access panel is interlocked with the ETD Module
power. When the ETD main access panel is removed all power to the
ETD Module will be turned off. However, the mechanical pump and
turbo pump will continue operating. ▲
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2. Remove the inlet valve lever (item 4 in Figure 3-25 on page 3-32) by
pulling it down and away from the ETD Module main access panel.
Do not rotate the lever upwards. It must remain in its down (closed)
position to avoid catastrophic venting of the system.
Caution Rotating the inlet valve lever upwards (to the open position)
without the inlet valve plug (item 5 in Figure 3-25) or the ion volume
tool in place will cause a catastrophic venting of the system. ▲
3. Remove the inlet valve knob (item 3 in Figure 3-25) and the inlet
valve plug (item 5 in Figure 3-25) by unscrewing the inlet valve
knob. Be sure that the inlet valve lever (item 4 in Figure 3-25)
remains in the down position.
4. Remove the four panel fasteners (items 6, 7, 8, and 9 in
Figure 3-25).
5. Tilt the top of panel towards you and lift it up and away from the
ETD Module.
Removing the ETD Side Access Panel
To remove the ETD side access panel, do the following:
1. If it is not already in Service mode, place the ETD Module in
Service mode as directed in topic “Place the Instrument in Off
Condition and Service Mode” on page 3-49.
Note In Service mode, all power to the LTQ Orbitrap XL ETD
electronics is turned off. There are no user accessible components that
carry a voltage in this mode. However, the vacuum pumps continue to
operate. ▲
Warning The reagent vial heaters can be at 108 °C (or set point); the
flow restrictor, the transfer line heaters, and the ion source heater can be
at 160 °C. These components may be too hot to touch. Verify that all of
these components are safe to touch before handling them. ▲
Note The ETD side access panel is interlocked with the ETD Module
power. When the ETD side access panel is removed, all power to the
ETD Module will be turned off. However, the mechanical pump and
turbo pump will continue operating. ▲
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2. Remove the grey plastic panel by removing the four screws that hold
it in place.
3. Remove the metal side access panel (item 2 in Figure 3-42 on
page 3-52) by removing the three screws that hold it in place.
Warning Reagent vial heaters, ion source heater, flow restrictor, and
transfer lines are accessible under the ETD side access panel. These are
heated components. Verify that they are safe to touch before handling
them. ▲
Replace the panels by following the above steps in reverse order and
reversing the instructions in each step.
Cleaning the Ion Source Lens Assembly
If cleaning the ion volume did not restore system performance, try
cleaning the ion source lens assembly. The ion source lens assembly
comes in direct contact with reagent ions introduced into the
ETD Module and needs to be cleaned periodically (though not as often
as the ion volume).
To clean the ion source lens assembly, do the following:
1. Prepare the ETD Module for maintenance:
a. Prepare a clean work area by covering the area with a clean
lint-free cloth.
b. Shut down and vent the ETD Module (see “Shutting Down the
Instrument” on page 2-7).
Caution Shut down and unplug the LTQ Orbitrap XL ETD before
proceeding with the next steps of this procedure. ▲
Note Wear clean, lint- and powder- free gloves when you handle parts
inside the vacuum manifold. ▲
Warning The ion source may be too hot to touch even if the cooling
nitrogen has completed its cycle. Be sure that the ion source has cooled
to room temperature before handling it. ▲
2. Remove the ion source assembly:
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a. Remove the main access panel of the ETD Module (item 1 in
Figure 3-25 on page 3-32). Follow the procedures in topic
“Removing the ETD Main Access Panel” on page 3-31.
Caution It is good practice to keep the inlet valve lever in the down
(closed) position whenever it is not explicitly required to be in the up
position (open), even if the vacuum manifold is at atmospheric pressure.
This is to be consistent with maintenance procedures that rely on the
inlet valve lever being closed at the appropriate step to prevent the
accidental loss of vacuum. If the vacuum is accidently lost the system
may be damaged. At a minimum, the components that were under
vacuum might have to be cleaned. ▲
Labeled components: 1=inlet valve plug, 2=vacuum manifold, 3=inlet valve
lever, 4=guide bar, 5=entry housing, 6=inlet valve knob, 7=inlet valve block,
8=foreline hose connection, 9=12 pin feedthrough, 10=vacuum manifold
probe plate, 11=ball valve housing, 12= inlet valve solenoid
Figure 3-26. Inlet valve components (ion volume tool not shown)
b. Remove all connectors between the components on the vacuum
manifold probe plate (item #10, Figure 3-26 on page 3-35) and
the ETD Control PCB (Figure 1-15 on page 1-20).
c. Remove the valve shield from the vacuum manifold probe plate
(Figure 3-27) by loosening the four screws at the corners of the
shield.
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1
Figure 3-27. Valve shield (1) covering the vacuum manifold probe plate
d. Remove the foreline hose on the source from its connection
(Figure 3-28 and item 8 in Figure 3-26).
Figure 3-28. Removing the foreline hose from its connection
e. Remove the four screws holding the vacuum manifold probe
plate (Figure 3-29 and item 10 in Figure 3-26 on page 3-35).
Support the plate with your hand as shown in Figure 3-29.
Arrows point to the four hex screw locations (items 1–4).
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1
4 (at lower left
2
3
Figure 3-29. Unscrewing the vacuum manifold probe plate
f. Remove the vacuum manifold probe plate (Figure 3-30).
Figure 3-30. Removing the vacuum manifold probe plate
g. Unplug the 12 pin feedthrough harness from the feedthrough
(Figure 3-31).
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1
2
4
3
2
Labeled components: 1=unplugged 12 pin feedthrough, 2=thumbscrews,
3=transfer line bellows, 4=ion source assembly
Figure 3-31. Interior of vacuum manifold
h. Remove the ion source assembly from the vacuum manifold
(Figure 3-32) by first loosening the ion source thumbscrews
(item 2 in Figure 3-31).
i. Second, as you remove the ion source assembly (item 1 in
Figure 3-32) gently shift it to the left (arrow 2 in Figure 3-32)
before and while pulling it out. This will allow the ion source
assembly to disengage from the transfer line bellows (item 3 in
Figure 3-32) as it is removed. Alternatively, gently depress the
transfer line bellows (Figure 3-31) to disengage it from the ion
source assembly.
The ion source assembly is held together with a clip (item 8 in
Figure 3-33). However, it is necessary to keep the tips of your gloved
fingers on both the front edge of the ceramic lens holder (item 11 in
Figure 3-33) and the back of the magnet yoke (item 3 in Figure 3-33)
when you handle the ion source assembly. This prevents unsecured
components inside of the ceramic lens holder from falling out.
Caution When handling the ion source assembly, it is important to
handle it with gentle finger pressure on each end (as instructed above) to
keep unsecured components from falling out of the assembly. ▲
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1
2
Figure 3-32. Removing the ion source assembly from the vacuum manifold*
* The ion source assembly (item 1) is gently shifted to the left (arrow 2) to allow the ion source assembly
to disengage from the transfer line bellows (item 3) as it is removed.
1
2
3
4
5
6
11
10
1
2
3
5
9
8
7
Labeled components: 1=thumbscrew, 2=springs, 3=magnet yoke, 4=Ion
Source PCB, 5=magnets, 6=ion source block, 7=ceramic lens holder, 8=spring
clip, 9=spring clip thumb screw, 10=12 pin feedthrough harness, 11=finger
over front edge of ceramic lens holder to keep unsecured components from
falling out of the ion source assembly.
Figure 3-33. Ion source assembly
An exploded view of the ion source assembly is shown in Figure 3-34.
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5
4
3
2
8
7
6
5
1
3
Labeled components: 1=thumbscrews, 2=springs, 3=E-clips , 4=magnet yoke,
5=magnets, 6=ion source, 7=ion source lens assembly, 8=ceramic lens holder
Figure 3-34. Ion source assembly exploded view
3. Separate the magnet yoke and the ion source.
4. Remove the ion source lens assembly from the ceramic lens holder
(Figure 3-34).
5. Clean the ion source lens assembly according to the procedure in
topic “Cleaning Stainless Steel Parts” on page 3-15. Pay particular
attention to the areas inside the tube and around the holes in the
lens assembly.
6. Replace the ion source assembly:
a. Insert the lens assembly into the ceramic lens holder.
b. Reassemble the ion source assembly.
c. Reinstall the ion source assembly into the vacuum manifold by
following step 2 in reverse order.
7. Restore the ETD Module to operational status. See topic “Starting
Up the System after a Shutdown” on page 2-9.
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Cleaning the Ion Source
If cleaning the ion volume and ion source lens assembly does not restore
system performance, you might need to clean the ion source. Clean the
ion source no more than once every six months.
Supplies needed for cleaning the ion source:
•
Cleaning supplies
•
Gloves (clean, lint-free, and powder-free)
•
Lint-free cloth
To clean the ion source block, do the following:
1. Prepare the ETD Module for maintenance:
a. Prepare a clean work area by covering the area with lint-free
cloth.
b. Shut down and vent the LTQ Orbitrap XL ETD. (See topic
“Shutting Down the LTQ Orbitrap XL ETD Completely” on
page 2-7.)
Caution Shut down and unplug the LTQ Orbitrap XL ETD before
proceeding with the next steps of this procedure. ▲
c. Remove the ion source assembly by following the procedures in
step 2 in topic “Cleaning the Ion Source Lens Assembly” on
page 3-34.
Note Wear clean, lint- and powder- free gloves when you handle parts
inside the vacuum manifold. ▲
2. Disassemble the ion source assembly (Figure 3-33 and Figure 3-34),
remove and disassemble the ion source (Figure 3-35).
a. Remove the magnet yoke and the ion source block with the ion
source lens assembly.
b. Remove the ion source lens assembly.
c. Remove the ion source.
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Labeled components: 1=ion source filament, 2=cartridge heaters, 3=base
studs (3×), 4=Ion Source PCB, 5=temperature sensor, 6=ion source block,
7=ion volume key thumbscrew, 8=ion volume pin, 9=ion volume, 10=spring
clip, 11=spring clip thumb screw, 12=heater ring, 13=sample inlet aperture (in
side of item 6), 14=ceramic spacer
Figure 3-35. Ion source, exploded view
d. Remove the three base studs (item 3 in Figure 3-35). Be careful
not to damage the leads on the Ion Source PCB (item 4 in
Figure 3-35).
e. Gently remove the Ion Source PCB (item 4 in Figure 3-35) from
the ion source by loosening the spring clip thumbscrew (item 11
in Figure 3-35) and the spring clip (item 10 in Figure 3-35) and
sliding the three cartridge heaters and the temperature sensor
(items 2 and 5 in Figure 3-35) off the ion source and pulling the
filament (item 1 in Figure 3-35) straight away from the three
filament connectors on the Ion Source PCB (item 4 in
Figure 3-35). Do not bend or twist the cartridge heaters or
temperature sensor.
f. Remove the filament and ceramic spacer (items 15 and 1 in
Figure 3-35) from the ion source block (item 6 in Figure 3-35).
g. Remove the ion volume key thumbscrew (item 7 in
Figure 3-35).
Note It is not necessary to remove the ion volume pin (item 8 in
Figure 3-35). If you remove it, you should reinsert it just far enough so
the ball will keep an ion volume (item 9 in Figure 3-35) from falling
out. If the ball extends too far, the ion volume will be difficult to
remove. ▲
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3. Clean the ion source parts and replace the ion source assembly:
a. Clean each component of the ion source, as described in topic
“Cleaning Stainless Steel Parts” on page 3-15 and “Cleaning
Non-Stainless Steel or Hybrid Parts” on page 3-17.
b. Reassemble the ion source block.
c. Reassemble the ion source assembly.
d. Reinstall the ion source assembly into the vacuum manifold by
following step 2 of topic “Cleaning the Ion Source Lens
Assembly” on page 3-34 in reverse order.
4. Restore the ETD Module to operational status. See topic “Starting
Up the System after a Shutdown” on page 2-9.
Replacing the Ion Source Filament
The number of ions produced in the ion source is approximately
proportional to the filament emission current. If you notice that ion
production is low, this might indicate that the filament has failed and
needs to be replaced. If the measured emission current is substantially
less than the value that the emission current is set to, or if the measured
emission current is decreasing over time, then the filament has failed or
is failing and needs to be replaced.
The ion source filament assembly is shown in Figure 3-36.
3
5
4
1
2
Labeled components: 1=ion source lens assembly, 2=ion source block, 3=Ion
Source PCB, 4=base studs (3x), 5=ion source filament
Figure 3-36. Ion source lens assembly and ion source
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Supplies needed for replacing the ion source filament:
•
Filament Assembly DSQ II (P/N 120320-0030)
•
Gloves, clean, lint-free, and powder-free
•
Lint-free cloth
To replace the ion source filament, do the following:
1. Prepare the ETD Module for maintenance.
a. Prepare a clean work area by covering the area with lint-free
cloth.
b. Shut down and vent the LTQ Orbitrap XL ETD. (See topic
“Shutting Down the LTQ Orbitrap XL ETD Completely” on
page 2-7.)
Caution Shut down and unplug the LTQ Orbitrap XL ETD before
proceeding with the next steps of this procedure. ▲
c. Remove the ion source assembly by following the procedures in
step 2 in topic “Cleaning the Ion Source Lens Assembly” on
page 3-34.
Note Wear clean, lint- and powder- free gloves when you handle parts
inside the vacuum manifold. ▲
2. Disassemble the ion source assembly (Figure 3-33 and Figure 3-34),
remove and disassemble the ion source (Figure 3-35).
a. Remove the ion source lens assembly (item 1 in Figure 3-36).
b. Remove the three base-studs (item 3 in Figure 3-35, item 4 in
Figure 3-36).
c. Remove the filament assembly (items 1 and 15 in Figure 3-35,
item 5 in Figure 3-36) and ion source block (item 2 in
Figure 3-36) from the three filament connectors and cartridge
heaters (item 2 in Figure 3-35) on the Ion Source PCB (item 4
in Figure 3-35) according to the procedure in step e of topic
“Cleaning the Ion Source“ on page 3-42 .
Note Now is a good time to clean the ion volume and ion source
lenses. ▲
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3. Inspect and install a new filament assembly:
a. Verify that the filament wire is centered in the electron lens hole.
Figure 3-37 shows the centered filament wire as seen from the
bottom of the filament through the electron lens hole.
Centered wire
Figure 3-37. Filament wire as seen from the bottom of the filament through
the electron lens hole
b. Insert the filament into the ceramic spacer of the ion source
block (item 14 in Figure 3-35).
c. Align the filament leads with the Ion Source PCB connectors
and gently press the leads into the connectors. Normally, there is
a small gap (about 0.020 in or 0.50 mm) between the filament
and the connectors. The gap allows the ceramic filament
centering ring (spacer) to properly position and align the
electron lens hole with the ion volume.
d. Reinstall the three base-studs (item 3 in Figure 3-35, item 4 in
Figure 3-36).
4. Reassemble ion source and ion source assembly.
5. Insert the ion source assembly into the vacuum manifold.
6. Restore the ETD Module to operational status. See topic “Starting
Up the System after a Shutdown” on page 2-9.
Note Tune Plus provides an evaluation procedure for CI gas pressure
under Diagnostics > Diagnostics > Tools > System evaluation >
Reagent CI gas pressure evaluation. Thermo Fisher Scientific
recommends performing this procedure after replacing the filament
and/or the ion volume. ▲
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Replacing Inlet Valve Components
This topic provides the procedure for replacing inlet valve components.
Perform this procedure when the inlet valve seal or the inlet valve is
being replaced.
Tools and supplies needed for replacing inlet valve components:
•
Ball Valve, complete (P/N A0101-02530)
•
Inlet Valve Seal Kit (P/N 119265-0003)
•
Lint-free cloth
•
Replacement Ball Valve O-ring and Seal Kit (P/N 76461-2002)
•
Wrench, open-ended, 5/16-in
•
Wrench, Allen, 4 mm
To replace inlet valve components, do the following:
1. Close the inlet valve by pulling the inlet valve lever down
(Figure 3-38).
1
2
3
4
Labeled components: 1=inlet valve knob, 2=inlet valve plug, 3=inlet valve
lever in the down (closed) position, 4=guide bar opening
Figure 3-38. Inlet valve
2. Remove the inlet valve knob, plug, and ferrule (Figure 3-39).
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9
1
8
2
7
6
3
5
4
Labeled components: 1=inlet valve plug, 2=vacuum manifold, 3=inlet valve
lever, 4=guide bar, 5=entry housing, 6=inlet valve knob, 7=inlet valve block,
8=foreline hose connection, 9=ball valve housing, 10=inlet valve solenoid
Figure 3-39. Inlet valve components (ion volume tool not shown)
3. Remove the existing inlet valve seal.
a. Insert the inlet valve seal removal tool (Figure 3-40) into the
inlet valve.
Figure 3-40. Inlet valve seal removal tool (P/N 119283-0001)
b. Press the button on the tool to engage the seal.
c. Pull out the seal and discard it.
4. Replace the inlet valve seal with a new one.
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User Maintenance
Maintenance of the ETD Module
5. Put ferrule, knob, and plug back into the inlet valve opening.
Caution Do not scratch the surface of the seal. Use the supplied tool
only. ▲
Changing the Reagent Vials
A significant drop of the m/z 202 signal within one hour with the
mission current at the correct level indicates a low reagent supply. In this
case, you should replace the fluoranthene vial.
Changing the reagent vials requires that the LTQ Orbitrap XL ETD be
placed in Service mode after the vials have cooled. (Vial cooling is done
in Off condition.) Refer to the following sections for procedures to be
used to change the reagent vials:
•
“Place the Instrument in Off Condition and Service Mode” on
page 3-49
•
“Removing the ETD Main Access Panel” on page 3-52
•
“Install/Exchange the Reagent Vials” on page 3-53
The ETD reagent vials are designed to keep the ETD reagent out the lab
environment. Removal and replacement of the ETD reagent vials when
they are not empty causes excessive puncturing of the septums and
reduces their integrity. This could result in ETD reagent (fluoranthene)
entering the lab environment. Prevent this from occurring by removing
and replacing the ETD reagent vials only when they are empty.
Caution To preserve the integrity of the ETD reagent vial septums,
remove and replace the ETD reagent vials only when they are empty. Do
not reinstall used vials. ▲
Note Store and handle all chemicals in accordance with standard safety
procedures. The Material Safety Data Sheet (MSDS) describing the
chemicals being used should be freely available to lab personnel for them
to examine at any time. Material Safety Data Sheets (MSDSs) provide
summarized information on the hazard and toxicity of specific chemical
compounds.
MSDSs also provide information on the proper handling of
compounds, first aid for accidental exposure, and procedures for
cleaning spills or dealing with leaks. Producers and suppliers of chemical
compounds are required by law to provide their customers with the
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User Maintenance
Maintenance of the ETD Module
most current health and safety information in the form of an MSDS.
Read the MSDS for each chemical you use. Dispose of all laboratory
reagents in the appropriate manner (see the MSDS). ▲
Safety information about fluoranthene is given in Appendix A:
“Fluoranthene”.
Place the Instrument in Off Condition and Service Mode
The power switches control power to the LTQ Orbitrap XL ETD (MS
and ETD Module). The ETD Module power switches control the
power to the ETD Module only. When the LTQ Orbitrap XL ETD is
fully operational (all systems On), the MS Main Power switch is in the
On position and the FT Electronics switch is in the operating (On)
position.
Normally, the ETD Module Power and Service switches remain On. Use
the FT Electronics switch on the MS unit to place the
LTQ Orbitrap XL ETD in Service mode. Turn On and Off the
instrument (both ETD Module and MS) with the MS Main Power
switch.
Warning When mass spectrometer and ETD Module system are turned
On, the flow restrictor, the transfer line heaters, and the ion source
heater can be at 160 °C. The vial heaters can be at 108 °C (or set point).
Do not attempt to replace reagent vials or to service heated components
until you have determined that they have cooled to a safe temperature
for handling. ▲
The instructions that follow assume that no analyte is flowing into
the API source.
To place the LTQ Orbitrap XL ETD in Off Condition and Service
mode and to verify that the vials are safe to handle, do the following:
1. If the Tune Plus window is not already open, choose Start >
Programs > Thermo Instruments > LTQ > LTQ Tune from the
taskbar. The Tune Plus window appears. (See Figure 3-9 on
page 3-20.)
On
Off
Standby
You can determine the state of the MS detector by observing the
state of the On/Standby button on the Control/Scan Mode toolbar.
The three different states of the On/Standby button are shown at
the left.
2. Choose Control > Off from the Tune Plus pull-down menu to place
the system in Off condition. When the MS detector is in Off
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LTQ Orbitrap XL ETD Hardware Manual
3-49
User Maintenance
Maintenance of the ETD Module
condition, the LTQ Orbitrap XL ETD turns off the ion source
sheath gas, auxiliary gas, high voltage, and all of the ETD Module
heaters.
Note It is important to choose Control > Off from the Tune Plus
pull-down menu in order to shut down all of the ETD Module
heaters. ▲
3. Click the reagent ion source portion of the instrument control icon
at the top of the Tune Plus window. The Reagent Ion Source dialog
box appears (Figure 3-41).
Observe the temperature of Vial 1 in the Actual column of the
Reagent Ion Source dialog box (Figure 3-41). Nitrogen cooling gas
will flow until the vial reaches 70 °C. (See topic “Turning Off the
Reagent Ion Source: What to Expect” on page 2-14.) Allow up to
90 minutes for the vial temperature to reach ambient temperature
(about 30 °C).
actual vial
temperature
in °C
Figure 3-41. Reagent Ion Source dialog box
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LTQ Orbitrap XL ETD Hardware Manual
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User Maintenance
Maintenance of the ETD Module
Warning Do not attempt to handle the vials or vial holders when the
cooling nitrogen stops. They are still too hot to handle when the cooling
nitrogen stops at a vial temperature of 70 °C.
Allow the vials to cool to about 30 °C (allow up to 90 minutes after the
cooling gas stops) before proceeding with the next step and handling the
vials. ▲
4. Toggle the FT Electronics switch to Service mode (Off ) when the
vial has reached a temperature that is safe for handling (about
30 °C). Toggling the FT Electronics switch to Service mode turns
off all components except the turbopumps and the forepumps in
both the mass spectrometer and the ETD Module.
Note Do not place the ETD Module Service switch into its Service
mode (Off ) position while the MS switches are left in their On
positions. This could cause communication problems between the MS
and the ETD Module. The ability to control the Service mode for both
the MS and the ETD Module at one point (at the FT Electronics
switch) is a safety feature. ▲
Warning Do not place the system in Service mode until the vials reach a
safe temperature (about 30 °C). System temperature monitoring will
stop when the system is placed in Service mode. Do not attempt to
handle the vials, the vial holders, or the heater assembly until a safe
temperature is reached (about 30 °C). ▲
The LTQ Orbitrap XL ETD is now in Service mode and the vials are at
a safe temperature for handling.
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LTQ Orbitrap XL ETD Hardware Manual
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User Maintenance
Maintenance of the ETD Module
Removing the ETD Main Access Panel
Figure 3-42 shows a schematical view of the rear side of the
ETD Module.
7
8
6
5
9
4
3
2
1
Labeled components: 1=ETD main access panel, 2=side access panel, 3=inlet
valve knob, 4=inlet valve lever (down is closed, up is open), 5=inlet valve
plug, 6, 7, 8, 9=panel fasteners
Figure 3-42. Schematical rear view of the ETD Module
To remove the ETD main access panel, do the following:
1. Place the ETD Module to Service mode as directed in topic “Place
the Instrument in Off Condition and Service Mode” on page 3-49.
Note In Service mode, all power to the LTQ Orbitrap XL ETD
electronics is turned Off. There are no user accessible components that
carry a voltage in this mode. However, the vacuum pumps continue to
operate. ▲
Warning The reagent vial heaters can be 108 °C (or set point); the
transfer line, the restrictor, and the ion source can be at 160 °C. These
components may be too hot to touch. Exercise caution and verify that
all of these components are safe to touch before handling them. ▲
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User Maintenance
Maintenance of the ETD Module
Note The ETD main access panel is interlocked with the ETD Module
power. When the ETD main access panel is removed, all power to the
ETD Module will be turned off. However, the mechanical pump
(ETD forepump) and ETD turbopump will continue operating. ▲
2. Remove the inlet valve lever (item 4 in Figure 3-42 on page 3-52) by
pulling it down and away from the ETD Module main access panel.
Caution Do not rotate the inlet valve lever upwards (to the open
position) without the inlet valve plug (item 5 in Figure 3-42) or the ion
volume tool in place. It must remain in its down (closed) position to
avoid catastrophic venting of the system. ▲
3. Remove the inlet valve knob (item 3 in Figure 3-42) and the inlet
valve plug (item 5) by unscrewing the inlet valve knob. Be sure that
the inlet valve lever (item 4) remains in the down position.
4. Remove the four panel fasteners (items 6, 7, 8, 9 in Figure 3-42).
5. Tilt the top of panel towards you and lift it up and away from the
ETD Module.
Replace the panel by following the above steps in reverse order and
reversing the instructions in each step.
Install/Exchange the Reagent Vials
After the reagent vial heaters have cooled to room temperature, the
reagent vials are ready to be installed or exchanged.
To install or exchange the reagent vials, do the following:
1. Remove the back panel from the ETD Module (see topic
“Removing the ETD Main Access Panel” on page 3-52). This
exposes the reagent inlet source heating unit, which has its own
cover (Figure 3-43 on page 3-54).
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LTQ Orbitrap XL ETD Hardware Manual
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User Maintenance
Maintenance of the ETD Module
Warning Follow the procedures described in topic “Place the
Instrument in Off Condition and Service Mode” on page 3-49 before
removing the back panel of the ETD Module. Removing the back panel
before the system is placed in Service mode will open the panel electrical
interlocks and stop all system activity including temperature
monitoring. In the absence of temperature monitoring, you might
attempt to handle the vials before it is safe to do so. ▲
2. Make sure that the vial heater cover is cool to the touch.
Warning The vial heaters can be at 108 °C (or set point). Allow
sufficient time for the vials to cool (up to 90 minutes) and then place
the system in Service mode. (See topic “Place the Instrument in Off
Condition and Service Mode” on page 3-49.) Verify that the vial heater
cover is safe to handle before attempting to remove the vial holders and
reagent vials. ▲
Reagent Inlet
Source Unit
Vial Heater Cover
Figure 3-43. ETD Module with back panel removed
3. Remove the vial heater cover. The screws that need to be removed
require a 3/32 inch or 2.38 mm hex driver. The vial heater cover is
located on the right side of the ETD Module as you view it from the
back of the LTQ Orbitrap XL ETD (Figure 3-43).
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User Maintenance
Maintenance of the ETD Module
4. Remove the vial holder by gently pulling it out of the vial heater.
Remove the empty vial if it is present. The vial holder is a cylindrical
tube with a handling knob at one end and ribs along its length. See
Figure 3-44. These ribs prevent the vial holder from rotating once it
is placed into the vial heater. Figure 3-45 on page 3-56 shows the tab
and ribs of a vial holder in the vial heater.
Note Dispose of an empty fluoranthene vial in accordance with its
MSDS. ▲
Figure 3-44. Reagent vials with holders
Note Store and handle all chemicals in accordance with standard safety
procedures. The Material Safety Data Sheet (MSDS) describing the
chemicals being used are to be freely available to lab personnel for them
to examine at any time. Material Safety Data Sheets (MSDSs) provide
summarized information on the hazard and toxicity of specific chemical
compounds. MSDSs also provide information on the proper handling
of compounds, first aid for accidental exposure, and procedures for
cleaning spills or dealing with leaks.
Producers and suppliers of chemical compounds are required by law to
provide their customers with the most current health and safety
information in the form of an MSDS. Read the MSDS for each
chemical you use. Dispose of all laboratory reagents in the appropriate
manner (see the MSDS). ▲
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
3-55
User Maintenance
Maintenance of the ETD Module
5. Take a vial containing the ETD reagent (fluoranthene) from its box
and place it into a vial holder.
Vial Heater ribs
Vial 1 Heater
Vial Holder Knob
Vial 2 Heater
Figure 3-45. ETD Module with vial heater cover removed
6. Place this ETD reagent vial and its vial holder into the Vial 1 heater
(top vial heater). Gently slide the vial holder into the vial heater.
7. Place the empty vial from the box into the other vial holder if an
empty vial is not already installed.
8. Place this empty vial and its vial holder into the Vial 2 heater
(bottom vial heater) if an empty vial is not already installed.
Warning The empty vial in the Vial 2 heater is an integral part of the
carrier/CI gas system. It is necessary to keep the carrier/CI gas system
closed to the laboratory. If no vial is placed in the Vial 2 heater:
3-56
LTQ Orbitrap XL ETD Hardware Manual
•
The carrier/CI gas containing the reagent may escape to the
laboratory causing a safety problem.
•
The ETD Module will not operate correctly and the filament will
burn out. ▲
Thermo Fisher Scientific
User Maintenance
Maintenance of the ETD Module
9. Replace the vial heater cover over the vial heaters.
10. Reinstall the back panel of the ETD Module. See topic “Removing
the ETD Main Access Panel” on page 3-52. The ETD Module will
not turn on unless the back panel is installed.
11. Start the system:
a. Toggle the FT Electronics switch to the On position.
The system will boot to Standby mode. Then ion source heater,
flow restrictor, and transfer line heaters will start heating.
Monitor these temperatures in the Status View on the right side
of the Tune Plus window. (See Figure 3-9 on page 3-20.) They
will have green check marks when they have reached their
operating temperatures.
b. Select the Reagent Ion Source On check box in the Reagent Ion
Source dialog box when the ion source heater, flow restrictor,
and transfer line heaters are at their operating temperatures. (See
Figure 3-41 on page 3-50.)
The LTQ Orbitrap XL ETD is now ready for use.
Changing the Reagent Ion Source Flow Restrictors
To change the reagent ion source flow restrictors, do the following:
1. Shut down completely the instrument according to the procedures
in topic “Shutting Down the LTQ Orbitrap XL ETD Completely”
on page 2-7.
Warning The reagent vial heaters can be 108 °C (or set point), the flow
restrictor, the transfer line heaters, and the ion source heater can be at
160 °C. These components may be too hot to touch. Verify that all of
these components are safe to touch before handling them. ▲
2. Remove the ETD side access panel according to the instructions in
topic “Removing the ETD Side Access Panel” on page 3-33.
Caution The ETD side access panel is interlocked with the
ETD Module power. When the ETD side access panel is removed, all
power to the ETD Module will be turned off. ▲
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User Maintenance
Maintenance of the ETD Module
3. Remove the four screws that hold the reagent inlet cover in place.
Warning The reagent inlet cover may be too hot to touch. Verify that
the reagent inlet cover is at or near room temperature before handling
it. ▲
4. Remove the five screws that hold the restrictor oven cover in place.
Warning The restrictor oven cover may be too hot to touch. Verify that
the restrictor oven cover is at or near room temperature before handling
it. ▲
5. Replace both fused silica restrictors and their ferrules by removing
their Swagelok® nuts. See Figure 3-46.
6
5
4
3
2
7
8
9
10
1
Labeled components: 1=PEEKsil® tubing, 2=fused silica tubing from lower
oven, 3=transfer line inlet, 4=Swagelok fitting with two hole ferrule, 5=fused
silica tubing from upper oven, 6=upper oven Swagelok fitting with a single
hole ferrule, 7=vial 1 (upper) and vial 2 (lower) heaters, 8=lower oven
Swagelok fitting with a single hole ferrule, 9=Tee below reagent inlet
assembly, 10=gas valves
Figure 3-46. Reagent inlet assembly
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User Maintenance
Maintenance of the ETD Module
6. Thread two pieces of fused silica tubing (P/N 98000-20060) into
the two hole ferrule (P/N 00101-08-00006) from the Installation
Kit for the Reagent Inlet Module (P/N 98000-62006). Place a
Swagelok fitting over the ferrule.
7. Insert the two hole ferrule and Swagelok fitting from step 6 onto the
transfer line inlet (item 3 in Figure 3-46) and tighten the Swagelok
fitting.
8. Thread the opposite end of one of the pieces of fused silica tubing
into a single hole ferrule. Place a Swagelok fitting over the ferrule.
9. Insert the ferrule and Swagelok fitting from step 8 on to one of the
oven outlets (items 6 or 8 in Figure 3-46) and tighten the Swagelok
fitting.
Caution Do not overtighten the ferrules. The ferrules may loosen after
they are first heated. If this occurs retighten them if necessary. ▲
10. Repeat step 9 for the other oven.
11. Replace the restrictor oven cover and reagent inlet cover removed in
step 3 and step 4.
12. Loosen the Swagelok fitting connecting the PEEKsil® tubing (item 1
in Figure 3-46) to the Tee below the reagent inlet assembly (item 9
in Figure 3-46) and from the gas valves (item 10 in Figure 3-46).
13. Replace the old PEEKsil tubing with new PEEKsil tubing
(P/N 00109-02-00020) from the Installation Kit for the Reagent
Inlet Module (P/N 98000-62006).
14. Close the ETD Module and restart the instrument. Follow the
procedures given in topic “Starting Up the System after a
Shutdown” on page 2-9.
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LTQ Orbitrap XL ETD Hardware Manual
3-59
User Maintenance
Maintenance of the ETD Module
Cleaning the Fan Filters of the ETD Module
You need to clean the fan filters every four months. The fan filters are
located at the rear of the ETD Module on the left side (as viewed from
the back of the ETD Module). See Figure 3-47.
Fan filters
Figure 3-47. ETD Module, top panel
To clean the fan filters of the ETD Module, do the following:
1. Remove the fan filter from the rear of the ETD Module by pulling it
out of the fan filter bracket.
2. Wash the fan filters in a solution of soap and water.
3. Rinse the fan filters with tap water.
4. Squeeze the water from the fan filters and allow them to air dry.
5. Reinstall the fan filter in the fan filter bracket.
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User Maintenance
Maintenance of the Recirculating Chiller
Maintenance of the Recirculating Chiller
For the NESLAB ThermoFlex™ 900 recirculating chiller, the checks
described in this section 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.
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LTQ Orbitrap XL ETD Hardware Manual
3-61
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 XL ETD 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 XL / LTQ Orbitrap Discovery
Preinstallation Requirements Guide.
Note Not all parts are available for purchase separately. Some parts may
only be available for purchase as part of a kit or assembly. ▲
This chapter contains the following topics:
Thermo Fisher Scientific
•
“Parts List for the Mass Analyzer” on page 4-2
•
“Parts Lists for the ETD System” on page 4-11
LTQ Orbitrap XL ETD Hardware Manual
4-1
Replaceable Parts
Parts List for the Mass Analyzer
Parts List for the Mass Analyzer
This topic contains parts lists for the mass analyzer portion of the
LTQ Orbitrap XL ETD.
Table 4-1.
Parts for the LTQ Orbitrap XL
Designation
Part No.
LTQ Orbitrap XL; 50 Hz*
072 3852
LTQ Orbitrap XL; 60 Hz
072 3862
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
†
OPTON-20026
APPI probe
* Module, for parts list see below.
† Optional equipment.
Table 4-2.
Parts LTQ Orbitrap XL; 50 Hz (P/N 072 3852)
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
Recirculating chiller Neslab ThermoFlex 900 PD-1 230V/50 Hz
101161010000004
Upgrade kit Orbitrap HCD option*
122 4800
* Module, for parts list see below.
Parts Basic System
This section contains parts lists for the mechanical components of the
LTQ Orbitrap XL ETD.
Table 4-3.
Pos. No.
4-2
LTQ Orbitrap XL ETD Hardware Manual
Parts basic system Orbitrap-2 (P/N 122 4790)
Qty.
Designation
Part No.
*
0010
1
Orbitrap-2 chamber; complete
0020
1
Orbitrap-D30; complete
116 5000
0030
1
CLT and lens system; complete
122 1200
122 4780
Thermo Fisher Scientific
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-3.
Pos. No.
Qty.
Designation
Part No.
*
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
1
Electronic parts Orbitrap-2*
800 1110
0100
*
Parts basic system Orbitrap-2 (P/N 122 4790)
Module, for parts list see below.
Table 4-4.
Parts Upgrade kit Orbitrap HCD option (P/N 122 4800)
Pos. No.
Qty.
Designation
Part No.
0010
1
Collision cell, with mount
122 1320
0020
1
Flange, for options; complete
122 1250
0030
1
Cable kit, Upgrade LTQ Orbitrap XL
122 5100
0040
1
Upgrade kit gas supply LTQ Orbitrap XL*
122 4820
0050
1
Cable, power distribution/valve
210 0310
* Module, for parts list see below.
Table 4-5.
Parts Orbitrap Installation Kit (P/N 118 8120)
Pos. No.
Qty.
Designation
Part No.
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
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.
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
4-3
Replaceable Parts
Parts List for the Mass Analyzer
Parts Orbitrap Analyzer
Table 4-6.
Parts Orbitrap-2 chamber; complete (P/N 122 4780)
Pos. No.
Qty.
Designation
Part No.
0010
1
UHV chamber; complete
116 6110
0020
1
Vacuum chamber, complete
116 6131
0040
4
Washer; 8.4×15×1.5, stainless steel
047 0860
0050
4
Screw; M8×25, 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 Orbitrap
Parts pumping system Orbitrap (P/N 118 4490)*
Table 4-7.
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 schematical overview of the vacuum system, refer to Figure 1-20 on page 1-28.
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.
4-4
LTQ Orbitrap XL ETD Hardware Manual
Parts pump kit Orbitrap (P/N 117 5000)
Pos. No.
Qty.
Designation
Part No.
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
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=1.6 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
Thermo Fisher Scientific
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-8.
Parts pump kit Orbitrap (P/N 117 5000), continued
Pos. No.
Qty.
Designation
Part No.
0100
1
Splinter shield for turbopumps, with DN 100 CF-F
flange
119 8590
0110
2
Centering ring, with integrated splinter shield;
DN 63 ISO
119 8600
Table 4-9.
Parts pump system Orbitrap (P/N 117 5010)
Pos. No.
Qty.
Designation
Part No.
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
Parts Gas and Water Supply
This topic contains parts lists for the gas and water supply of the
LTQ Orbitrap XL ETD. For a schematical overview of the gas supply,
refer to Figure 1-26 on page 1-36.
Table 4-10. Parts gas supply (P/N 117 7881)
Thermo Fisher Scientific
Pos. No.
Qty.
Designation
Part No.
0010
2
Bulkhead union; 1/16”, for hose 4 x 1 (for
P/N 069 1130)
115 3660
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
LTQ Orbitrap XL ETD Hardware Manual
4-5
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-10. Parts gas supply (P/N 117 7881)
Pos. No.
Qty.
*
Designation
Part No.
Capillary 1/16" ID-SS
060 5470
0050
0.5 m
0060
2
Plug-in T-piece; 3 x 6mm
112 8140
0070
1
Stainless steel 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
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)
Pos. No.
Qty.
*
Designation
Part No.
Capillary 1/16" ID-SS
060 5470
0050
0.10 m
0070
1
Stainless steel 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.
Table 4-12. Parts water supply (P/N 117 8460) *
Pos. No.
Qty.
Designation
Part No.
0010
2
Quick coupling insert; 9.6 mm
114 1640
0020
2
Quick coupling body; 9.6 mm
113 8960
Hose; 9 x 3, black, PVC
104 9540
Hose clamp; 1-ear, 14.6–16.8 mm
114 4910
Hose; 4 x 1, Teflon
069 0280
0030
10 m
0040
4
0050
4-6
LTQ Orbitrap XL ETD Hardware Manual
†
1.5 m
†
Thermo Fisher Scientific
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-12. Parts water supply (P/N 117 8460), continued*
Pos. No.
Qty.
Designation
Part No.
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 schematical overview of the cooling water circuit, refer to Figure 1-30 on page 1-40.
†
Specify required length.
Table 4-13. Kit gas-water assembly (P/N 208 7351)
Pos. No.
Qty.
Designation
Part No.
0010
1
Bulkhead union; 1/16”, for hose 4 x 1 (for
P/N 069 1130)
115 3660
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
Hose; 9 x 3, black, PVC
104 9540
Hose clamp; 1-ear, 14.6–16.8 mm
114 4910
0090
6.0 m
0100
2
*
* Specify required length.
Electronic Parts
This section contains parts list for the electronic components of the
LTQ Orbitrap XL ETD.
Table 4-14. Electronic parts Orbitrap-2 (P/N 800 1110)
Pos. No.
Thermo Fisher Scientific
Qty.
Designation
Part No.
*
0050
1
Orbitrap-2 Electronics; right panel
210 1480
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
210 1690
0110
1
Cable kit LTQ-Orbitrap grounding
208 1070
LTQ Orbitrap XL ETD Hardware Manual
4-7
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-14. Electronic parts Orbitrap-2 (P/N 800 1110)
Pos. No.
Qty.
Designation
Part No.
0120
1
Kit Orbitrap assembly material
208 1080
0130
1
Subpackage Orbitrap-2 assembly
210 1660
1
Kit gas-water assembly†
208 7351
0140
*
Module, for parts list see below.
†
Module, see Table 4-13 on page 4-7.
Electronics – Right Panel
The following replaceable parts are available for the electronics at the
right panel of the LTQ Orbitrap XL ETD.
Table 4-15. Parts Orbitrap-2 electronics; right panel (P/N 210 1480)
*
Pos. No.
Qty.
Designation
Part No.
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
Module, for parts list see below.
Table 4-16. Parts Unit data acquisition (P/N 206 4132)
4-8
LTQ Orbitrap XL ETD Hardware Manual
Pos. No.
Qty.
Designation
Part No.
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
Thermo Fisher Scientific
Replaceable Parts
Parts List for the Mass Analyzer
Table 4-16. Parts Unit data acquisition (P/N 206 4132), continued
Pos. No.
Qty.
Designation
Part No.
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 XL ETD.
Table 4-17. Parts Orbitrap-2 electronics; left panel (P/N 208 1020)
Pos. No.
Qty.
Designation
Part No.
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 XL ETD.
Table 4-18. Parts electronics analyzer Orbitrap-2 (P/N 210 0160)
Thermo Fisher Scientific
Pos. No.
Qty.
Designation
Part No.
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
LTQ Orbitrap XL ETD Hardware Manual
4-9
Replaceable Parts
Parts List for the Mass Analyzer
Electronics Main Supply
The following replaceable parts are available for the electronics main
supply of the LTQ Orbitrap XL ETD.
Table 4-19. Parts electronics main supply Orbitrap (P/N 208 1040)
4-10
LTQ Orbitrap XL ETD Hardware Manual
Pos. No.
Qty.
Designation
Part No.
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
Thermo Fisher Scientific
Replaceable Parts
Parts Lists for the ETD System
Parts Lists for the ETD System
This section contains parts lists for the components of the ETD System
of the LTQ Orbitrap XL ETD.
Table 4-20. Parts ETD Option for Orbitrap XL (P/N 072 3890)
*
Pos. No.
Qty.
Designation
Part No.
0010
1
ETD Upgrade kit for Orbitrap XL*
124 1480
0020
1
Software LTQ Orbitrap XL 2.5.5 DVD
124 4030
Module, for parts list see below.
Table 4-21. Parts ETD Upgrade kit for Orbitrap XL (P/N 124 1480)
Pos. No.
Qty.
Designation
Part No.
0010
1
Upgrade kit Orbitrap XL to ETD*
124 4690
0020
1
UNIT_CLT RF MAINBOARD
207 9581
0030
1
Packaging ETD
124 7040
* Module, for parts list see below.
Table 4-22. Parts Upgrade kit Orbitrap XL to ETD (P/N 124 4690)
Pos. No.
Qty.
Designation
Part No.
0010
1
ETD-Unit Mechanics*
123 9920
0020
1
Collision cell (axial field) with mount, complete
124 0850
0030
1
Connections; antechamber Orbitrap-3
124 1400
0040
1
Quadrupole Orbitrap, complete
123 9200
0050
1
Mounting parts; ETD*
123 9300
0060
1
ETD housing, complete
123 3750
0070
1
Kit ETD electronics*
210 8880
*
0080
1
ETD upgrade from LTQ XL
0090
1
Cross beam for ETD frame
117 2210
0100
1
Unit CLT-Offset-Filter
211 0470
OPTON-97103
* Module, for parts list see below.
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
4-11
Replaceable Parts
Parts Lists for the ETD System
Mechanical Parts for ETD System
Table 4-23. ETD unit mechanics (P/N 123 9920)
Pos. No.
*
Qty.
Designation
Part No.
1
1
Transfer tube with flatapole for ETD*
121 7000
2
1
Housing HCD/ETD*
123 1780
Module, for parts list see below.
Table 4-24. Parts for transfer tube with flatapole for ETD (P/N 121 7000)
Pos. No.
Qty.
Designation
Part No.
0010
1
Tube with flatapole for ETD, complete
121 7400
0020
1
Mount 1, for ETD flatapole
121 7130
0030
3
Rubber bumper; 20x15-M6
121 7370
0040
1
Support, for ETD tube
121 7380
0050
4
Washer 6.4; stainless steel
047 0060
0060
2
Allen screw, stainless steel; M6; 20 long
045 3420
0070
1
Counter support, for ETD tube
121 7490
0080
2
Cylindrical Screw ISO4762-M6X12-A4
045 3300
0090
2
Nut, stainless steel; M6
046 0520
Table 4-25. Parts Housing HCD/ETD (P/N 123 1780)
4-12
LTQ Orbitrap XL ETD Hardware Manual
Pos. No.
Qty.
Designation
Part No.
0010
1
Housing HCD/ETD
123 1740
0020
1
Separating plate HCD/ETD
123 1770
0030
6
Screw M 4 x 8 DIN912
104 4420
0040
1
O-ring 129 X 4 A Viton
124 0520
0050
1
Lid HCD/ETD
123 1760
0060
2
Screw-in connector; 1/16”
118 6150
0070
3
Gasket; NW 63 ISO, aluminum/Viton
055 4060
0080
2
Blank flange; stainless steel, NW 63
065 2620
0090
8
Clamping screw; DN63-100, aluminum
102 8380
0100
4
Washer 8.4; stainless steel
047 0070
0110
4
Screw, hexagonal; M 8 x 35, stainless steel
045 4400
0120
4
Washer 8.4 x 11 x 1.5, stainless steel
047 0860
0130
4
Screw M8 x 35; stainless steel
045 4250
0140
1
Centering ring NW 16 Viton
052 2140
0150
1
Feedthrough; 8-fold 1,5kV DN16KF
123 1750
0160
1
O-ring; 118 X 5 A, Viton
116 8240
Thermo Fisher Scientific
Replaceable Parts
Parts Lists for the ETD System
Table 4-25. Parts Housing HCD/ETD (P/N 123 1780), continued
Pos. No.
Qty.
Designation
Part No.
0170
1
Box f. feedthrough; KF16 / Sub-D9
123 1800
0180
6
Cylindrical Screw ISO4762-M6X12-A4
045 3300
0190
1
Flange clamp; KF16
114 5860
0200
2
Washer, stainless steel, ID 6.4
047 0850
0210
2
Allen screw, stainless steel; M6; 20 long
045 3420
0220
1
Adapter flange
116 8050
0230
4
Clamping screw; DN63-100 ISO, aluminum
104 2670
0240
3
Guide bolt
124 3930
0300
1
Cable set; HCD/ETD box
123 9660
0400
1
Cable set; HCD/ETD feedthrough
123 9670
Table 4-26. Mounting parts ETD (P/N 123 9300)
Pos. No.
Qty.
Designation
Part No.
0010
1
Pfeiffer - Kit for ETD*
124 1510
0020
1
ILMVAC - Kit for ETD*
124 1520
0030
1
Springer - Kit for ETD*
0040
1
124 1530
Mounting parts - Kit for ETD
*
124 1540
* Module, for parts list see below.
Table 4-27. Pfeiffer - Kit for ETD (P/N 124 1510)
Pos. No.
Qty.
Designation
Part No.
0010
1
TURBOPUMP TMH 071 P
114 1500
0020
1
Splinter guard, DN_63_ISO
119 8600
0030
1
Water cooling, for TMH 071 P
079 4742
Table 4-28. ILMVAC - Kit for ETD (P/N 124 1520)
Thermo Fisher Scientific
Pos. No.
Qty.
Designation
Part No.
0010
2
Metal hose, DN 16 ISO-KF x500
118 1410
0020
3
Centering ring with o-ring; DN 16, Viton
052 2140
0030
2
Clamping ring; NW 10/16, KF
052 1830
0040
1
Hose flange; NW 25 KF
104 2330
0050
2
Centering ring, with o ring; DN 25, Viton
052 2150
0060
2
Clamping ring, DN 25
052 1560
0070
1
Flange, KF16 - hose OD 19
123 9340
0080
1
Reducer; DN 16/DN 25, aluminum
052 2160
LTQ Orbitrap XL ETD Hardware Manual
4-13
Replaceable Parts
Parts Lists for the ETD System
Table 4-29. Springer - Kit for ETD (P/N 124 1530)
Pos. No.
Qty.
Designation
Part No.
0010
1
Plug-in T-piece; 3 x 6mm
112 8140
0020
1
Sleeve 6 mm
104 7320
0030
1
Reducing hose connector, 3.2−>6
123 9220
0040
1
Hose cutter
123 9280
0050
1
Allen wrench 5 mm; long with ball head
123 9290
0060
1
Ring wrench; 10x11, cranked
123 9310
0070
1
Mounting paste; MoS2 - Tube 50 g
124 3890
Table 4-30. Mounting parts - Kit for ETD (P/N 124 1540)
Pos. No.
Qty.
Designation
Part No.
0010
1
T-piece 13 mm
051 2360
0020
2m
Hose 9 X 3; PVC, black
104 9540
0030
4
Clamping piece 8/16
037 0130
0040
2m
Hose 13 X 3.5; PVC
069 0720
0050
2
Allen screw, stainless steel; M6; 20 long
045 3420
0060
9
Spring washer; DIN127-B 6-A4
047 0560
0070
1
Cylinder screw; stainless steel, M 4, 12 long
045 0810
0080
2
Spring washer; DIN127-B 4-1.4310
047 0580
0090
1
Nut, stainless steel, M4
046 0220
0100
2
Allen screw, stainless steel; M 6; 25 long
045 3720
0110
3
Allen screw; stainless steel; M6; 45 long
045 3440
0120
2
Nut, stainless steel; M6
046 0520
0130
2
Water draining hose, for ETD
124 4080
0140
0.5 m
Hose; 4 X 1, Teflon
069 0280
0150
1
Clamping ring; stainless steel, NW10/16
114 9200
0160
0.25 m
PEEK capillary; 1/16” x 0.040
124 5940
0170
1
Ferrule, 1/16”, for GVF/16
067 4800
0180
1
Ferrule 1/16" - CTFE, collapsible
122 4700
Electronic Parts of ETD System
Table 4-31. Parts KIT_ETD-ELECTRONICS (P/N 210 8880)
4-14
LTQ Orbitrap XL ETD Hardware Manual
Pos. No.
Qty.
Designation
Part No.
0010
1
INTERCONNEC_ETD-LTQ-ORBITRAP
210 8890
0020
1
Cable Y-ADAPTER/T.PUMP
210 8630
0030
1
Coupling; RJ45 BU/2BU
207 5210
Thermo Fisher Scientific
Replaceable Parts
Parts Lists for the ETD System
Table 4-31. Parts KIT_ETD-ELECTRONICS (P/N 210 8880), continued
Pos. No.
Qty.
Designation
Part No.
0040
1
Patch cable; 0.51MT RJ45 gray SFTP
208 0870
0050
1
Cable POWER DIS./T-PUMP
208 1200
0060
1
Cable CLT-OFFSET-A
210 8710
0080
1
Cable IOS ETD/ION OPTIC-S
210 8820
0090
1
UNIT_ION OPTIC SUPPLY ETD
210 8920
0100
1
PCB LTQ CABLE DRIVER
209 7780
0110
1
PCB ORBITRAP CABLE RECEIVER
209 7830
0120
1
PCB ETD CABLE RECEIVER
209 7800
0130
1
Cable ETD/LTQ/ORBITRAP-INTERCONNECT 60
210 8940
0140
1
Cable ETD/LTQ/ORBITRAP-INTERCONNECT 36
210 8950
0150
1
Cable ETD/LTQ/ORBITRAP-INTERCON SUPPLY
210 8960
0160
1
Traverse 2, with plate
123 8440
0170
1
Coaxial cable; ETD IOS/ANALOG CTRL, J5554
210 8990
0180
1
Coaxial cable; ETD IOS/ANALOG CTRL, J5555
210 9000
0190
1
Coaxial cable; ETD IOS/ANALOG CTRL, J5556
210 9010
0200
1
Cable ANALOG CTRL / ETD IOS
210 8970
0210
1
Cable ETD IOS/HCD multipole
210 8980
0220
1
Extension cable; 16A C20-C19 2M
209 7050
0230
20
Cable tie; 20 maximum
008 1710
0260
1
ADAPTER_IOS/MULTIPOLE-HCD
210 0410
Parts Lists for the ETD Module
Table 4-32. ETD upgrade from LTQ XL (P/N OPTON-97103)
Pos. No.
Qty.
Designation
Part No.
0010
1
KIT, INTEGRATION, LTQ XL-ETD
98000-62003
0020
1
ASSY, SYSTEM, ETD
98000-60000
0030
1
Kit, Mechanical Pump, ETD*
98000-62005
0040
1
KIT, SHIP, ETD
98000-62004
0050
1
ETD Accessory Kit
98000-62002
0060
1
ETD Reagent Kit*
98000-62008
0070
1
ASSY, TOOL, ION VOLUME
INSERTION/REMOVAL
98000-60028
0080
1
Kit, Common Software
97355-62020
0090
1
KIT, SWRE, BIOWORKS 3.3.1 SP1
97355-62005
* Module. see below.df
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
4-15
Replaceable Parts
Parts Lists for the ETD System
Table 4-33. Parts Kit, Mechanical Pump, ETD (P/N 98000-0005)
Pos. No.
Designation
Part No.
0010
PUMP, ROTARY VANE, EDWARDS RV3
00108-01-0008
0020
KIT, ACCESSORY, MECHANICAL PUMP, RV3
98000-620007
Table 4-34. Parts Installation Kit Reagent Inlet Module (P/N 98000-62006)
Pos. No.
Qty.
Designation
Part No.
0010
1
TUBING, PEEKsil, 1/16"OD, 100mm LONG, RoHS
00109-02-00020
0020
2
FRLE, 1HOLE, 1/16OD, 0.4mmID, VESP/GRPHT,
RO
00101-08-00005
0030
1
FRLE, 2HOLS, 1/16OD, 0.4mmID, VESP/GRPHT,
RO
00101-08-00006
Table 4-35. Parts Inlet Valve Seal Kit (P/N 119265-0003)
Pos. No.
Designation
Part No.
0010
Inlet valve seal removal tool
119283-0001
0020
Spool inlet valve seal
119683-0100
0030
O-ring Viton, 0530 ID × 0.082 W
3814-6530
Table 4-36. Parts Filament Assembly DSQ II (P/N 120320-0030)
4-16
LTQ Orbitrap XL ETD Hardware Manual
Pos. No.
Designation
Part No.
0010
Base, filament
119701-20513
0020
Reflector, filament
70001-20517
0030
Filament wire, formed
70001-20516
0040
Shroud, filament
70001-20518
0050
Extraction lens, filament
119701-20520
0060
Box, pastic, 1”×1”×1”, clear/wht
A0301-07532
Thermo Fisher Scientific
Replaceable Parts
Parts Lists for the ETD System
ETD Reagent Kit
The ETD Reagent Kit (P/N 98000-62008) contains angiotensin I and
fluoranthene. See Table 4-37.
Table 4-37. ETD Reagent Kit (P/N 98000-62008)
Pos. No.
Qty.
Designation
Part No.
1
1
Angiotensin I, 1mg
00301-15517
2
1
Fluoranthene, 150mg
00301-01-0013
The fluoranthene in your ETD Reagent Kit is Sigma/Aldrich Supelco
#48535. The fluoranthene MSDS is obtained from the MSDS link at:
www.sigmaaldrich.com/catalog/search/ProductDetail/SUPELCO/48535
Thermo Fisher Scientific supplies fluoranthene as a two vial kit. One
vial contains 150 mg of fluoranthene and the other is the required
empty vial.
The angiotensin I in your ETD Reagent Kit is Angiotensin I human
acetate hydrate (Sigma/Aldrich #A9650). Angiotensin I is potentially
hazardous. Handle it in accordance with its MSDS. The angiotensin I
MSDS is obtained from the MSDS link at:
www.sigmaaldrich.com/catalog/search/ProductDetail/SIGMA/A9650
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
4-17
Appendix A
Fluoranthene
Fluoranthene is used as the Electron Transfer Dissociation (ETD)
reagent in the ETD Module portion of the LTQ Orbitrap XL ETD.
The fluoranthene radical anion is generated according to the reaction
shown in Figure A-1.
Fluoranthene
Figure A-1. ETD Reagent (fluoranthene radical anion) generation from
fluoranthene
Fluoranthene is potentially hazardous. Use it in accordance with its
Material Safety Data Sheet (MSDS).
Note Store and handle all chemicals in accordance with standard safety
procedures. The MSDS describing the chemicals being used should be
freely available to lab personnel for them to examine at any time.
Material Safety Data Sheets (MSDSs) provide summarized information
on the hazard and toxicity of specific chemical compounds. The MSDS
also provides information on the proper handling of compounds, first
aid for accidental exposure, and procedures for cleaning spills or dealing
with leaks. Producers and suppliers of chemical compounds are required
by law to provide their customers with the most current health and
safety information in the form of an MSDS. Read the MSDS for each
chemical you use. Dispose of all laboratory reagents in the appropriate
way (see the MSDS). ▲
The fluoranthene contained in the ETD Reagent Kit
(P/N 98000-62008, see page 4-17) is Sigma/Aldrich Supelco #48535.
The fluoranthene MSDS is obtained from the MSDS link at:
www.sigmaaldrich.com/catalog/search/ProductDetail/SUPELCO/48535
Thermo Fisher Scientific supplies fluoranthene as a two vial kit. One
vial contains 150 mg of fluoranthene and the other is the required
empty vial.
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
A-1
Glossary
This section lists and defines terms used in this
manual. It also includes acronyms, metric prefixes,
symbols, and abbreviations.
A ampere
ac alternating current
ADC analog-to-digital converter
Automatic Gain Control™ (AGC) Sets the ion
injection time to maintain the optimum quantity
of ions for each scan. With AGC on, the scan
function consists of a prescan and an analytical
scan.
auxiliary gas The outer-coaxial gas (nitrogen) that
assists the sheath (inner-coaxial) gas in dispersing
and/or evaporating sample solution as the sample
solution exits the APCI, ESI, or H-ESI nozzle.
AGC™ See Automatic Gain Control™ (AGC).
b bit
APCI See atmospheric pressure chemical
ionization (APCI).
API See atmospheric pressure ionization (API).
APPI See Atmospheric Pressure Photoionization
(APPI).
ASCII American Standard Code for Information
Interchange
B byte (8 b)
baud rate data transmission speed in events per
second
BTU British thermal unit, a unit of energy
°C degrees Celsius
cfm cubic feet per minute
atmospheric pressure chemical ionization
(APCI) A soft ionization technique done in an ion
source operating at atmospheric pressure.
Electrons from a corona discharge initiate the
process by ionizing the mobile phase vapor
molecules. A reagent gas forms, which efficiently
produces positive and negative ions of the analyte
through a complex series of chemical reactions.
chemical ionization (CI) The formation of new
ionized species when gaseous molecules interact
with ions. The process can involve transfer of an
electron, proton, or other charged species
between the reactants.
CI See chemical ionization (CI).
atmospheric pressure ionization (API)
Ionization performed at atmospheric pressure by
using atmospheric pressure chemical ionization
(APCI), electrospray ionization (ESI), or
nanospray ionization (NSI).
CID See collision-induced dissociation (CID).
Atmospheric Pressure Photoionization (APPI)
A soft ionization technique in which an ion is
generated from a molecule when it interacts with
a photon from a light source.
cm3 cubic centimeter
Thermo Fisher Scientific
CLT curved linear trap
cm centimeter
collision gas A neutral gas used to undergo
collisions with ions.
LTQ Orbitrap XL ETD Hardware Manual
G-1
Glossary: collision-induced dissociation (CID)
collision-induced dissociation (CID) An ion/
neutral process in which an ion is dissociated as a
result of interaction with a neutral target species.
consecutive reaction monitoring (CRM) scan
type A scan type with three or more stages of mass
analysis and in which a particular multi-step
reaction path is monitored.
Convectron™ gauge A thermocouple bridge gauge
that is sensitive to the pressure as well as the
thermal conductivity of the gas used to measure
pressures between X and Y.
CPU central processing unit (of a computer)
CRM See consecutive reaction monitoring (CRM)
scan type.
C-Trap curved linear trap
<Ctrl> control key on the terminal keyboard
EI electron ionization
electron multiplier A device used for current
amplification through the secondary emission of
electrons. Electron multipliers can have a discrete
dynode or a continuous dynode.
electron transfer dissociation (ETD) A method
of fragmenting peptides and proteins. In electron
transfer dissociation (ETD), singly charged
reagent anions transfer an electron to multiply
protonated peptides within the ion trap mass
analyzer. This leads to a rich ladder of sequence
ions derived from cleavage at the amide groups
along the peptide backbone. Amino acid side
chains and important modifications such as
phosphorylation are left intact.
electrospray ionization (ESI) A type of
atmospheric pressure ionization that is currently
the softest ionization technique available to
transform ions in solution into ions in the gas
phase.
d depth
EMBL European Molecular Biology Laboratory
Da dalton
<Enter> Enter key on the terminal keyboard
DAC digital-to-analog converter
ESD electrostatic discharge
damping gas Helium gas introduced into the ion
trap mass analyzer that slows the motion of ions
entering the mass analyzer so that the ions can be
trapped by the RF voltage fields in the mass
analyzer.
ESI See electrospray ionization (ESI).
ETD See electron transfer dissociation (ETD).
eV electron volt
data-dependent scan A scan mode that uses
specified criteria to select one or more ions of
interest on which to perform subsequent scans,
such as MS/MS or ZoomScan.
dc direct current
divert/inject valve A valve on the mass
spectrometer that can be plumbed as a divert
valve or as a loop injector.
DS data system
DSP digital signal processor
G-2
LTQ Orbitrap XL ETD Hardware Manual
f femto (10-15)
°F degrees Fahrenheit
.fasta file extension of a SEQUEST® search
database file
ft foot
Fast Fourier Transform (FFT) An algorithm that
performs a Fourier transformation on data. A
Fourier transform is the set of mathematical
formulae by which a time function is converted
Thermo Fisher Scientific
Glossary: FFT
into a frequency-domain function and the
converse.
FWHM Full Width at Half Maximum
g gram
FFT See Fast Fourier Transform (FFT).
fluoranthene A reagent anion that is used in an
electron transfer dissociation (ETD) experiment.
G Gauss; giga (109)
GC gas chromatograph; gas chromatography
firmware Software routines stored in read-only
memory. Startup routines and low-level input/
output instructions are stored in firmware.
GC/MS gas chromatography / mass spectrometer
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump.
h hour
GUI graphical user interface
h height
Fourier Transform - Ion Cyclotron Resonance
Mass Spectrometry (FT-ICR MS) A technique
that determines the mass-to-charge ratio of an ion
by measuring its cyclotron frequency in a strong
magnetic field.
fragment ion A charged dissociation product of an
ionic fragmentation. Such an ion can dissociate
further to form other charged molecular or
atomic species of successively lower formula
weights.
fragmentation The dissociation of a molecule or
ion to form fragments, either ionic or neutral.
When a molecule or ion interacts with a particle
(electron, ion, or neutral species) the molecule or
ion absorbs energy and can subsequently fall
apart into a series of charged or neutral
fragments. The mass spectrum of the fragment
ions is unique for the molecule or ion.
handshake A signal that acknowledges that
communication can take place.
HCD Higher Energy Collision Induced
Dissociation
header information Data stored in each data file
that summarizes the information contained in the
file.
H-ESI source Heated-electrospray ionization
(H-ESI) converts ions in solution into ions in the
gas phase by using electrospray ionization (ESI)
in combination with heated auxiliary gas.
high performance liquid chromatography
(HPLC) Liquid chromatography in which the
liquid is driven through the column at high
pressure. Also known as high pressure liquid
chromatography.
FT Fourier Transformation
FT-ICR MS See Fourier Transform - Ion
Cyclotron Resonance Mass Spectrometry (FTICR MS).
HPLC See high performance liquid
chromatography (HPLC).
HV high voltage
FTMS Fourier Transformation Mass Spectroscopy
Hz hertz (cycles per second)
full-scan type Provides a full mass spectrum of
each analyte or parent ion. With the full-scan
type, the mass analyzer is scanned from the first
mass to the last mass without interruption. Also
known as single-stage full-scan type.
ID inside diameter
Thermo Fisher Scientific
IEC International Electrotechnical Commission
LTQ Orbitrap XL ETD Hardware Manual
G-3
Glossary: IEEE
IEEE Institute of Electrical and Electronics
Engineers
in inch
instrument method A set of experiment
parameters that define Xcalibur operating settings
for the autosampler, liquid chromatograph (LC),
mass spectrometer, divert valve, syringe pump,
and so on. Instrument methods are saved as file
type .meth.
I/O input/output
ion gauge Measures the pressure in the mass
analyzer region (high vacuum region) of the
vacuum manifold.
ion optics Focuses and transmits ions from the
API source to the mass analyzer.
ion source A device that converts samples to gasphase ions.
k kilo (103, 1000)
K kilo (210, 1024)
KEGG Kyoto Encyclopedia of Genes and
Genomes
kg kilogram
l length
L liter
LAN local area network
lb pound
LC See liquid chromatography (LC).
LC/MS See liquid chromatography / mass
spectrometry (LC/MS).
LED light-emitting diode
G-4
LTQ Orbitrap XL ETD Hardware Manual
liquid chromatography (LC) A form of elution
chromatography in which a sample partitions
between a stationary phase of large surface area
and a liquid mobile phase that percolates over the
stationary phase.
liquid chromatography / mass spectrometry
(LC/MS) An analytical technique in which a highperformance liquid chromatograph (LC) and a
mass spectrometer (MS) are combined.
μ micro (10-6)
m meter; milli (10-3)
M mega (106)
M+ molecular ion
MALDI See matrix-assisted laser desorption/
ionization (MALDI).
matrix-assisted laser desorption/ionization
(MALDI) Ionization by effect of illumination with
a beam of laser generated light onto a matrix
containing a small proportion of analyte. A mass
spectrometric technique that is used for the
analysis of large biomolecules.
MB Megabyte (1048576 bytes)
MH+ protonated molecular ion
min minute
mL milliliter
mm millimeter
MRFA A peptide with the amino acid sequence
methionine–arginine–phenylalanine–alanine.
MS mass spectrometer; mass spectrometry
MS MSn power: where n = 1
MS scan modes Scan modes in which only one
stage of mass analysis is performed. The scan
types used with the MS scan modes are full-scan
Thermo Fisher Scientific
Glossary: MSDS
type and selected ion monitoring (SIM) scan
type.
by the ion.
For example, for the ion C7H72+, m/z=45.5.
MSDS Material Safety Data Sheet
n nano (10-9)
MS/MS Mass spectrometry/mass spectrometry, or
tandem mass spectrometry is an analytical
technique that involves two stages of mass
analysis. In the first stage, ions formed in the ion
source are analyzed by an initial analyzer. In the
second stage, the mass-selected ions are
fragmented and the resultant ionic fragments are
mass analyzed.
nanospray ionization (NSI) A type of
electrospray ionization (ESI) that accommodates
very low flow rates of sample and solvent on the
order of 1 to 20 nL/min (for static nanospray) or
100 to 1000 nL/min (for dynamic nanospray).
MSn scan mode The scan power equal to 1 to 10,
where the scan power is the power n in the
expression MSn. MSn is the most general
expression for the scan mode, which can include
the following:
NIST National Institute of Standards and
Technology (USA)
•
•
•
The scan mode corresponding to the one stage
of mass analysis in a single-stage full-scan
experiment or a selected ion monitoring (SIM)
experiment
The scan mode corresponding to the two stages
of mass analysis in a two-stage full-scan
experiment or a selected reaction monitoring
(SRM) experiment
The scan mode corresponding to the three to
ten stages of mass analysis (n = 3 to n = 10) in a
multi-stage full-scan experiment or a
consecutive reaction monitoring (CRM)
experiment.
See also MS scan modes and MS/MS.
multipole A symmetrical, parallel array of
(usually) four, six, or eight cylindrical rods that
acts as an ion transmission device. An RF voltage
and dc offset voltage are applied to the rods to
create an electrostatic field that efficiently
transmits ions along the axis of the multipole
rods.
m/z Mass-to-charge ratio. An abbreviation used to
denote the quantity formed by dividing the mass
of an ion (in u) by the number of charges carried
Thermo Fisher Scientific
NCBI National Center for Biotechnology
Information (USA)
NMR Normal Mass Range
NSI See nanospray ionization (NSI).
octapole An octagonal array of cylindrical rods
that acts as an ion transmission device. An RF
voltage and dc offset voltage applied to the rods
create an electrostatic field that transmits the ions
along the axis of the octapole rods.
OD outside diameter
OT Orbitrap
Ω ohm
p pico (10-12)
Pa pascal
PCB printed circuit board
PDA detector Photodiode Array detector is a
linear array of discrete photodiodes on an
integrated circuit chip. It is placed at the image
plane of a spectrometer to allow a range of
wavelengths to be detected simultaneously.
PE protective earth
PID proportional / integral / differential
LTQ Orbitrap XL ETD Hardware Manual
G-5
Glossary: P/N
P/N part number
p-p peak-to-peak voltage
ppm parts per million
RF voltage An ac voltage of constant frequency
and variable amplitude that is applied to the ring
electrode or endcaps of the mass analyzer or to
the rods of a multipole. Because the frequency of
this ac voltage is in the radio frequency (RF)
range, it is referred to as RF voltage.
PQD pulsed-Q dissociation
RMS root mean square
psig pounds per square inch, gauge
ROM read-only memory
PTM posttranslational modification
quadrupole A symmetrical, parallel array of four
hyperbolic rods that acts as a mass analyzer or an
ion transmission device. As a mass analyzer, one
pair of opposing rods has an oscillating radio
frequency (RF) voltage superimposed on a
positive direct current (dc) voltage. The other
pair has a negative dc voltage and an RF voltage
that is 180 degrees out of phase with the first pair
of rods. This creates an electrical field (the
quadrupole field) that efficiently transmits ions of
selected mass-to-charge ratios along the axis of
the quadrupole rods.
RAM random access memory
raw data Uncorrected liquid chromatograph and
mass spectrometer data obtained during an
acquisition. Xcalibur and Xcalibur-based software
store this data in a file that has a .raw file
extension.
resolution The ability to distinguish between two
points on the wavelength or mass axis.
retention time (RT) The time after injection at
which a compound elutes. The total time that the
compound is retained on the chromatograph
column.
RF radio frequency
RF lens A multipole rod assembly that is operated
with only radio frequency (RF) voltage on the
rods. In this type of device, virtually all ions have
stable trajectories and pass through the assembly.
rotary-vane pump A mechanical vacuum pump
that establishes the vacuum necessary for the
proper operation of the turbomolecular pump.
(Also called a roughing pump or forepump.)
RS-232 An accepted industry standard for serial
communication connections. This
Recommended Standard (RS) defines the specific
lines and signal characteristics used by serial
communications controllers to standardize the
transmission of serial data between devices.
RT An abbreviated form of the phrase retention
time (RT). This shortened form is used to save
space when the retention time (in minutes) is
displayed in a header, for example, RT: 0.00-3.75.
s second
selected ion monitoring (SIM) scan type A scan
type in which the mass spectrometer acquires and
records ion current at only one or a few selected
mass-to-charge ratio values.
See also selected reaction monitoring (SRM) scan
type.
selected reaction monitoring (SRM) scan type A
scan type with two stages of mass analysis and in
which a particular reaction or set of reactions,
such as the fragmentation of an ion or the loss of
a neutral moiety, is monitored. In SRM a limited
number of product ions is monitored.
SEM secondary electron multiplier
Serial Peripheral Interface (SPI) hardware and
firmware communications protocol
G-6
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Glossary: serial port
serial port An input/output location (channel) for
serial data transmission.
sheath gas The inner coaxial gas (nitrogen), which
is used in the API source to help nebulize the
sample solution into a fine mist as the sample
solution exits the ESI or APCI nozzle.
signal-to-noise ratio (S/N) The ratio of the signal
height (S) to the noise height (N). The signal
height is the baseline corrected peak height. The
noise height is the peak-to-peak height of the
baseline noise.
SIM See selected ion monitoring (SIM) scan type.
skimmer A vacuum baffle between the higher
pressure capillary-skimmer region and the lower
pressure region. The aperture of the skimmer is
offset with respect to the bore of the ion transfer
capillary.
source CID A technique for fragmenting ions in
an atmospheric pressure ionization (API) source.
Collisions occur between the ion and the
background gas, which increase the internal
energy of the ion and stimulate its dissociation.
SPI See Serial Peripheral Interface (SPI).
SRM See selected reaction monitoring (SRM) scan
type.
sweep gas Nitrogen gas that flows out from
behind the sweep cone in the API source. Sweep
gas aids in solvent declustering and adduct
reduction.
syringe pump A device that delivers a solution
from a syringe at a specified rate.
target compound A compound that you want to
identify or quantitate or that a specific protocol
(for example, an EPA method) requires that you
look for. Target compounds are also called
analytes, or target analytes.
Torr torr
total ion current (TIC) The sum of the ion
current intensities across the scan range in a mass
spectrum.
tube lens offset The voltage offset from ground
that is applied to the tube lens to focus ions
toward the opening of the skimmer.
See also source CID.
Tune Method A defined set of mass spectrometer
tune parameters for the ion source and mass
analyzer. Tune methods are defined by using the
Tune Plus (LCQ Series, LXQ, and LTQ) or Tune
Master (TSQ Quantum) window and saved as
the file type .LCQTune, .LTQTune, or.TSQTune,
respectively.
A tune method stores tune parameters only.
(Calibration parameters are stored separately, not
with the tune method.)
tune parameters Instrument parameters whose
values vary with the type of experiment.
turbomolecular pump A vacuum pump that
provides a high vacuum for the mass spectrometer
and detector system.
TWA time weighted average
u atomic mass unit
UHV ultra high vacuum
Ultramark 1621 A mixture of
perfluoroalkoxycyclotriphosphazenes used for ion
trap calibration and tuning. It provides ESI singly
charged peaks at m/z 1022.0, 1122.0, 1222.0,
1322.0, 1422.0, 1522.0, 1622.0, 1722.0, 1822.0,
and 1921.9.
UMR Universal Mass Range
V volt
TIC See total ion current (TIC).
V ac volts alternating current
Thermo Fisher Scientific
LTQ Orbitrap XL ETD Hardware Manual
G-7
Glossary: V dc
V dc volts direct current
vacuum manifold A thick-walled, aluminum
chamber with machined flanges on the front and
sides and various electrical feedthroughs and gas
inlets that encloses the API stack, ion optics, mass
analyzer, and ion detection system.
vacuum manifold, pumps, pressure gauges, and
associated electronics.
vent valve A valve that allows the vacuum
manifold to be vented to filtered air or to the gas
supply. A solenoid-operated valve.
vol volume
vacuum system Components associated with
lowering the pressure within the mass
spectrometer. A vacuum system includes the
w width
W watt
G-8
LTQ Orbitrap XL ETD Hardware Manual
Thermo Fisher Scientific
Index
Numerics
00101-08-00006 3-59
00109-02-00020 3-59
00301-01-0013 4-17
00301-15517 4-17
017 2350 3-12
105 0160 3-12
117 5000 4-4
117 5010 4-4–4-5
118 4490 4-4
119265-0003 3-46
119283-0001 3-47
12 pin feedthrough 3-35, 3-38
harness 3-39
120320-0030 3-44
205 4221 1-50
205 5810 1-56
206 0501 1-48
206 1440 1-50
206 2130 1-52
206 4132 1-47
206 4150 1-49
207 6470 1-47
207 7991 1-65
207 8900 1-46
207 8930 1-61
207 9581 1-62
207 9591 1-62
207 9611 1-64
207 9640 1-60
208 1480 1-67
208 2540 1-63
209 9810 1-59
210 8920 1-44
211 0470 1-63
32000-60340 3-15
76461-2002 3-46
98000-20060 3-59
98000-62006 3-59
98000-62008 4-17, A-1
A
A0101-02530 3-46
A0301-02000 3-15
A0301-15101 3-5
Active Pirani gauge (APG) 1-33
Thermo Fisher Scientific
active temperature control 1-17
actual vial temperature 3-50
aluminum oxide abrasive, number 600 3-15
analog signals 1-50
analyzer
chamber temperature 1-61
system 2-11
temperature 1-40
angiotensin I 4-17
anti-aliasing filters 1-49
API source
safety interlock switch 2-10
settings 2-13
applicators, cotton-tipped 3-15
Automatic Gain Control (AGC) 1-12, 2-15
autosampler 2-8–2-9
auxiliary gas 1-36
axial ion ejection 1-12
axial oscillations 1-13
frequency 1-16
B
bakeout
controls 1-7–1-8
timer 1-8, 3-4–3-5
bakeout procedure
indication 1-8
starting 1-7, 3-5
stopping 1-7, 3-5
ball valve
housing 3-35, 3-47
replacement kit 3-46
base studs 3-42–3-43
basic system operations 2-1
bath gas 1-14, 1-36
bayonet guide 3-28
bayonet lock 3-28
bayonet pin 3-28
burnout, of filament 3-56
buttons
Display Status View 2-11
On/Standby 2-6
system bakeout 1-7
C
cable tie 1-10
LTQ Orbitrap XL ETD Hardware Manual I-1
Index: D
calibration parameters 2-13
CAN bus 1-54
capillaries 1-36
cartridge heaters 3-42
central electrode 1-13
location 1-13
power supply box 1-40
voltages 1-15, 1-64
central electrode power supply board
cooling 1-17
diagnostic LEDs 1-65
location 1-58, 1-64
central electrode pulser board
diagnostic LEDs 1-61
location 1-58, 1-60
ceramic lens holder 3-39–3-40
ceramic spacer 3-42
changing
chiller operating fluid 3-61
reagent vials 3-48
charge-sign independent trapping 1-12, 1-19
circuit breakers 1-7–1-8
cleaning
instrument surface 3-3
ion source 3-41
ion source lens assembly 3-34
ion volume 3-19
CLT compartment 1-28
CLT Offset connector 1-58, 1-63
CLT RF main board 1-14
diagnostic LEDs 1-63, 1-65
location 1-58, 1-62
CLT RF unit
function 1-62
housing 1-30
CLT RF voltage 1-14
Cold Ion Gauge 1-28, 1-30, 1-34–1-35, 1-43, 1-46
collision cell 1-36
collision gas
C-Trap 1-14
HCD 1-14
inlet 1-11
linear trap 1-37
Orbitrap 1-36
collisional damping 1-18
Communication LED 1-53
communication link 1-6
condenser filter, of recirculating chiller 3-61
connector, to ETD Interface board 1-20
control elements
inlet valve 1-20
instrument 1-6
control panel 1-7
control unit, for turbopumps 1-29
Convectron gauge
I-2
LTQ Orbitrap XL ETD Hardware Manual
ETD Module 1-20–1-21, 1-23, 1-34
linear trap 1-34
cooling water
circuit 1-17, 1-40–1-41
flow control sensor 1-40
properties 1-41
temperature 1-40
cover lid, for bakeout controls 1-8
CSIT 1-12, 1-19
C-Trap 1-13–1-14, 1-18, 1-38
cycle time 1-5
D
data acquisition analog board
diagnostic LEDs 1-50
layout 1-48
location 1-47, 1-49
data acquisition digital PCI board
diagnostic LEDs 1-49
layout 1-48
location 1-47–1-48
data acquisition unit 1-47
data communication 1-43
data system 1-6, 1-11, 1-34, 1-48, 1-50, 2-8, 2-12
log file 2-3
DC HV Supply PCB 1-20–1-21, 1-23
default values, of tune and calibration parameters 2-13
deflector electrode (DE) voltages 1-64
Display Status View button 2-11
distilled water 3-3
drip pan, of ETD forepump 1-32–1-33
dynamic range, of instrument 1-5
E
E-clips 3-40
electric power, for recirculating chiller 1-41
electrodynamic squeezing 1-15
electronic boards
data acquisition analog 1-49
data acquisition digital PCI 1-48
instrument control 1-50
ion optic supply 1-59
left side 1-58
power distribution 1-52
preamplifier 1-46
right side 1-44
electronic connections, to linear trap 1-43
emergency shutdown 2-2
entry housing 3-35, 3-47
error messages 1-34, 1-53, 1-55
ETD Control PCB 1-20–1-24
ETD forepump
Thermo Fisher Scientific
Index: F
cabinet 1-20
connections 1-21, 1-32
electrical cord 1-32
power supply 1-21
ETD Ion Optic Supply board 1-21, 1-44, 1-47
ETD main access panel 3-23, 3-52–3-53
ETD Module
forepump receptacle 1-22
ion gauge 1-21
maintenance 3-13
power panel 1-7, 1-22
power receptacle 1-22
power switch 1-22
service switch 1-22
Standby condition 2-4
ETD Module Heater Control PCB 1-23
ETD Module interface board 1-21–1-22
ETD power module
function 1-21
panel 1-21–1-22
ETD Reagent Kit 4-17
ETD side access panel
interlocks 3-57
removing 3-33
ETD tube 1-30
ETD turbopump
connections 1-21, 1-32
controller 1-33
function 1-31
location 1-20
maintenance 3-12
Ethernet 1-10–1-11
evacuating, after a complete shut down 3-4
exchanging, the lubricant reservoir of the turbopumps 3-12
exhaust
hose 1-11, 1-33
system 1-11, 1-31–1-32
external calibration 1-5
external connections 1-11
extracting voltage 1-14
extraction, of ion packets 1-14
F
fan filters 1-20, 3-60
ferrules, tightening 3-59
filament
assembly 3-19, 3-44
burnout 3-56
emission current 3-43
function 1-24, 1-26
wire 3-45
fingerprints, removing 3-3
flatapole 1-30
Thermo Fisher Scientific
flow control
sensor 1-40
UHP nitrogen 1-21, 1-23
flow rates
cooling water 1-40
HCD collision gas 1-38
nitrogen 1-38
flow restrictors 1-27
fluid bag filter, of chiller 3-61
fluoranthene 4-17, A-1
focusing potentials 1-66
foreline hose connection 3-35, 3-47
forepump electrical cord 1-33
forepumps
cabinet 1-2, 1-7, 1-31
effluent 1-32
linear trap 1-28–1-29, 1-31–1-32
location 1-7, 1-12, 1-31
oil level 1-32
oil mist filters 1-31, 3-12
power supply 1-32
switches 1-32
forevacuum tube 1-32–1-33
front panel 1-4
front side, LEDs 1-6
FT Electronics switch
functions 1-55
location 1-9
fused silica tubing
from lower oven 3-58
from upper oven 3-58
in ETD Module 1-26
G
gas ballast 1-32
gas flow dividers
HCD collision gas 1-38
location 1-38
nitrogen 1-37
schematics 1-36
gas pressures 2-11
gas supply
helium 1-10
nitrogen 1-10
schematics 1-36
gas valves 3-58
gate voltage 1-59
gloves 3-2
ground wires 1-44
guide bar 1-20, 3-35, 3-47
handle 3-21–3-22
opening 3-21, 3-23, 3-46
LTQ Orbitrap XL ETD Hardware Manual
I-3
Index: H
H
handling, hot pump oil 3-10
harmonic oscillations, in Orbitrap 1-13
hazardous materials 1-32
HCD
collision cell 1-59
collision gas 1-37
collision gas port 1-36
collision gas supply 1-10
collision gas valve 1-38, 1-53
flow rate, of collision gas 1-38
fragment spectra 1-18
housing 1-28, 1-30
heated dual restrictor enclosure 1-26
heated transfer line 1-26
heater control 1-55
Heater Control PCB 1-20–1-21, 1-24
heater ring 3-42
heating element 1-40
helium
gas capillary 1-37
inlet 1-11, 1-36
purging the line 2-11
supply 1-10
high voltage power supply board
diagnostic LEDs 1-67
function 1-14
layout 1-66
location 1-58, 1-65
voltages 1-66
high voltage, at PCBs 1-42
I
image current 1-13, 1-15–1-16, 1-46
inlet port, for UHP nitrogen 1-20
inlet valve
block 3-35, 3-47
knob 3-23, 3-35, 3-46–3-47, 3-52
lever 1-20, 3-21–3-23, 3-35, 3-46–3-47, 3-52
plug 3-23, 3-35, 3-46–3-47, 3-52
seal kit 3-46
seal removal tool 3-47
solenoid 1-20, 3-35, 3-47
installation kit, for the reagent inlet module 3-59
instrument
controls 1-7
diagnostics 1-42
forevacuum measurement 1-33
high vacuum measurement 1-34
parts 4-2
rear side 1-7
right side 1-10
shutdown 1-53
switching off 1-10, 2-2
I-4
LTQ Orbitrap XL ETD Hardware Manual
instrument control board
diagnostic LEDs 1-51
location 1-44, 1-47, 1-50
software status LEDs 1-52
internal calibration 1-5
internal computer
add-ons 1-48–1-49
data communication 1-43
location 1-44, 1-47
rebooting 2-12
timer 1-48
ion dephasing 1-16
ion gauge, for ETD Module 1-20
ion optic supply board 1-14, 1-18, 1-59
diagnostic LEDs 1-60
location 1-58–1-59
ion optics 1-12
ion oscillation 1-15
ion packets 1-15
shape 1-16
ion source
assembly 3-38
block 3-19, 3-39, 3-42–3-43
filament 3-42–3-43
filament assembly 3-43
lens assembly 3-40, 3-43
lenses 3-19
PCB 3-39, 3-42–3-43
schematics 1-21
springs 3-39–3-40
ion trajectory 1-13
ion volume 1-21, 1-26, 3-27
alignment arrow 3-28
assembly 3-28
cleaning 3-19
key thumbscrew 3-42
ion volume assembly, cleaning frequency 3-19
ion volume tool 3-20, 3-24, 3-26, 3-53
alignment arrow 3-28
components 3-21
handle 1-20, 3-23
ionization techniques 1-12
ions
detection 1-15
electrodynamic squeezing 1-15
image current 1-15
packet shape 1-16
L
laboratory
exhaust system 1-31–1-32
gas supply 1-37
LC 2-6–2-7
LEDs
power control 1-9
Thermo Fisher Scientific
Index: M
system status 1-6, 1-9
vacuum 1-6
left side panel, of instrument 1-4
lens voltages 1-65
line power 1-10
linear trap
collision gas 1-37
Communication LED 2-10, 2-12
connections 1-50
description 1-12
electronics 1-43
forepumps 1-29, 1-32
LEDs 1-6
location 1-2
maintenance 3-1
Power LED 2-10, 2-12
power panel 1-7, 1-32
Reset button 2-12
System LED 2-10, 2-12
turbopump 1-31
Vacuum LED 2-10
vacuum measurement 1-34
vent valve 1-35, 1-37–1-38, 2-2–2-3
Link Port Signal line 1-50
log file 2-3
lower oven 3-58
lubricant reservoir, of turbopumps 3-12
M
magnet support 3-19
magnet yoke 3-39–3-40
magnets, in ion source 3-19, 3-39–3-40
main circuit breaker 2-8
main power switch 1-6–1-7, 1-10, 1-55
Off position 2-2
securing 1-10
main RF supply 1-62
mains failure 1-56, 2-2, 3-4
mains supply, for the ETD Module 1-11
maintenance
API source 1-12
linear trap 3-1
procedures 3-2
reagent ion source 3-18
recirculating chiller 3-61
vacuum system 3-4
mass accuracy 1-5
mass range 1-5
Material Safety Data Sheet 3-48
micro controller 1-50–1-51
MS/MS 1-5
MSDS 3-48
multiple socket outlets 1-8, 1-55, 2-2
Thermo Fisher Scientific
N
nitrogen
CLT 1-36
cooling 1-25
cooling gas 1-25
flow rates 1-38
gas flow 1-37
inlet 1-11
pressure 1-37
pressure regulator 1-37–1-39
supply 1-10
tubing 1-38
venting 1-36
O
oil
level 1-32
mist filters 1-31–1-33, 3-12
On/Standby button 2-4, 2-6, 3-20
open-split interface 1-37
operating vacuum 1-6
Orbitrap
applied voltages 1-14
central electrode 1-61
chamber 1-29
control LEDs 1-7
detection electrodes 1-61
differential pumping 1-14
electrodes 1-13
Instrument Control board 1-21
ion extraction 1-14
ion trajectories 1-16
layout 1-14
lenses 1-14
measuring principle 1-13
voltages 1-16
output current, of preamplifier 1-46
P
padlock, for main power switch 1-10
panel fasteners 3-52
parameters
calibration 2-13
default values 2-13
tune 2-13
part numbers 4-1
Peltier element 1-17, 1-40, 1-61–1-62
location 1-64
water supply 1-30, 1-46
Penning gauge 1-55
peripherals power outlet 1-21
Pirani gauge 1-28–1-29, 1-34, 1-55
position, of inlet valve lever 3-35
LTQ Orbitrap XL ETD Hardware Manual
I-5
Index: Q
power
connector 1-7, 1-11
connector for linear trap 1-12
control LEDs 1-9
control panel 1-9
panel 1-7
supply for linear trap 1-12
power distribution
operating states 1-55
resetting 1-35
working modes 1-55
power distribution board 1-6, 1-8–1-9, 1-36, 1-40, 1-50, 1-52, 155
location 1-44, 1-52
status LEDs 1-54
power fail detector 2-3
Power LED 1-6
power module 1-20
power outlet, for peripheral devices 1-11
power supply 1 board
diagnostic LEDs 1-57
layout 1-57
location 1-44, 1-56
power supply 2 board
diagnostic LEDs 1-50
location 1-47
preamplifier
diagnostic LEDs 1-45, 1-47
location 1-30, 1-44, 1-46
pressure readings, in ETD Module 1-34
pressure regulator
location 1-39
nitrogen 1-37, 1-39
preventive maintenance 2-8, 3-2
printed circuit boards 1-42
proton transfer reactions 1-19
pumping, the system 2-9, 3-4
pumps
exhaust 1-11
forevacuum 1-31
manuals 3-5, 3-12
oil mist filters 1-31
purging, helium line 2-11
Q
quadrupole mass filter 1-19
quality, of vacuum 1-53
R
reagent heaters 1-20–1-21, 1-23–1-24, 1-26
reagent inlet cover 3-58
reagent inlet source 3-54
I-6
LTQ Orbitrap XL ETD Hardware Manual
heating unit 3-53
reagent ion source 1-26–1-27
cleaning frequency 3-14
flow restrictors 3-57
maintenance 3-18
maintenance tools 3-14
temperature 3-52
Reagent Ion Source dialog box 1-24, 2-4
Reagent Ion Source instrument control icon 2-4, 3-20
Reagent Ion Source On check box 1-24–1-25
reagent vapor, in the carrier gas 1-24
reagent vial heaters, temperature 3-52
reagent vials 1-27
rebooting, of instrument 2-3
recirculating chiller 1-41
condenser filter 3-61
connections 1-4
description 1-41
fluid bag filter 3-61
maintenance 3-61
reflector dc voltages 1-59
removing
ETD main access panel 3-32
ETD side access panel 3-33
gases 2-11, 3-4
stains 3-3
repair covering letter 3-3
replaceable parts
electronics (left panel) 4-9
electronics (right panel) 4-8
electronics analyzer Orbitrap 4-9
electronics main supply 4-10
pumping system Orbitrap 4-4
Replacement Ball Valve O-ring and Seal Kit 3-46
replacing
inlet valve components 3-46
ion source filament 3-44
turbopump lubricant reservoirs 3-12
reservoir, of recirculating chiller 3-61
resetting
instrument 2-12
system parameters 2-13
tune and calibration parameters 2-13
resolution, of instrument 1-5
restrictor
oven cover 3-58
oven heater 1-23
temperature 3-52
RF CLT main board 1-65
RF off & feedback board 1-58, 1-63
RF output control 1-59
RF voltage supply 1-62
RF voltages, to the quadrupole mass filter 1-14
right side panel, of instrument 1-4
routine maintenance 2-8
sequence for ETD system 3-13
Thermo Fisher Scientific
Index: S
S
safety
features 1-22
interlock switch 2-10
problem 3-56
sample inlet aperture 3-42
secondary electrons 1-24
SEM detector 1-12
serial port connector 1-50
service switch, of linear trap 1-10
setting up, conditions for operation 2-10
sheath gas 1-36
shutdown 1-56, 2-7, 2-9
side access panel 3-52
signal communication 1-43
software
debugging 1-51
function 1-40, 1-42
status LEDs of the instrument control board 1-52
Tune Plus window 2-6
specifications, of instrument 1-5
spectrum 1-16
SPI bus 1-43, 1-61, 1-64, 1-66
termination board 1-62–1-63, 1-65, 1-67
spring clip thumb screw 3-39, 3-42
stainless steel parts, cleaning 3-15
stains, removing 3-3
Standby condition 1-25, 2-4
starting up
ETD Module 2-11
instrument 2-9
status LEDs, of power distribution board 1-54
Status View 3-20
sweep gas 1-36
switches
forepumps 1-32
FT Electronics 1-9, 3-4
linear trap 1-10
main power 1-10
vacuum pumps 1-9
switching on, the vacuum system 1-34
system
bakeout 1-6–1-7, 1-35, 2-9, 3-4
bakeout timer 1-7
buttons for bakeout 1-7
heating 1-35
pump down time 2-10
rebooting 2-3
resetting 2-12
shutdown 2-2
Standby 2-4
starting up 2-9
status LEDs 1-6, 1-53
timing 1-48
Thermo Fisher Scientific
venting 1-38, 2-2
system status LEDs
linear trap 1-2
LTQ Orbitrap XL ETD 1-2
T
temperature
analyzer chamber 1-61
control 1-17
differential 1-17
monitoring 3-54
reagent vial heaters 3-52
sensor 3-42
temperature controller board 1-17, 1-37, 1-58, 1-61
diagnostic LEDs 1-62
location 1-61
thermoelectric elements 1-17
three way valve 1-36
thumbscrews 3-38–3-40
TMP 1 1-28–1-29
TMP 2 1-28–1-30
TMP 3 1-29–1-30
TMP 4 1-29
tools
cleanliness 3-3
for cleaning stainless steel parts 3-15
for cleaning the ion volume 3-19
reagent ion source 3-14
top lids
ETD Module 1-4
MS 1-4
transfer chamber 1-12
transfer line 1-21, 3-52
bellows 3-38
heater 1-23
inlet 3-58
transfer multipole 1-3, 1-19, 1-30
trap voltage 1-59
tune parameters 2-13
Tune Plus window 1-42
buttons 2-6, 2-11
diagnostics 1-42
turbopumps
connections 1-50
controllers 1-29, 1-33
error 1-54
linear trap 1-31, 1-33
maintenance 3-12
maintenance intervals 3-12
TMH 071 1-28, 1-36, 1-40
TMP 4 1-30
TMU 262 1-28, 1-36, 1-40
vent valves 1-35
LTQ Orbitrap XL ETD Hardware Manual
I-7
Index: U
U
UHP nitrogen 1-21, 1-36
inlet port 1-39
supply 1-39
UHV chamber 1-28–1-29
components 1-29
location 1-28
temperature control 1-17
uninterruptible power supply (UPS) 2-3
upper control panel 1-7–1-8
user maintenance 3-1–3-2, A-1
V
vacuum
compartments 1-28
deterioration 1-35
failure 1-34–1-35, 1-53
gauges 1-33, 1-50
quality 1-53
safety threshold 1-34–1-35
system 1-10, 1-28
vacuum chamber 1-28–1-29
vacuum components
left instrument side 1-29
UHV chamber 1-30
Vacuum LED
instrument 1-6
linear trap 2-10
vacuum manifold
location 1-20
probe plate 3-35–3-36
schematics 3-47
Vacuum Pumps switch 1-6, 1-9, 1-55
I-8
LTQ Orbitrap XL ETD Hardware Manual
vacuum system
controls 1-33
heating 1-35
maintenance 3-12
moisture 1-35
valve, for HCD collision gas 1-38, 1-53
vent valve
control 1-38
function 2-2, 2-8
linear trap 1-37, 2-3
nitrogen supply 1-36
venting pressure 1-39
venting, the system 2-3, 3-33
vial heaters 3-56, 3-58
cover 3-54
ribs 3-56
vial holder 3-55–3-56
vial temperature 1-25
W
water
chiller 1-4
hoses 1-41
ports 1-11
temperature 1-41
water cooler, for TMH 071 1-40
wheels, of instrument 1-4
working modes, of power distribution 1-55
working principle, of the Orbitrap 1-3
X
Xcalibur 1-42, 2-15
Thermo Fisher Scientific
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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