LTQ Orbitrap Velos Hardware Manual

LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
LTQ Orbitrap Velos™
Hardware Manual
Revision A - 1250580
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
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Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate
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For Research Use Only. Not for use in diagnostic procedures.
Place Declaration of Conformity here
Regulatory Compliance
Thermo Fisher Scientific 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 in the next sections by product name.
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 Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
LTQ Velos/ETD System (November 2008)
EMC Directives 2004/108/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-4: 2004
EN 55011: 2007
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 2005
EN 61000-4-11: 2004
EN 61000-4-2: 2001
FCC Part 15: 2007
EN 61000-4-3: 2006
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 18 OF THE FCC RULES.
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Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol:
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information on Thermo Fisher Scientific products which may assist the detection of substances
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substances sujettes à la directive RoHS sont disponibles sur www.thermo.com/WEEERoHS.
Read This First
Welcome to the Thermo Scientific LTQ Orbitrap Velos™ system! The
LTQ Orbitrap Velos is a member of the family of LTQ™ mass
spectrometer (MS) hybrid instruments.
All information in this guide concerning the LTQ Orbitrap Velos also
applies to the LTQ Orbitrap Velos ETD™ system where the
ETD Module is physically coupled to the back of the LTQ Orbitrap
Velos.
About This Guide
This LTQ Orbitrap Velos Hardware Manual contains a description of the
modes of operation and principle hardware components of your
LTQ Orbitrap Velos instrument. In addition, this manual provides
step-by-step instructions for cleaning and maintaining your instrument.
Who Uses This Guide
This LTQ Orbitrap Velos 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 Velos.
•
Chapter 2: “Basic System Operations” provides procedures for
shutting down and starting up the LTQ Orbitrap Velos.
•
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
Velos ETD.
LTQ Orbitrap Velos 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 Velos and LTQ Orbitrap
Velos ETD:
•
LTQ Orbitrap Series Preinstallation Requirements Guide
•
LTQ Orbitrap Velos Getting Started Guide
•
LTQ Velos manual set
You can access PDF files of the documents listed above from the data
system computer. The software also provides Help.
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LTQ Orbitrap Velos 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 (Bremen) GmbH
Hanna-Kunath-Str. 11
28199 Bremen
Germany
•
Send an e-mail message to the Technical Editor at
[email protected]
You are encouraged to report errors or omissions in the text or index.
Thank you.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
iii
Read This First
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 Velos 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.
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.
Safety and Special Notices
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. ▲
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
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Safety and EMC Information
Identifying Safety Information
The LTQ Orbitrap Velos 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:
vi
LTQ Orbitrap Velos Hardware Manual
•
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.
•
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.
Thermo Fisher Scientific
Read This First
Safety and EMC Information
Thermo Fisher Scientific
•
Do not change the external or internal grounding connections.
Tampering with or disconnecting these connections could endanger
you and/or damage the system.
•
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.
•
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.
•
Do not place any objects – especially not containers with liquids –
upon the instrument. Leaking liquids might get into contact with
electronic components and cause a short circuit.
LTQ Orbitrap Velos Hardware Manual
vii
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.
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LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Contents
Thermo Fisher Scientific
Chapter 1
Functional Description.............................................................1-1
General Description .......................................................... 1-2
Mechanical Characteristics ............................................. 1-3
Specifications ................................................................. 1-4
Control Elements.............................................................. 1-5
System Status LEDs ....................................................... 1-5
Control Panels ............................................................... 1-6
Linear Ion Trap............................................................... 1-12
Orbitrap Analyzer ........................................................... 1-13
Curved Linear Trap ..................................................... 1-13
Extraction of Ion Packets ............................................. 1-14
Measuring Principle ..................................................... 1-15
Ion Detection............................................................... 1-16
Active Temperature Control ........................................ 1-17
HCD Collision Cell........................................................ 1-18
HCD and ETD ........................................................... 1-18
ETD System ................................................................... 1-19
Principle of Operation ................................................. 1-21
ETD Module ............................................................... 1-21
Vacuum System .............................................................. 1-30
Turbomolecular Pumps................................................ 1-31
Forepumps of the Linear Trap ..................................... 1-33
Forepump of the ETD Module.................................... 1-34
Vacuum System Controls............................................. 1-35
Vacuum System Heating during a System Bakeout ...... 1-36
Gas Supply...................................................................... 1-37
Gas Supply for the Mass Analyzers ............................... 1-37
Gas Supply of the Reagent Ion Source ......................... 1-40
Cooling Water Circuit .................................................... 1-42
Recirculating Chiller .................................................... 1-43
Properties of Cooling Water......................................... 1-43
Printed Circuit Boards .................................................... 1-44
Linear Ion Trap Electronics.......................................... 1-45
Electronic Boards at the Right Side of the
Instrument ................................................................... 1-46
Electronic Boards on the Left Side of the Instrument ... 1-59
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 Instrument in Standby Condition................... 2-4
Placing the ETD Module in Standby Condition............ 2-4
LTQ Orbitrap Velos Hardware Manual
ix
Contents
Placing the MS in Standby Condition............................ 2-6
Shutting Down the LTQ Orbitrap Velos 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................................. 3-11
Maintenance of the ETD Module ................................... 3-12
Handling and Cleaning Reagent Ion Source Parts........ 3-13
Removing the Access Panels ......................................... 3-18
Maintenance of the Reagent Ion Source ....................... 3-20
Replacing Inlet Valve Components .............................. 3-44
Changing the Reagent Vials ......................................... 3-47
Cleaning the Fan Filters of the ETD Module............... 3-56
Maintenance of the Recirculating Chiller ........................ 3-57
Reservoir ...................................................................... 3-57
Fluid Bag Filter ............................................................ 3-57
Condenser Filter .......................................................... 3-57
Chapter 4
Replaceable Parts.................................................................... 4-1
Ion Sources ....................................................................... 4-2
Parts for the Basic System.................................................. 4-3
Parts Lists for the ETD System ......................................... 4-5
ETD Reagent Kit ........................................................... 4-7
Appendix A Fluoranthene ............................................................................ A-1
Glossary ................................................................................... G-1
Index ............................................................................................I-1
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LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Figures
LTQ Orbitrap Velos front view ............................................................ 1-2
Schematical view of the LTQ Orbitrap Velos ........................................ 1-3
Top lid of MS portion opened .............................................................. 1-4
System status LEDs ............................................................................... 1-5
Right side of the LTQ Orbitrap Velos ................................................... 1-6
Upper control panel .............................................................................. 1-7
Power control panel with power control LEDs and switches ................. 1-8
Main power switch ................................................................................ 1-9
External connections to the LTQ Orbitrap Velos ................................ 1-10
Schematical view of the Orbitrap cell and example of a stable ion
trajectory ............................................................................................. 1-13
Layout of the LTQ Orbitrap Velos, 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 Velos ETD front view ................................................. 1-19
Schematical view of the LTQ Orbitrap Velos ETD ............................. 1-20
LTQ Orbitrap Velos ETD, rear side ................................................... 1-22
Rear view of the ETD Module, with major component locations ........ 1-22
ETD Module functional block diagram .............................................. 1-23
Right side of the LTQ Orbitrap Velos ETD ....................................... 1-24
ETD Power Module panel .................................................................. 1-24
Reagent Ion Source dialog box ............................................................ 1-27
Reagent ion source schematics ............................................................. 1-29
Schematical view of Orbitrap vacuum system (CLT compartment
and Orbitrap chamber not shown) ...................................................... 1-30
Vacuum components on the left instrument side ................................ 1-31
Vacuum components on the right instrument side .............................. 1-32
Forepumps cabinet .............................................................................. 1-33
Forepump for ETD Module ............................................................... 1-34
Schematical view of gas supply for LTQ Orbitrap Velos ETD ............ 1-37
Proper orientation of the Swagelok-type nut and two-piece ferrule ...... 1-38
Gas regulators ..................................................................................... 1-39
ETD reagent carrier gas port at the ETD Module ............................... 1-40
Schematical view of cooling water circuit ............................................ 1-42
Electronic connections to linear trap ................................................... 1-45
Electronic boards on the right side of the LTQ Orbitrap Velos ........... 1-46
ETD Ion Optic Supply board ............................................................. 1-47
Preamplifier board ............................................................................... 1-48
Data Acquisition unit .......................................................................... 1-49
Data Acquisition Digital PCI board .................................................... 1-50
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LTQ Orbitrap Velos Hardware Manual
xi
Figures
Data Acquisition Analog board ........................................................... 1-51
Instrument Control board ................................................................... 1-52
Power Distribution board ................................................................... 1-54
Power Supply 1 board ......................................................................... 1-57
Electronic boards on the left side of the instrument ............................. 1-59
Ion Optic Supply board ...................................................................... 1-60
Central Electrode Pulser board ............................................................ 1-61
Temperature Controller board ............................................................ 1-62
CLT RF unit (cover removed) ............................................................. 1-64
Central Electrode Power Supply board ................................................ 1-65
High Voltage Power Supply board (cover removed) ............................ 1-67
High Voltage Power Supply board with SPI Bus Termination
board ................................................................................................... 1-68
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 .................................................................. 3-9
Routine maintenance sequence for ETD system .................................. 3-12
Rear view of the ETD Module ............................................................ 3-18
Ion source components (left view) ....................................................... 3-21
Tune Plus window .............................................................................. 3-22
Ion volume tool components ............................................................... 3-23
Guide bar being inserted into guide bar opening ................................. 3-23
Guide bar insertion complete .............................................................. 3-24
Rear view of the ETD Module, showing the inlet valve ....................... 3-24
Ion volume tool handle in the unlock position .................................... 3-25
Ion volume tool guide bar first stop ..................................................... 3-25
Reagent Ion Source dialog box, Open Probe Interlock button. ............ 3-26
Instrument Message box: The Ball Valve can now be opened .............. 3-26
Ion volume tool inserted into the inlet valve ........................................ 3-27
Detail of ion volume tool fully inserted into the inlet valve ................. 3-27
Ion volume tool handle in the locked position .................................... 3-28
Ion volume assembly ........................................................................... 3-29
Separating ion volume and ion volume holder .................................... 3-29
Placing the ion volume on the ion volume tool ................................... 3-30
Ion volume tool handle in the unlock position .................................... 3-31
Ion volume tool handle in the locked position .................................... 3-32
Inlet valve components (ion volume tool not shown) .......................... 3-34
Valve shield (1) covering the vacuum manifold probe plate ................. 3-34
Removing the foreline hose from its connection .................................. 3-35
Unscrewing the vacuum manifold probe plate ..................................... 3-35
Removing the vacuum manifold probe plate ....................................... 3-36
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Thermo Fisher Scientific
Figures
Interior of vacuum manifold ............................................................... 3-36
Removing the ion source assembly from the vacuum manifold ........... 3-37
Ion source assembly ............................................................................. 3-38
Ion source assembly exploded view ...................................................... 3-38
Ion source, exploded view ................................................................... 3-40
Ion source lens assembly and ion source .............................................. 3-42
Filament wire as seen from the bottom of the filament through
the electron lens hole ........................................................................... 3-43
Inlet valve components ........................................................................ 3-44
Inlet valve seal tool .............................................................................. 3-45
Inlet valve seal tool inserted in the inlet valve ...................................... 3-45
Inlet valve seal on the inlet valve seal tool ............................................ 3-46
Inlet valve seal disengaged from tool .................................................... 3-46
Reagent Ion Source dialog box ............................................................ 3-49
ETD Module with back panel removed .............................................. 3-51
Reagent vials with holders ................................................................... 3-52
ETD Module with vial heater cover removed ...................................... 3-52
Reagent inlet assembly ........................................................................ 3-55
ETD Module, top panel ...................................................................... 3-56
ETD Reagent (fluoranthene radical anion) generation from
fluoranthene ..........................................................................................A-1
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Tables
System status LEDs of the LTQ Orbitrap Velos .................................... 1-5
Circuit breakers of the LTQ Orbitrap Velos .......................................... 1-7
Typical pressure readings in the ETD Module .................................... 1-35
Diagnostic LEDs on the ETD Ion Optic Supply board ....................... 1-47
Diagnostic LEDs on the Preamplifier board ........................................ 1-48
Diagnostic LEDs of the Data Acquisition Digital PCI board .............. 1-50
Diagnostic LEDs of the Data Acquisition Analog board ...................... 1-51
Diagnostic LEDs of the Power Supply 2 board ................................... 1-52
Diagnostic LEDs of the Instrument Control board ............................. 1-53
Software status LEDs of the Instrument Control board ....................... 1-53
Status LEDs of the Power Distribution board ..................................... 1-55
Working modes of the Power Distribution board ................................ 1-56
Operating states of the Power Distribution board ............................... 1-56
Diagnostic LEDs of the Power Supply 1 board ................................... 1-58
Diagnostic LEDs of the Ion Optic Supply board ................................. 1-60
Diagnostic LEDs of the Central Electrode Pulser board ...................... 1-62
Diagnostic LEDs of the Temperature Controller board ....................... 1-63
Diagnostic LEDs of the CLT RF Main board ..................................... 1-64
Diagnostic LEDs of the Central Electrode Power Supply board .......... 1-66
Diagnostic LEDs of the High Voltage Power Supply board ................ 1-67
User maintenance procedures ................................................................ 3-2
Indications requiring maintenance of the ETD system ........................ 3-13
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Chapter 1
Functional Description
This chapter provides an overview of the functional elements of the
LTQ Orbitrap Velos. It contains the following topics:
Thermo Fisher Scientific
•
“General Description” on page 1-2
•
“Control Elements” on page 1-5
•
“Linear Ion Trap” on page 1-12
•
“Orbitrap Analyzer” on page 1-13
•
“ETD System” on page 1-19
•
“Vacuum System” on page 1-30
•
“Gas Supply” on page 1-37
•
“Cooling Water Circuit” on page 1-42
•
“Printed Circuit Boards” on page 1-44
LTQ Orbitrap Velos Hardware Manual
1-1
Functional Description
General Description
General Description
LTQ Orbitrap Velos is a hybrid mass spectrometer incorporating the
LTQ Velos™ dual cell linear trap and the Orbitrap™ analyzer. Figure 1-1
shows a front view of the instrument.
System status LEDs of linear trap
System status LEDs of LTQ Orbitrap Velos
Orbitrap Analyzer
Linear Trap
Forepumps cabinet
Figure 1-1.
LTQ Orbitrap Velos front view
The LTQ Orbitrap Velos consists of four main components (See
Figure 1-2 on page 1-3.), which are described in the following topics:
•
A dual cell linear ion trap (Thermo Scientific LTQ Velos) 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.
The LTQ Orbitrap Velos ETD has an additional reagent ion source for
enabling post-translational modification analyses of peptides by
Electron Transfer Dissociation (ETD). See “ETD System” on page 1-19.
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Functional Description
General Description
LTQ Velos
Electrospray Ion Source
S-Lens
Square Quadrupole
Octopole
Orbitrap
High Pressure Cell
Low Pressure Cell
Multipole
C-Trap
HCD Collision Cell
Orbitrap Mass Analyzer
Figure 1-2.
Schematical view of the LTQ Orbitrap Velos
Mechanical Characteristics
Wheels at the bottom side of the instrument facilitate positioning the
LTQ Orbitrap Velos 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 forepumps for the
vacuum system of the linear trap and the Orbitrap are hidden under the
linear trap and accessible from the front. The forepump 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.
In the LTQ Orbitrap Velos ETD, after removing the cables the top lid
of the ETD Module is also removable to allow accessing its electronic
components.
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LTQ Orbitrap Velos Hardware Manual
1-3
Functional Description
General Description
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.
Specifications
The LTQ Orbitrap Velos 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,
<1 ppm RMS with internal calibration
Dynamic Range >10000 between mass spectra,
>5000 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 Velos 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 1-6.) The Power LED is directly controlled by the
3 × 230 V input and all other LEDs are controlled by the power
distribution board (See “Power Distribution Board” on page 1-53).
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 Series Hardware Manual.
Table 1-1. System status LEDs of the LTQ Orbitrap Velos
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 “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 Velos. Located here
are the control panels, switches, and the ports for the external
connections (mains supply, gases, Ethernet communication, and cooling
water).
Power panel of linear trap
Bakeout timer
Cover lid for
bakeout controls
Switches and
control LEDs
Main power
switch
Forepumps cabinet
Figure 1-5.
Power connector
Right side of the LTQ Orbitrap Velos
For more information about the external connections, see “External
Connections” on page 1-9.
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 1-7.
The timer allows setting the duration for the bakeout of the system.
After the duration is set, the bakeout procedure is started by pressing the
green button on the right. A running bakeout procedure can be stopped
by pressing the orange button on the left side. For instructions about
performing a bakeout, see “Baking Out the System” on page 3-4.
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Functional Description
Control Elements
Bakeout timer
Bakeout control
buttons
Cover lid
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 1-5. ▲
Three circuit breakers are located at the bottom of this control panel.
Table 1-2 shows the parts of the LTQ Orbitrap Velos that are protected
by the respective circuit breaker. The proper function of each circuit
breaker is signaled by a dedicated LED in the power control panel (for
example, F1 corresponds to L1).
Table 1-2. Circuit breakers of the LTQ Orbitrap Velos
Circuit breaker
Ampere
LED
Instrument parts
F1
10
L1
Power Distribution
F2
15
L2
Linear ion trap
F3
15
L3
Multiple socket outlets (Peripherals, LC, heater,
etc.)
Power Control Panel
In addition to the system status LEDs at the front side (see Figure 1-4
on page 1-5), the LTQ Orbitrap Velos 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 1-7.)
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Functional Description
Control Elements
Power control LEDs
Vacuum Pumps switch
FT Electronics switch
Figure 1-7.
Power control panel with power control LEDs and switches
The use of the switches below the power control LEDs changes the
working mode of the power distribution. (See “Working Modes of the
Power Distribution” on page 1-48.)
The Vacuum Pumps switch can be set into the positions ON or OFF.
When the switch is in the OFF position, everything but the multiple
socket outlet is switched off.
The FT Electronics switch can be set into the operating position (ON)
or into the service position (OFF). When the switch is in the service
position, all components are switched off with exception of the
following:
•
Fans
•
Heater control
•
Power distribution (See “Power Distribution Board” on page 1-53)
•
Pumps (See “Vacuum System” on page 1-30)
•
Temperature controller (See “Temperature Controller Board” on
page 1-62)
•
Vacuum control
The linear ion trap also remains on because it has a separate Service
switch.
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Functional Description
Control Elements
Main Power Switch
The main power switch must be turned 90° clockwise/anti-clockwise to
switch on/off the instrument (see Figure 1-8). Placing the main power
switch in the Off position turns off all power to the LTQ Orbitrap
Velos, the linear ion trap, and the vacuum pumps. In the LTQ Orbitrap
Velos ETD, power to the ETD Module is also turned off.
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 1-10 shows the lower right side of the instrument
with the external connections for mains supply, gases, cooling water, and
Ethernet communication.
Located at the top are two ports for Ethernet cables for connecting the
LTQ Orbitrap Velos and the linear ion trap via an Ethernet hub with
the data system computer.
The power outlet for peripheral devices is located below the Ethernet
ports. In the LTQ Orbitrap Velos, the outlet provides the mains supply
for the data system. In the LTQ Orbitrap Velos ETD, the outlet
provides the mains supply for the ETD Module whereas the data system
is connected to a wall outlet.
The power connector for the mains supply is located at the center. The
LTQ Orbitrap Velos instrument is designed to operate at a nominal
voltage of 230 V ac, 50/60 Hz. Line voltages can vary between a
minimum of 207 V ac and a maximum of 253 V ac.
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Functional Description
Control Elements
Caution Systems installed in areas with 208 V power experience voltage
sags during high use periods that might place the line voltage below the
operating parameters discussed in this section. In this case, you must
protect your instrument by using a buck/boost transformer to ensure
that power is within the specified parameters at all times. ▲
1
Ethernet ports
Power outlet for
peripheral devices
Power connector
Helium gas inlet
Collision gas inlet1
Nitrogen gas inlet
Figure 1-9.
Cooling water inlet port
Cooling water outlet port
External connections to the LTQ Orbitrap Velos
The cooling water ports are located below the power connector. (See
also “Cooling Water Circuit” on page 1-42.)
The port for nitrogen gas allows connecting a Teflon® hose from the gas
supply of the laboratory to the instrument. The required gas pressure for
nitrogen is 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi). Helium
(40 ±10 psi [275 ±70 kPa], 99.999% [ultra-high] purity) enters the
instrument through a 1/8 inch port. Metal tubing from the helium gas
supply must be terminated with 1/8 inch, female, Swagelok-type
connectors. See “Gas Supply” on page 1-37 for information about
connecting the gas supplies to the instrument.
1
The port named Collision Gas is not used in the LTQ Orbitrap Velos.
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Functional Description
Control Elements
Caution Do not connect other gases than nitrogen or helium to the
LTQ Orbitrap Velos! The maximum pressure for the nitrogen gas inlet
is 830 kPa (8.3 bar, 120 psi); the maximum pressure for the helium inlet
is 345 kPa (3.45 bar, 50 psi). ▲
In the LTQ Orbitrap Velos ETD, the ETD reagent carrier gas supply of
the laboratory is connected via metal tubing to an1/8 inch inlet port at
the rear side of the instrument. Metal tubing from the gas supply must
be terminated with 1/8 inch, female, Swagelok-type connectors. The
required gas pressure is 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi). See
“Gas Supply of the Reagent Ion Source” on page 1-40.
The exhaust hose from the rotary pumps comes out the back of the
instrument, and connects the pumps to the exhaust system in the
laboratory.
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Functional Description
Linear Ion Trap
Linear Ion Trap
The LTQ Orbitrap Velos system can utilize a variety of ionization
techniques such as ESI, APCI, or APPI. Maintenance of the Ion Max
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 Velos), 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 Series 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 1-26 on page 1-33. The LTQ Orbitrap Velos
provides power for the linear ion trap. The LTQ Orbitrap Velos ETD
also provides the power 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 Velos 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
Curved Linear Trap
On their way from the linear trap to the Orbitrap, ions move through
the gas-free RF-only octapole 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
collision gas (bath gas) is used for dissipating the kinetic energy of
injected ions 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 1-63.) Trap and gate dc voltages as well
as RF voltages to the octapole are all provided by the ion optic supply
board. (See page 1-59.) High voltages to the lenses are provided by the
high voltage power supply board. (See page 1-66.)
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LTQ Orbitrap Velos Hardware Manual
1-13
Functional Description
Orbitrap Analyzer
Octapole
Gate C-Trap Trap
Collision Cell
TMP 1
TMP 2
Static
Pulsing from LTQ
Squeezing in C-Trap
TMP 3
Figure 1-11. Layout of the LTQ Orbitrap Velos, 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
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 C-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 (See Figure 1-12.),
these packets start coherent axial oscillations without the need for any
additional excitation cycle.
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Functional Description
Orbitrap Analyzer
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.
Measuring Principle
In the mass analyzer shown in Figure 1-10 on page 1-13, stable ion
trajectories combine rotation 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 amplified image current, the instrument obtains the
frequencies of these axial oscillations and therefore the mass-to-charge
ratios of the ions.
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LTQ Orbitrap Velos Hardware Manual
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Functional Description
Orbitrap Analyzer
Ion Detection
During ion detection, both the central electrode and deflector are
maintained at very stable voltages so that no mass drift can take place.
The outer electrode is split in half at z=0, allowing the ion image current
in the axial direction to be collected. The image current on each of half
of the outer electrode is differentially amplified and then undergoes
analog-to-digital conversion before processing using the fast Fourier
transform algorithm.
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
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Functional Description
Orbitrap Analyzer
a period of only 50–100 oscillations. After this, the ion packet of a given
m/q assumes the shape of a thin ring, with ions uniformly distributed
along its circumference. (See Figure 1-13.) Because of this angular and
radial smearing, radial and rotational frequencies cannot appear in the
measured spectrum. Meanwhile, axial oscillations will persist, with axial
thickness of the ion ring remaining small compared with the axial
amplitude. Moving from one half outer electrode to the other, this ring
will induce opposite currents on these halves, thus creating a signal to be
detected by differential amplification.
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 1-62.
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 1-43 on page 1-59.
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 Velos. See
“Cooling Water Circuit” on page 1-42 for further information.
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Functional Description
HCD Collision Cell
HCD Collision Cell
The HCD 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 to provide increased gas pressure inside
the multipole. See “Gas Supply” on page 1-37 for details. The ETD Ion
Optic Supply board provides the voltages for the HCD collision cell.
(See page 1-46.)
For HCD (Higher Energy Collisional Dissociation), ions are passed
through the C-Trap into the HCD collision cell. The offset between the
C-Trap and HCD is used to accelerate the parent ions into the gas-filled
collision cell. A potential gradient is applied to the collision cell to
provide fast extraction of ions, such that it transmits ions at a reliable
rate.
The fragment spectra generated in the HCD collision cell and detected
in the Orbitrap show a fragmentation pattern comparable to the pattern
of typical triple quadrupole spectra. See the LTQ Orbitrap Velos Getting
Started manual for more information.
HCD and ETD
In the LTQ Orbitrap Velos ETD, 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 Velos, 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
In the LTQ Orbitrap Velos ETD, an ETD Module is physically coupled
to the back of the LTQ Orbitrap Velos. See Figure 1-14. A quadrupole
mass filter replaces the octapole of the LTQ Orbitrap Velos. See
Figure 1-2 on page 1-3. The linear trap provides the voltages for the
quadrupole mass filter. A tube, which contains the transfer multipole,
connects the HCD housing to the ETD Module. See Figure 1-23 on
page 1-30. The ETD Ion Optic Supply board is mounted on top of the
data acquisition unit on the right side of the instrument. See
Figure 1-35 on page 1-47.
ETD Module
Orbitrap
Analyzer
Linear Trap
Figure 1-14. LTQ Orbitrap Velos ETD front view
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.
Note The ETD system is also available as an upgrade on new and
existing LTQ Velos and LTQ Orbitrap XL systems. The ETD system is
not available for LTQ Orbitrap Discovery or LTQ Orbitrap systems. ▲
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LTQ Velos
Electrospray Ion Source
S-Lens
Square Quadrupole
Orbitrap
Octopole
High Pressure Cell Low Pressure Cell
Quadrupole Mass Filter
C-Trap
ETD System
HCD Collision Cell
Transfer Multipole
Reagent Ion Source
e-
Orbitrap Mass Analyzer
Reagent 1
Heated Inlet
Figure 1-15. Schematical view of the LTQ Orbitrap Velos ETD
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LTQ Orbitrap Velos Hardware ManualThermo Fisher Scientific
Reagent 2
Heated Inlet
Functional Description
ETD System
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 1-15 on page 1-20.)
The reagent ions pass a quadrupole mass filter 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 1-16 on page 1-22 shows the rear side of the ETD Module. 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.
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Functional Description
ETD System
Fan filter
Control elements
of inlet valve
Inlet port for ETD reagent
carrier gas
Cabinet for
ETD forepump
Figure 1-16. LTQ Orbitrap Velos 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 1-17. 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 1-23 on page 1-30
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
ETD Reagent
Carrier Gas
Convectron Gauge
3 = Transfer line
4 = Ion volume
Figure 1-18. ETD Module functional block diagram
The following sections describe the major ETD Module components
that are shown in Figure 1-17 on page 1-22 and Figure 1-18.
ETD Power Module
The ETD power module (item #1 in Figure 1-17) receives 220 V, 10 A,
from the peripherals power outlet. See Figure 1-9 on page 1-10. 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 1-19.
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LTQ Orbitrap Velos Hardware Manual
1-23
Functional Description
ETD System
ETD Module
ETD Module
power panel
Figure 1-19. Right side of the LTQ Orbitrap Velos ETD
Figure 1-20 shows a close up picture of the ETD Power Module panel.
Power In is connected to the peripherals power outlet of the
MS portion. See Figure 1-9 on page 1-10. Forepump is a receptacle to
power the ETD forepump (220 V AC, 5 A).
ETD Module Service switch
ETD Module Power switch
ETD Module Forepump receptacle
ETD Module Power receptacle
ETD Module Power Panel
Figure 1-20. ETD Power Module panel
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Functional Description
ETD System
The ETD power module panel contains the main breaker and the
service switch for the ETD Module. During normal operation, the
ETD Power switch is left On and the service switch is left in the
Operating Mode position. As a safety feature, both components of the
LTQ Orbitrap Velos ETD system (the MS detector and the
ETD module) are shut down with one set of switches, the MS detector
switches. When you perform maintenance on components inside the
ETD module as described in “Maintenance of the ETD Module” on
page 3-12, you set the MS detector’s service switch to the Service
position. The service switch turns On or Off power to all ETD Module
components except the turbopump and forepump.
ETD Module Interface Board
The ETD Module Interface board (item #2 in Figure 1-17 on
page 1-22) 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 Velos 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 1-17) controls most of the
ETD Module functions. The ETD Control PCB consists of circuits that
control:
Thermo Fisher Scientific
•
ETD Module operating logic
•
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
LTQ Orbitrap Velos Hardware Manual
1-25
Functional Description
ETD System
The DC HV Supply PCB (item #3 in Figure 1-17 on page 1-22) is
plugged in to the ETD Control PCB.
ETD Heater Control PCB
The ETD Module Heater Control PCB (item #6 in Figure 1-17)
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 1-18 on page 1-23, and items #9 and #10 in
Figure 1-17), the transfer line heater (#3 in Figure 1-17), and the
restrictor oven heater (not shown in Figure 1-17). 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.
Reagent Carrier Gas Flow Control for ETD
The ETD Module contains a digital flow control for the chemical
ionization (CI) gas/reagent carrier gas provided by the ETD Control
PCB (See Figure 1-17 on page 1-22.) and an electronic pressure
regulator. The gas serves two functions in the ETD Module:
•
As a carrier gas, the nitrogen sweeps the reagent (fluoranthene) from
the vial to the ion source where the reagent radical anions are
formed.
•
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.
Thermo Fisher Scientific strongly recommends a mixture of
25% helium and 75% nitrogen. The helium in this mixture serves as a
tracer gas to enable leak checking of gas connections using conventional
thermal conductivity-based leak detectors, which are widely used to
check leaks in gas chromatography equipment. See “Gas Supply of the
Reagent Ion Source” on page 1-40 for detailed information.
The reagent carrier gas supply in the laboratory is connected to the
ETD reagent carrier gas port at the rear side of the ETD Module. See
Figure 1-31 on page 1-40.
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Functional Description
ETD System
Reagent Heaters
The reagent heaters (items #9 and #10 in Figure 1-17 on page 1-22, H1
and H2 in Figure 1-18 on page 1-23) 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. See Figure 1-21.
Figure 1-21. Reagent Ion Source dialog box
When you deselect the Reagent Ion Source On check box, the reagent
heaters and filament immediately turn off and the reagent ion source
goes into Standby mode.
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 “Turning
Off the Reagent Ion Source: What to Expect” on page 2-14.
Warning Burn Hazard. When the reagent ion source is in Off mode,
restrictor oven, transfer line, and ion source remain at 160 °C. ▲
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Functional Description
ETD System
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 “Changing the Reagent Vials” on page 3-47.
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 Burn Hazard. 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 “Changing the Reagent Vials” on page 3-47 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 1-21 on page 1-27). 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
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.
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 1-21 on page 1-27.)
•
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 1-17 on page 1-22 and inside of the vacuum
manifold, see item #14 in Figure 1-17) 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
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Thermo Fisher Scientific
Functional Description
ETD System
react with the reagent to form reagent ions. The reagent ion volume is
the space where this reaction takes place. See Figure 1-22. 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 1-22. Reagent ion source schematics
The reagent ion source contains two reagent vials, CI/carrier gas
(nitrogen) handling hardware and flow restrictors, 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 Velos Hardware Manual
1-29
Functional Description
Vacuum System
Vacuum System
Figure 1-23 shows a schematical overview of the Orbitrap vacuum
system.
HCD Housing
UHV Chamber
Vacuum Chamber
LTQ Velos
ETD Module
Vacuum System,
see Figure 1-18 on
page 1-23
TMP 4
Cold Ion Gauge
Pirani Gauge
TMP 2
Forepump
TMP 3
TMP 1
Forepump
Figure 1-23. Schematical view of Orbitrap vacuum system (CLT compartment and Orbitrap chamber not shown)*
*
For an abridged version of the parts list, see Table on page 4-3.
The LTQ Orbitrap Velos has the following vacuum compartments:
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LTQ Orbitrap Velos 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 –
turbomolecular pump TMH 071, TMP 1, manufacturer: Pfeiffer)
•
Ultra high vacuum chamber (UHV chamber, pumped by a
water-cooled 60 L/s turbomolecular pump 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
turbomolecular pump TMU 262, TMP 3, manufacturer: Pfeiffer)
•
HCD housing (pumped by a water-cooled 60 L/s turbomolecular
pump TMH 071, TMP 4, manufacturer: Pfeiffer)
The forepumps of the linear trap provide the forevacuum for the
turbomolecular pumps TMP 1 to TMP 4.
Turbomolecular Pumps
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
turbomolecular pump (TMP 1, see Figure 1-24). The rotary vane
pumps of the linear trap (see page 1-33) provide the forevacuum for this
pump. This chamber is bolted to a stainless steel welded UHV chamber,
which accommodates Orbitrap, lenses, and corresponding electrical
connections.
TMP 4
Gas Regulator
for Vent Valve
Pirani Gauge
TMP 1
Figure 1-24. 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 turbomolecular pump (TMP 2, see Figure 1-25 on
page 1-32). 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
turbomolecular pump (TMP 3, see Figure 1-25). The HCD housing is
evacuated by a 60 L/s UHV turbomolecular pump (TMP 4, see
Figure 1-24) that is mounted to its bottom via an elbow. This dedicated
pump for the HCD cell protects the low pressure cell of the linear trap
from gas overload.
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LTQ Orbitrap Velos Hardware Manual
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Functional Description
Vacuum System
In the LTQ Orbitrap Velos ETD, a tube that contains the transfer
multipole (flatapole) connects the HCD housing to the ETD Module.
Preamplifier
HCD housing
Cold ion
gauge
Cooling water
supplies for
Peltier element
and Preamplifier
TMP 3
TMP 2
Figure 1-25. Vacuum components on the right instrument side
All turbomolecular pumps are equipped with TC 100 control units
(manufacturer: Pfeiffer). A 24 V switch mode power supply provides the
electric power for all four turbomolecular pumps of the system.
Linear Trap Turbomolecular Pump
A separate turbomolecular pump 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 Series
Hardware Manual.
ETD Module Turbomolecular Pump
In the LTQ Orbitrap Velos ETD, a separate turbomolecular pump
(BOC Edwards EXT75DX) provides the high vacuum for the
ETD reagent ion source. See Figure 1-17 on page 1-22. It is backed up
by a dedicated rotary vane pump at the bottom of the ETD Module. See
Figure 1-27 on page 1-34. This air-cooled turbomolecular pump
contains no user-serviceable parts.
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Functional Description
Vacuum System
Forepumps of the Linear Trap
The rotary vane pumps from the linear trap serve as forepumps for the
three smaller turbomolecular pumps (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 1-26.
Oil mist filters
Forepumps
Figure 1-26. 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 3-11 on
instructions about returning the collected oil to the forepumps.
The forepumps of the linear trap are powered by the power panel of the
linear ion trap.
Warning Hazardous materials 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:
Thermo Fisher Scientific
•
The forevacuum pumps are filled with oil,
•
They are connected to the power supply, and
•
The gas ballast is shut.
LTQ Orbitrap Velos Hardware Manual
1-33
Functional Description
Vacuum System
For a detailed description of the forepumps, refer to the handbook of
the manufacturer.
Forepump of the ETD Module
In the LTQ Orbitrap Velos ETD, a rotary vane pump (BOC Edwards
RV 3) provides the forevacuum for the ETD turbomolecular pump. (See
“ETD Module Turbomolecular Pump” on page 1-32.) It is located in a
cabinet at the bottom of the ETD Module. The ETD forepump is
equipped with an oil mist filter and stands on a drip pan. See
Figure 1-27 on page 1-34.
An exhaust hose connects the forepump to the exhaust system in the
laboratory. A forevacuum tube connects the ETD forepump to the
ETD TMP. The forepump electrical cord is plugged into the Forepump
receptacle on the ETD Module power panel. See Figure 1-20 on
page 1-24.
For maintenance instructions for the ETD forepump, see “Maintenance
of the ETD Forepump” on page 3-5 and the manual that came with the
forepump.
Exhaust hose
Forevacuum tube
Oil mist filter
Drip pan
Forepump electrical cord
Figure 1-27. Forepump for ETD Module
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Functional Description
Vacuum System
Vacuum System Controls
The power distribution board controls all turbopumps via voltage levels.
See “Power Distribution Board” on page 1-53. An interface for RS485
data via the instrument control board connects the turbopumps with
the linear ion trap. (See “Instrument Control Board” on page 1-52.)
The turbomolecular pump of the linear ion trap and the
ETD turbomolecular pump have individual controllers.
Vacuum Gauges
Several vacuum gauges monitor the vacuum within the instrument:
•
The forevacuum of the LTQ Orbitrap Velos is monitored by an
Active Pirani gauge (TPR 280, manufacturer: Pfeiffer) connected to
the LTQ Orbitrap Velos forevacuum line. See Figure 1-24 on
page 1-31.
•
The high vacuum of the LTQ Orbitrap Velos is monitored by a
Cold Ion Gauge (IKR 270, manufacturer: Pfeiffer) connected to the
UHV chamber. See Figure 1-25 on page 1-32. 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 Series Hardware Manual for
more information.
•
In the LTQ Orbitrap Velos ETD, two dedicated vacuum gauges
monitor the vacuum in the ETD Module. A Convectron gauge (see
Figure 1-17 on page 1-22 and Figure 1-18 on page 1-23) monitors
the pressure in the ETD forevacuum line and an ion gauge (see
Figure 1-17) 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
Ion Gauge Reading
CI gas pressure set to 20 psi
0.1–0.01 Torr
20–35×10-5 Torr
The vacuum gauges of the LTQ Orbitrap Velos are connected to the
power distribution board that directly responds to the pressure values.
(See “Power Distribution Board” on page 1-53.) The analog values are
digitized by the instrument control board. (See “Instrument Control
Board” on page 1-52.) They are then sent as readout values to the data
system.
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LTQ Orbitrap Velos Hardware Manual
1-35
Functional Description
Vacuum System
Switching on the Vacuum System
When the vacuum system is switched on, the following occurs:
1. After the Vacuum Pumps switch is switched On, the pumps of the
linear ion trap and the LTQ Orbitrap Velos are run up. The Pirani
gauge (see above) controls the LTQ Orbitrap Velos low vacuum
pressure as well as the pressure at the forevacuum pumps. Within a
short time, a significant pressure decrease must be observed. The
goodness of the vacuum can be estimated by means of the rotation
speed of the turbopumps (e.g. 80% after 15 min.).
2. If the working pressure is not reached after the preset time, the
complete system is switched off. At the status LED panel of the
power distribution board, an error message (Vacuum Failure) is put
out (see below).
3. The Cold Ion Gauge is only switched on after the low vacuum is
reached. It is then used to monitor the vacuum in the Orbitrap
region.
Vacuum Failure
In case the pressure in the LTQ Orbitrap Velos 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.
(See “Power Distribution Board” on page 1-53.) It can be reset by
switching the main power switch off and on. (See “Main Power Switch”
on page 1-9.)
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.
(See “Vent Valve of the Linear Ion Trap” on page 1-39.)
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. See “Baking Out the System” on page 3-4.
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Functional Description
Gas Supply
Gas Supply
This section describes the gas supplies for the mass analyzers of the
LTQ Orbitrap Velos and the reagent ion source of the LTQ Orbitrap
Velos ETD.
Gas Supply for the Mass Analyzers
Figure 1-28 shows a schematical view of the gas supply for the
instrument. The gas supply of the ETD system is highlighted in gray.
1
Nitrogen (N2)
ETD reagent carrier gas
Helium (He)
Collision gas1
ETD Module
Linear Trap
Regulator with
manometer
Analyzer
Turbopump TMH 071
Turbopump TMU 262
C-Trap
Turbopump TMH 071
Cooling Gas
N2 venting
Turbopump TMH 071
Collision Cell
Vent valve
Figure 1-28. Schematical view of gas supply for LTQ Orbitrap Velos ETD*
*
For parts lists of the gas supply, see page 4-4 and page 4-5.
Gas Inlet Ports of the Instrument
On its right side (See Figure 1-9 on page 1-10.), the instrument provides
three gas inlet ports for the gas supply of the mass analyzers:
•
Nitrogen: The linear trap requires high-purity (99%) nitrogen for
the API sheath gas and auxiliary/sweep gas. The required gas
pressure is 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi).
1
The port named Collision Gas is not used in the LTQ Orbitrap Velos.
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LTQ Orbitrap Velos Hardware Manual
1-37
Functional Description
Gas Supply
In the LTQ Orbitrap Velos ETD, the ETD system uses the
high-purity nitrogen for cooling the reagent vials when the reagent
ion source is turned off.
•
Helium: The linear trap requires ultra-high purity (99.999%)
helium for the collision gas. The required gas pressure is
275 ± 70 kPa (2.75 ± 0.7 bar, 40 ±10 psi).
Warning Danger of Asphyxiation. Accumulation of nitrogen gas could
displace sufficient oxygen to suffocate personnel in the laboratory.
Ensure that the laboratory is well ventilated. ▲
❖
To connect the nitrogen source to the LTQ Orbitrap Velos
1. Connect an appropriate length of Teflon™ tubing to the nitrogen
source in the laboratory. The Installation Kit contains 6 m (20 ft) of
suitable Teflon tubing (OD 6 mm, P/N 0690280). The connection
for the Teflon hose to the nitrogen gas supply is not provided in the
kit; you have to supply this part.
2. Connect the opposite end of the Teflon tubing to the press-in fitting
labeled Nitrogen, which is located at the right side of the
instrument. See Figure 1-9 on page 1-10. To connect the tubing,
align the Teflon tubing with the opening in the fitting and firmly
push the tubing into the fitting until the tubing is secure.
❖
To connect the helium source to the LTQ Orbitrap Velos
1. Connect an appropriate length of 1/8-in ID copper or stainless steel
tubing with a brass Swagelok-type 1/8-in nut (P/N 00101-15500)
and a 2-piece brass 1/8-in ID ferrule [P/N 00101-08500 (front),
P/N 00101-2500 (back)] to the Helium gas inlet. See Figure 1-29
for the proper orientation of the fitting and ferrule.
2. Connect the opposite end of the tubing to the helium gas source,
using an appropriate fitting.
Gas hose
Swagelok-type nut
Front ferrule
Back ferrule
Figure 1-29. Proper orientation of the Swagelok-type nut and two-piece
ferrule
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Thermo Fisher Scientific
Functional Description
Gas Supply
Gas Distribution Within the Instrument
Helium gas is led from the helium port through a stainless steel capillary
to the right rear side of the linear trap. See Figure 1-28 on page 1-37.
High purity nitrogen gas is led from the nitrogen port via Teflon tubing
to the right side of the LTQ Orbitrap Velos. Here, two T-pieces divide
the nitrogen gas flow into three parts.
The first 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 Figure 1-30 on page 1-39.) The second part of the nitrogen flow is
directed through Teflon tubing to the API source. The third part of the
nitrogen flow enters a a gas regulator with manometer, which keeps the
gas pressure to the C-Trap and HCD collision cell constant. (See
Figure 1-30, background.) From the regulator, the collision gas is led
through red PEEKSil™ tubing (100 mm ID silica capillary in 1/16 inch
PEEK tubing) to the collision octapole next to the curved linear trap
(flow rate: ~0.5 mL/min). The nitrogen gas leaking from the
HCD collision cell (3–5 mbar) is used for ion trapping and cooling in
the C-Trap.
Gas for HCD
and C-Trap
Gas for Vent Valve
Figure 1-30. Gas regulators
In the LTQ Orbitrap Velos ETD, 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.
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 Series Hardware
Manual contains further information about the vent valve.
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LTQ Orbitrap Velos Hardware Manual
1-39
Functional Description
Gas Supply
The instrument is vented with high purity nitrogen from the same
tubing that supplies the LTQ Velos sheath gas. See Figure 1-28 on
page 1-37. The vent valve of the LTQ Velos is supplied via 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 Velos. (See
Figure 1-30, front.)
Gas Supply of the Reagent Ion Source
In addition to high purity nitrogen for cooling, the reagent ion source of
the LTQ Orbitrap Velos ETD uses a mixture of 25% helium and 75%
nitrogen gas as carrier gas and chemical ionization (CI) vehicle. This gas
mixture must be ultra high-purity (minimum purity 99.999%) with less
than 3.0 ppm each of water, oxygen, and total hydrocarbons. The
required gas pressure is 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi). The
ETD carrier gas supply of the laboratory is connected via metal tubing
to the inlet port at the rear side of the instrument. See Figure 1-31.
Figure 1-31. ETD reagent carrier gas port at the ETD Module
The helium in this mixture serves as a tracer gas to enable leak checking
of gas connections using conventional thermal conductivity-based leak
detectors, which are widely used to check leaks in gas chromatography
equipment.
Note If the helium/nitrogen mixture is not available, then use a nitrogen
supply that is ultra high-purity (99.999%) with less than 3.0 ppm each
of water, oxygen, and total hydrocarbons. ▲
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Functional Description
Gas Supply
Triple Gas Filter
A triple (oxygen/water/hydrogen) gas filter is installed between the
regulator on the reagent carrier gas source and the ETD module to
ensure that the reagent carrier gas (either nitrogen or helium/nitrogen) is
better than 99.999% pure with much less than 1 ppm of oxygen, water,
and hydrocarbons.
Refer to the filter manufacturer’s instructions for information about how
to monitor the color changes in the filters that indicated when the filters
need to be replaced, as well as information about where to order new
filters. If there are no leaks in the reagent carrier gas plumbing, you can
expect the filters to last a year or more. Thermo Fisher Scientific
strongly recommends that a Thermo Fisher Scientific Field Service
Engineer replace the gas filters.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
1-41
Functional Description
Cooling Water Circuit
Cooling Water Circuit
Figure 1-32 on page 1-42 shows a schematical view of the cooling water
circuit in the LTQ Orbitrap Velos. 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 1-10. First, the fresh water passes through the
turbomolecular pumps 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. After
that, the cooling water passes through the preamplifier cooling unit.
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
Preamplifier cooling
Heating element
(Peltier element)
TMP 3
Analyzer
Flow control sensor
Peltier element Central Electrode
Power Supply Box
TMP 1
TMP 4
TMP 2
Water cooler for
TMH 071 (2x)
Figure 1-32. Schematical view of cooling water circuit*
* For a parts list of the cooling water circuit, see Table
on page 4-4.
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 Velos 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
“Maintenance of the Recirculating Chiller” on page 3-57. 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 Burn Hazard. 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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LTQ Orbitrap Velos Hardware Manual
1-43
Functional Description
Printed Circuit Boards
Printed Circuit Boards
The LTQ Orbitrap Velos 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 Velos. 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 “ETD Module” on page 1-21.
The electronics of the LTQ Orbitrap Velos 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 Electrical Shock Hazard. Parts of the printed circuit boards
are at high voltage. Shut down the instrument and disconnect it from
line power before performing service. 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 Velos 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 Velos main power
switch. The linear ion trap has a sheet metal back cover. Figure 1-33
shows the electronic connections at the rear side of the linear trap.
Cold Ion Gauge
Figure 1-33. Electronic connections to linear trap
The linear ion trap electronics has two connections with the
LTQ Orbitrap Velos electronics:
•
Data communication with the internal computer of the
LTQ Orbitrap Velos. See “Electronic Boards at the Right Side of the
Instrument” on page 1-46.
•
Signal communication (SPI bus) with supply information for the
instrument control board. See “Instrument Control Board” on
page 1-52.
For further information about the linear ion trap electronics, refer to the
LTQ Series Hardware Manual.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
1-45
Functional Description
Printed Circuit Boards
Electronic Boards at the Right Side of the Instrument
Figure 1-34 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 1-34. Electronic boards on the right side of the LTQ Orbitrap Velos
The side panel is connected to the instrument frame by two
green/yellow ground wires. See bottom of Figure 1-34. 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 is mounted on top of the data
acquisition unit. See Figure 1-35. It supplies the voltages for the HCD
collision cell. In the LTQ Orbitrap Velos ETD, this board also 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.
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Functional Description
Printed Circuit Boards
Figure 1-35. ETD Ion Optic Supply board
The diagnostic LEDs on the ETD ion optic supply board are listed in
Table 1-4 on page 1-47. The positions of the diagnostic LEDs on the
board are indicated by white rectangles in Figure 1-36.
Table 1-4. Diagnostic LEDs on the ETD Ion Optic Supply board
Thermo Fisher Scientific
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 Velos Hardware Manual
1-47
Functional Description
Printed Circuit Boards
Preamplifier
The preamplifier is located in a housing next to the Cold Ion Gauge. See
Figure 1-36. It is water cooled to protect it during a system bakeout.
Cooling water supply
for Preamplifier
Cooling water supply
for Peltier element
Cold Ion Gauge
Figure 1-36. 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 1-48. The positions of the diagnostic LEDs on the board are
indicated by white rectangles in Figure 1-36.
Table 1-5. Diagnostic LEDs on the Preamplifier board
1-48
LTQ Orbitrap Velos Hardware Manual
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
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Internal Computer
Figure 1-37 shows the components of the data acquisition unit. 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 1-37. Data Acquisition unit
The internal computer 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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1-49
Functional Description
Printed Circuit Boards
Data Acquisition Digital PCI Board
Figure 1-38 shows the data acquisition digital PCI board. It is an add-on
board to the internal computer. (See Figure 1-37 on page 1-49.)
Figure 1-38. 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 are 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 linear ion trap and
the internal computer of the LTQ Orbitrap Velos system, but also
between the linear ion trap and the data system computer. For further
information about the data system, refer to the LTQ Series Hardware
Manual.
The diagnostic LEDs listed in Table 1-6 show the status of the board.
The position of the LEDs on the board is indicated by a red rectangle in
Figure 1-38.
Table 1-6. Diagnostic LEDs of the Data Acquisition Digital PCI board
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LTQ Orbitrap Velos Hardware Manual
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
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Data Acquisition Analog Board
Figure 1-39 shows the data acquisition analog board. This board is an
add-on board to the mainboard of the internal computer. See
Figure 1-37 on page 1-49. 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.
Figure 1-39. Data Acquisition Analog board
The diagnostic LEDs listed in Table 1-7 on page 1-51 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 1-39.
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 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 1-37 on page 1-49.
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Functional Description
Printed Circuit Boards
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 1-40 shows the instrument control board. The instrument
control board is located in a housing next to the internal computer. It is
connected to the LTQ Orbitrap Velos main power.
Diagnostic LEDs
Status LEDs
Figure 1-40. Instrument Control board
The instrument control board is used to interface the LTQ Velos control
electronics to the Orbitrap control electronics. Three signal lines are
passed from the LTQ Velos: 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.
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Functional Description
Printed Circuit Boards
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 1-53.) Turbopumps (See
“Vacuum System” on page 1-30.) are attached to a serial port connector
and this is connected via the signal lines to the linear ion trap.
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 1-40 on page 1-52.
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. The position of the status LEDs on the board is indicated
by a white oval in Figure 1-40 on page 1-52.
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 Velos SPI bus enabled
On
6.4
Orbitrap SPI bus enabled
On
Flashing on error
Power Distribution Board
Figure 1-41 on page 1-54 shows the power distribution board. It is
located at the bottom of the right side of the instrument.
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.
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LTQ Orbitrap Velos Hardware Manual
1-53
Functional Description
Printed Circuit Boards
Figure 1-41. Power Distribution board
The power distribution board indicates all system states and error
messages by status LEDs (See Table 1-11 on page 1-55.) 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 1-41.
The system status LEDs on the front side of the instrument (See
Figure 1-4 on page 1-5.) 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).
(See “Instrument Control Board” on page 1-52.)
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 1-41.
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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 Velos failure
Control signal < 0.5 V
Ion Gauge On
Penning LTQ Orbitrap Velos
Off
Forevacuum > 10-2 mbar
Ion Gauge OK
Penning LTQ Orbitrap Velos
failure
Control signal < 0.5 V
LT Vacuum Work
LTQ Velos vacuum failure
Vacuum forepump LTQ Velos
>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
TMP 1 failure
Turbopump defective/error*
Rotation 1 OK
TMP 1 failure
80% rotation speed of turbopump
not reached
Turbo P. 2 On
TMP 2 failure
Turbopump defective/error*
Rotation 2 OK
TMP 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 TMP 3 is indicated by an LED directly located on the pump controller. An error of TMP 4 is
indicated in the software.
Depending on user actions, the power distribution is switched to various
working modes by the hardware. See Table 1-12 on page 1-56.
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LTQ Orbitrap Velos Hardware Manual
1-55
Functional Description
Printed Circuit Boards
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 Velos (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
Velos forevacuum pumps:
If not ok: switch off system and light
error LED*; power distribution remains
switched on
10-0 mbar after 30 s.
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
7.
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 Velos
>10-1 mbar
Rebooting of the system by switching
off/on of the main switch.
• Penning gauge LTQ Orbitrap Velos
>10-3 mbar
• Pirani gauge LTQ Velos forepump
>10-1 mbar
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Functional Description
Printed Circuit Boards
Table 1-13. Operating states of the Power Distribution board, continued
8.
9.
Action
Consequences
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 Velos without data link,
keeps on running
10.
FT Electronics switch LTQ Orbitrap Velos
off
LTQ Orbitrap Velos electronics
switched off, pumps keep on running;
LTQ Orbitrap Velos without data link,
keeps on running
11.
Failure of linear ion trap or LTQ Orbitrap
Velos (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 1-42 shows the power supply 1 board. This board is located next
to the power distribution board. It provides the power for the ion optic
supply board (See “Ion Optic Supply Board” on page 1-59.) and the
instrument control board. (See “Instrument Control Board” on
page 1-52.)
Figure 1-42. Power Supply 1 board
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LTQ Orbitrap Velos Hardware Manual
1-57
Functional Description
Printed Circuit Boards
Warning Electrical Shock Hazard. Parts of the power supply 1 board
are at high voltage. Shut down the instrument and disconnect it from
line power before performing service. ▲
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 1-42.
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
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LTQ Orbitrap Velos Hardware Manual
+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
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Electronic Boards on the Left Side of the Instrument
Figure 1-43 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
Temperature
Controller board
CLT RF Main board housing
with RF Off & Feedback board
and CLT Offset Connector
Central Electrode
Power Supply board
housing
High Voltage Power Supply
board housing
Figure 1-43. Electronic boards on the left side of the instrument
The main components on this side are described starting from the top.
Ion Optic Supply Board
Figure 1-44 on page 1-60 shows the ion optic supply board. 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 Velos. It
has an RF detector for the RF output control. The board also provides
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
1-59
Functional Description
Printed Circuit Boards
the trap voltage, the gate voltage, and the reflector dc voltages as well as
the RF voltages to the octapole of the Orbitrap. See “Orbitrap Analyzer”
on page 1-13 for further information.
Figure 1-44. Ion Optic Supply board
The diagnostic LEDs listed in Table 1-15 show the status of applied
voltages to the board. The position of the LEDs on the board is
indicated by white rectangles in Figure 1-44.
Warning Electrical Shock Hazard. Parts of the board are at high
voltage. Shut down the instrument and disconnect it from line power
before performing service. ▲
Table 1-15. Diagnostic LEDs of the Ion Optic Supply board
1-60
LTQ Orbitrap Velos Hardware Manual
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
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Table 1-15. Diagnostic LEDs of the Ion Optic Supply board, continued
No.
Name
Color
Description
Normal Operating
Condition
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 is located in a housing that is
mounted to the flange of the UHV chamber. See Figure 1-45.
Figure 1-45. Central Electrode Pulser board
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 on page 1-62 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.
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Functional Description
Printed Circuit Boards
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 is located on the top left side of the
instrument, next to the CLT RF main board. See Figure 1-43 on
page 1-59. 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 1-46. Temperature Controller board
The diagnostic LEDs listed in Table 1-17 on page 1-63 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 1-46.
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Functional Description
Printed Circuit Boards
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 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 is located in a housing in the center of the left
side of the instrument. See Figure 1-43 on page 1-59. 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 “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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LTQ Orbitrap Velos Hardware Manual
1-63
Functional Description
Printed Circuit Boards
CLT Offset Connector
RF Off & Feedback board
Figure 1-47. 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 1-47.
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 is an add-on board to the CLT RF main
board. It is located in the same housing. See Figure 1-47 on page 1-64.
The CLT Offset connector, which removes interfering signals from the
circuit, is also mounted in the housing.
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Functional Description
Printed Circuit Boards
Central Electrode Power Supply Board
The central electrode power supply board is mounted in a housing on
the bottom left side of the instrument. See Figure 1-48.
Figure 1-48. 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.
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1-65
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 1-48 on
page 1-65.
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 is mounted in a housing on the
bottom left side of the instrument. See Figure 1-43 on page 1-59. This
board provides five dc voltages for the ion optics of the LTQ Orbitrap
Velos. Two voltages supply the lenses of the instrument. Three voltages
are applied to the RF CLT main board to be used as focusing potentials
for the curved linear trap. See “Orbitrap Analyzer” on page 1-13 for
further information. The board communicates via the SPI bus.
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Functional Description
Printed Circuit Boards
Warning Electrical Shock Hazard. The high voltage power supply
board creates voltages up to 3.5 kV! Shut down the instrument and
disconnect it from line power before performing service. ▲
Figure 1-49. 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 1-49.
Table 1-20. Diagnostic LEDs of the High Voltage Power Supply board
Thermo Fisher Scientific
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)
LTQ Orbitrap Velos Hardware Manual
1-67
Functional Description
Printed Circuit Boards
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 is located below the High Voltage
Power Supply board, at the bottom left side of the instrument. See
Figure 1-50.
SPI bus termination board
Figure 1-50. High Voltage Power Supply board with SPI Bus Termination
board
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Chapter 2
Basic System Operations
Many maintenance procedures for the LTQ Orbitrap Velos system
require that the MS detector be shut down. In addition, the
LTQ Orbitrap Velos 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 Instrument in Standby Condition” on page 2-4
•
“Shutting Down the LTQ Orbitrap Velos 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 Velos 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 Velos) 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. See “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. See
“Baking Out the System” on page 3-4.
It is not possible to check whether the system was vented. The log file of
the data system indicates a reboot of the system. In case of frequent but
short power failures we recommend installing an uninterruptible power
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LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Basic System Operations
Shutting Down the System in an Emergency
supply (UPS). If main power failures occur frequently while the system
is not attended (e.g. in the night), we recommend installing a power fail
detector.
Note The intentional venting of the system is performed with the vent
valve of the linear ion trap. ▲
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LTQ Orbitrap Velos Hardware Manual
2-3
Basic System Operations
Placing the Instrument in Standby Condition
Placing the Instrument in Standby Condition
The LTQ Orbitrap Velos 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.
In case of an LTQ Orbitrap Velos ETD, first place the ETD Module in
Standby condition. Then place the mass spectrometer in Standby
condition according to the procedures described in the following topics.
Placing the ETD Module in Standby Condition
❖
To place the ETD Module in Standby condition
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, clear 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.
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.
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Thermo Fisher Scientific
Basic System Operations
Placing the Instrument in Standby Condition
Figure 2-3.
Reagent Ion Source dialog box with Reagent Ion Source On
box and Actual condition circled
If the reagent ion source is on when you place the LTQ Orbitrap
Velos ETD in Standby mode, the filament turns off immediately. In
contrast, the vial heaters stay on for 60 minutes before they turn off
and the cooling gas begins. Because the filament is turned off, you
can perform minor maintenance procedures on the ETD Module
without cooling the reagent inlet.
Warning Burn Hazard. Install or exchange the reagent vials by
following the procedure in “Changing the Reagent Vials” on page 3-47.
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 “Reagent Heaters” on page 1-27.
Warning Burn Hazard. The restrictor, the transfer line, and the ion
source heater operate at 160 °C. Do not attempt to touch them unless
the LTQ Orbitrap Velos is shut down (See “Shutting Down the
LTQ Orbitrap Velos Completely” on page 2-7.) and these heaters have
had sufficient time to cool down to room temperature. ▲
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
2-5
Basic System Operations
Placing the Instrument in Standby Condition
Placing the MS in Standby Condition
❖
To place the LTQ Orbitrap Velos 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 Series Hardware Manual. The
System LED on the front panel of the LTQ Velos 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 Velos main power switch in the On
position.
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Thermo Fisher Scientific
Basic System Operations
Shutting Down the LTQ Orbitrap Velos Completely
Shutting Down the LTQ Orbitrap Velos Completely
The LTQ Orbitrap Velos 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
1. Place the ETD Module in Standby condition as described in
“Placing the ETD Module in Standby Condition” on page 2-4.
2. Shut down the instrument as described in “Shutting Down the
Instrument“ below. This also shuts down the ETD Module because
its power controls are linked to the LTQ Orbitrap Velos power
controls through the ETD Module Interface board. See
“ETD Module Interface Board” on page 1-25.
Shutting Down the Instrument
❖
To shut down the LTQ Orbitrap Velos 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 1-8.
5. Put the Vacuum Pumps switch to the Off position. See Figure 1-7.
When you place the switch in the Off position, the following occurs:
a. All power to the instrument, including the turbomolecular
pumps and the rotary-vane pumps, is turned off.
b. After 30 s, power to the vent valve solenoid of the ion trap is
shut off. The vent valve opens and the vacuum manifold is
vented with nitrogen to atmospheric pressure through a filter.
You can hear a hissing sound as the gas passes through the filter.
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LTQ Orbitrap Velos Hardware Manual
2-7
Basic System Operations
Shutting Down the LTQ Orbitrap Velos Completely
6. Leave the main power switch of the LTQ Orbitrap Velos in the On
position.
7. During service or maintenance operations that require opening the
vacuum system of the LTQ Velos or the LTQ Orbitrap Velos, 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 Burn Hazard. 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 Velos 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. ▲
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LTQ Orbitrap Velos Hardware Manual
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 Velos 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. ▲
❖
To start up the LTQ Orbitrap Velos
1. Start up the (optional) LC and autosampler as is described in the
manual that came with the LC and autosampler.
2. Start up the data system and the chiller.
3. Turn on the flows of helium and nitrogen at the tanks, if they are
off.
4. Make sure that the main power switch of the LTQ Velos is in the On
position and the electronics service switch of the LTQ Velos is in the
Operating position.
5. Place the main power switch at the right side of the LTQ Orbitrap
Velos in the On position.
6. Put the Vacuum Pumps switch to the On position. See Figure 1-7
on page 1-8. The rotary-vane pumps and the turbomolecular pumps
are started.
Note Pumping the system after a complete shut down takes hours and
requires overnight baking of the system. ▲
7. Put the FT Electronics switch to the On position. See Figure 1-7.
When you place the FT Electronics switch to the On position, the
following occurs:
a. Power is provided to all electronic boards. (The electron
multiplier, conversion dynode, 8 kV power to the API source,
main RF voltage, and quadrupole RF voltage remain off.)
b. The internal computer reboots. After several seconds, the
Communication LED on the front panel is illuminated yellow
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LTQ Orbitrap Velos Hardware Manual
2-9
Basic System Operations
Starting Up the System after a Shutdown
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 Velos 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 Velos to establish the
communication link between LTQ Velos 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 “Setting Up
Conditions for Operation“. If you do not have either, go to the topic
directly.
Setting Up Conditions for Operation
❖
To set up your LTQ Orbitrap Velos for operation
1. Before you begin data acquisition with your LTQ Orbitrap Velos
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.
Note The vacuum in the analyzer system can be improved by an
overnight baking of the system. See “Baking Out the System” on
page 3-4. ▲
2. Ensure that the gas pressures are within the operational limits:
2-10
LTQ Orbitrap Velos Hardware Manual
•
Helium: 275 ± 70 kPa (2.75 ± 0.7 bar, 40 ±10 psi),
•
Nitrogen: 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi).
Thermo Fisher Scientific
Basic System Operations
Starting Up the System after a Shutdown
In case of an LTQ Orbitrap Velos ETD, also check the pressure of
the reagent carrier gas: 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. In case of an LTQ Orbitrap Velos ETD, start up the ETD Module
as described in “Starting the ETD Module After a Complete
Shutdown“. In case of an LTQ Orbitrap Velos, continue to set up
for ESI or APCI operation as described in LTQ Orbitrap Velos
Getting Started.
Starting the ETD Module After a Complete Shutdown
❖
To start up the ETD Module after a complete shutdown
1. Start the LTQ Orbitrap Velos ETD according to the start up
procedures given in “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
“ETD Module Interface Board” on page 1-25).
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
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.
3. Click the Display Status View button in the Tune Plus window.
Check the reagent vacuum parameters:
•
Reagent ion gauge pressure: 20 to 35 × 10-5 Torr
•
Reagent Convectron gauge pressure: <0.08 Torr
•
Reagent turbomolecular pump speed : > 90%
4. Continue to set up the instrument for operation as described in
LTQ Orbitrap Velos Getting Started manual.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
2-11
Basic System Operations
Resetting the System
Resetting the System
If the communication link between LTQ Orbitrap Velos and data
system computer is lost, it may be necessary to reset the system using the
Reset button of the LTQ Velos.
The procedure given here assumes that the LTQ Orbitrap Velos and
data system computer are both powered on and are operational. If the
instrument, data system computer, or both are off, see “Starting Up the
System after a Shutdown” on page 2-9.
To reset the LTQ Orbitrap Velos, press the Reset button of the
LTQ Velos. See the LTQ Series 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.
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LTQ Orbitrap Velos Hardware Manual
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 Velos 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 Velos tune and calibration parameters
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. ▲
Thermo Fisher Scientific
LTQ Orbitrap Velos 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
In the LTQ Orbitrap Velos ETD, the reagent ion source controls can be
accessed as described in “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 Burn Hazard. 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 Velos 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 Velos 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 Velos ETD completes the Xcalibur Sequence step in
progress before going into Standby mode.
LTQ Orbitrap Velos 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 Velos.
For instructions on maintaining the LTQ Velos linear trap, refer to the
LTQ Series Hardware Manual. For instructions on maintaining LCs or
autosamplers, refer to the manual that comes with the LC or
autosampler.
Note 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:
Thermo Fisher Scientific
•
“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 3-12
•
“Maintenance of the Recirculating Chiller” on page 3-57
LTQ Orbitrap Velos 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 3-11
Recirculating chiller
Check cooling fluid level
See manufacturer’s documentation
Manufacturer’s documentation
page 3-57
Check cooling fluid filter
Check air inlet filter
ETD Module
Clean the ion volume
As needed*
page 3-21
Replace the inlet valve
components
As needed*
page 3-44
Clean the ion source lenses
As needed*
page 3-33
Clean the ion source
As needed*
page 3-39
Replace the ion source
filament
As needed*
page 3-41
Check the rotary-vane pump
oil and add when needed
Every month
page 3-8
Change the rotary-vane
pump oil
Every four months
page 3-9
Clean the rear cooling fans
Every four months
page 3-56
*
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:
3-2
LTQ Orbitrap Velos 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
Thermo Fisher Scientific recommends the following gloves: white
nitrile clean room gloves (Fisher Scientific P/N 19-120-2947B [size
medium] or P/N 19-120-2947C [size large]; Thermo Scientific
P/N 23827-0008) [size medium] or P/N 23827-0009 [size large]).
•
Never re-use gloves after you remove them because the surface
contaminants on them will re-contaminate clean parts.
•
Always wear protective eye wear when you clean parts.
•
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 Velos.
•
Never insert a test probe (for example, an oscilloscope probe) into
the sockets of female cable connectors on PCBs.
Returning Parts
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. See ”Safety Advice
for Possible Contamination” on page viii 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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3-3
User Maintenance
Maintenance of the Vacuum System
Maintenance of the Vacuum System
This section 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 noticeably 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. See “Behavior of
the System in Case of a Main Failure” on page 2-2.
Bakeout Procedure
❖
To perform a system bakeout
1. Place the system in Standby condition as described in “Placing the
Instrument 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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LTQ Orbitrap Velos Hardware Manual
Bakeout start button
Bakeout timer
Thermo Fisher Scientific
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 Velos 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 1-5.
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 Series 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.
The rotary-vane pump major components are shown in Figure 3-2 on
page 3-6.
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LTQ Orbitrap Velos Hardware Manual
3-5
User Maintenance
Maintenance of the Vacuum System
1
2
3
3
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 “Forepump of the ETD Module” on page 1-34, 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 on page 3-7.
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User Maintenance
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. The
panel hangs on the hooks and comes off if lifted up a little and getting
pulled on into the backwards direction.
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 on page 3-8.
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LTQ Orbitrap Velos Hardware Manual
3-7
User Maintenance
Maintenance of the Vacuum System
Figure 3-5.
❖
Lugs for fixing the bottom panel
To remove the panel
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 on page 3-6. If the ETD forepump oil level is low,
follow these steps to add more oil.
❖
To add oil to the ETD forepump
1. Shut down and vent the LTQ Orbitrap Velos 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.
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
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LTQ Orbitrap Velos Hardware Manual
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User Maintenance
Maintenance of the Vacuum System
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
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 on page 3-6.) 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 (0), as shown in Figure 3-6.
High Flow (Position II)
Low Flow (Position I)
Closed (Position 0)
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:
Thermo Fisher Scientific
•
Rotary-vane pump oil (P/N A0301-15101)
•
Suitable container for removing spent or excess oil
LTQ Orbitrap Velos Hardware Manual
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User Maintenance
Maintenance of the Vacuum System
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 Burn Hazard. Handle hot pump oil carefully to avoid being
burned or injured. ▲
❖
To change the ETD forepump oil
1. Shut down and vent the LTQ Orbitrap Velos 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.
a. Disconnect the foreline vacuum hose. (See Figure 3-2 on
page 3-6.)
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.
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User Maintenance
Maintenance of the Vacuum System
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.
Maintenance of the Turbopumps
The turbopumps in the MS portion of the LTQ Orbitrap Velos need
maintenance work that is briefly outlined below. In contrast, the
turbopump in the ETD Module of the LTQ Orbitrap Velos ETD
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 0172350; TMU 262: P/N 1050160) are available from Thermo
Fisher Scientific.
The disposal of used oil is subject to the relevant regulations.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
3-11
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. See also the ETD Module Hardware Manual
for additional information.
Figure 3-7 illustrates the sequence in which to perform routine
maintenance on the ETD system.
Vent
MS/ETD System
Remove
ETD Module
Covers
Remove
Reagent Ion Source
Block Assembly
Remove
Vacuum Manifold
Cover
Start
Remove
Ion Source from
Vacuum Manifold
Remove
Ion Volume
Remove
Lenses
No
Yes
Clean
Reagent Ion Source
Block Assembly
?
No
Disassemble
Remaining
Reagent Ion Source
Components
Clean
Reagent Ion Source
Block Assembly
Clean
Remaining
Reagent Ion Source
Components
Reassemble
Reagent Ion Source
Block Assembly
Clean
Lenses
Clean
Ion Volume
Clean
Ion Source
Lenses
?
Disassemble
Reagent Ion Source
Block Assembly
Yes
Clean
Remaining
Reagent Ion Source
Components
?
No
Yes
Reassemble
Remaining
Reagent Ion Source
Components
Reinstall
Reagent Ion Source
Block Assembly
Replace
Ion Volume
Reinstall
Lenses
End
Reinstall
Reagent Ion Source
Replace
Vacuum Manifold
Cover
Reinstall
ETD Module
Covers
Start Up
MS/ETD System
Figure 3-7.
Routine maintenance sequence for ETD system
Table 3-2 on page 3-13 gives advice for correcting frequent problems
with the ETD system.
3-12
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User Maintenance
Maintenance of the ETD Module
Table 3-2. Indications requiring maintenance of the ETD system
Symptom
Cause
Fix
No ions at m/z 202 with the emission
current at the correct level.
The m/z 202 is outside the mass range.
Set the starting mass lower.
The m/z 202 signal intensity drops
slowly over several days when the
emission current is at the correct level.
The ion volum needs to be cleaned or replaced.
Clean or replace the ion volume when the
injection time is over 100 ms. See
page 3-21.
A system error message advising that
the maximum injection time has been
reached for the ETD AGC.
The AGC target has not been reached within the
specified time limit. The ion volume needs to be
cleaned or replaced.
Clean the ion volume. Increase the
maximum injection time limit.
Sudden and complete drop of m/z 202
level, low emission current.
The filament may just have blown out.
Check the filament. Replace it if necessary.
See page 3-41.
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. ▲
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3-13
User Maintenance
Maintenance of the ETD Module
The following tools and supplies are needed for reagent ion source
maintenance:
•
Clean, dry gas (air or nitrogen)
•
New, white nitrile clean room gloves (Fisher Scientific
P/N 19-120-2947B [size medium] or P/N 19-120-2947C [size
large]; Thermo Scientific P/N 23827-0008 ) [size medium] or
P/N 23827-0009 [size large])
•
Lint-free cloth or paper
•
Nut driver, 5.5 mm
•
Protective eyewear
•
Screwdriver, Phillips #2
•
Screwdriver, flat blade
•
Wrench, adjustable
•
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. To clean these parts, follow 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:
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LTQ Orbitrap Velos Hardware Manual
•
Acetone, analytical grade (or other suitable solvent)
•
Aluminum oxide abrasive, number 600 (P/N 32000-60340)
•
Applicators, cotton-tipped
•
Beaker, 450 mL
•
Clean, dry gas
•
De-ionized water
•
Detergent (Alconox®, Micro, or equivalent)
•
Dremel® rotary tool or equivalent (recommended)
Thermo Fisher Scientific
User Maintenance
Maintenance of the ETD Module
•
Foil, aluminum
•
Forceps
•
New, white nitrile clean room gloves
•
Glycerol, reagent grade
•
Lint-free cloth
•
Protective eyewear
•
Tap water
•
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 Hand and Eye Hazard. Wear impermeable laboratory gloves
and eye protection when performing these cleaning procedures. ▲
❖
To clean reagent ion source stainless steel parts
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
often 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.
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User Maintenance
Maintenance of the ETD Module
Warning Injury Hazard. 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.
3. 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.
4. Place the parts in a warm detergent solution in an ultrasonic bath
and sonicate them.
a. Make a solution of detergent and warm tap water in a 400 mL
glass beaker.
b. Using forceps, place the parts in a beaker containing the warm
detergent solution.
c. Place the beaker and contents in an ultrasonic bath for five
minutes.
d. Rinse the parts with tap water to remove the detergent.
5. 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.
6. 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.
7. Blow-dry the parts immediately. Use clean, dry gas (air or nitrogen)
to blow the acetone off the parts.
8. Complete the drying process, doing one of the following:
•
3-16
LTQ Orbitrap Velos Hardware Manual
Using forceps, place the parts in a 500 mL glass beaker, cover the
beaker with aluminum foil, and put the beaker in an oven set at
100 °C for 30 minutes.
Thermo Fisher Scientific
User Maintenance
Maintenance of the ETD Module
•
Lay the parts on clean aluminum foil (dull side up) and allow to
dry for 30 minutes.
9. Allow the parts to cool before reassembling them.
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 3-15. 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 Hand and Eye Hazard. Wear impermeable laboratory gloves
and eye protection when performing these cleaning procedures. ▲
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
1. Scrub all of the parts with a warm detergent solution.
a. Make a solution of detergent and warm tap water in a 500 mL
glass beaker.
b. Dip a clean cotton-tipped applicator in the detergent mixture
and use the applicator to scrub the parts.
Note Do not soak or sonicate the parts in detergent. ▲
c. 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.
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User Maintenance
Maintenance of the ETD Module
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.
Removing the Access Panels
During some ETD Module maintenance activities, it is necessary to
remove either the ETD main access panel, or the side access panel, or
both (see Figure 3-8). Follow the subsequent procedures to remove these
panels.
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 3-8.
Rear view of the ETD Module
Removing the ETD Main Access Panel
❖
To remove the ETD main access panel
1. Place the ETD Module to Service mode as directed in “Placing the
Instrument in Off Condition and Service Mode” on page 3-47.
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User Maintenance
Maintenance of the ETD Module
Note In Service mode, all power to the LTQ Orbitrap Velos 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 Burn Hazard. 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. ▲
2. Remove the inlet valve lever (item 4 in Figure 3-8 on page 3-18) 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 3-8) or the ion volume
tool in place will cause a catastrophic venting of the system. ▲
3. Unscrew the inlet valve knob (item 3 in Figure 3-8) and remove the
inlet valve plug (item 5 in Figure 3-8), the inlet valve knob, and the
internal ferrule.
4. Loosen the four panel fasteners (items 6, 7, 8, and 9 in Figure 3-8).
5. The top panel rests on hooks pointing into the upward direction.
Tilt the top 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
1. If it is not already in Service mode, place the ETD Module in
Service mode as directed in “Placing the Instrument in Off
Condition and Service Mode” on page 3-47.
Note In Service mode, all power to the LTQ Orbitrap Velos 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. ▲
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Warning Burn Hazard. 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
turbopump will continue operating. ▲
2. Using an Allen wrench, loosen the captive screws at the top and
remove the screws at the bottom of gray plastic side panel and
remove the panel.
3. Using a #2 Phillips screwdriver, loosen the three captive screws on
the metal side access panel (item 2 in Figure 3-8 on page 3-18) and
remove the panel.
Warning Burn Hazard. 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.
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 3-21
•
“Cleaning the Ion Source Lens Assembly” on page 3-33
•
“Cleaning the Ion Source Block” on page 3-39
•
“Replacing the Ion Source Filament” on page 3-41
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•
“Replacing Inlet Valve Components” on page 3-44
The ion source, the ion trap, and their components are shown in
Figure 3-9.
2
4
3
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 3-9.
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:
•
Cleaning supplies for stainless steel parts (See “Cleaning Stainless
Steel Parts” on page 3-14.)
•
Gloves (clean, lint-free, and powder-free)
•
Ion volume tool and guide bar
•
Lint-free cloth
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.
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❖
To clean the ion volume with an inlet valve
1. Click the On/Standby button in the Tune Plus window to place the
LTQ Orbitrap Velos ETD in Standby mode. See Figure 3-10.
On
On/Standby button
Off
Standby
Reagent Ion Source instrument control icon
Status View
Figure 3-10. Tune Plus window
2. Open the Reagent Ion Source dialog box (Figure 3-17 on page 3-26)
in Tune Plus by clicking the Reagent Ion Source instrument control
icon.
3. Place the guide bar handle (item 13 in Figure 3-11 on page 3-23) to
the 3 o’clock position (Figure 3-12 on page 3-23).
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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 3-11. Ion volume tool components
4. Insert the guide bar (item 9 in Figure 3-11) into the guide bar
opening in the back of the ETD Module (Figure 3-12).
Inlet valve lever in
down (closed) position
Guide bar handle
Guide bar opening
Figure 3-12. 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.
5. Push the guide bar in as far as it will go, then rotate it 90° clockwise
to lock in the guide bar (Figure 3-13 on page 3-24). The guide bar
handle faces the floor at the completion of this step.
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Inlet valve lever in
down (closed) position
Guide bar handle
Figure 3-13. 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.
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 3-14. Rear view of the ETD Module, showing the inlet valve
Make sure the inlet valve is closed (inlet valve lever is down, as
shown in Figure 3-13) and remove the inlet valve plug (item 2 in
Figure 3-14). Do this by rotating (loosening) the inlet valve knob
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(item 1 in Figure 3-14 on page 3-24) until the inlet valve plug will
slide out easily. The inlet valve plug prevents air from entering the
vacuum manifold in case the inlet valve is inadvertently opened.
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 3-15.
Figure 3-15. 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.
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 3-16. Ion volume tool guide bar first stop
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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 3-11 on page 3-23 and Figure 3-16 on page 3-25.
c. Slide the ion volume tool so the guide ball is in the groove at the
first stop (Figure 3-11 and Figure 3-16). This prevents the probe
from being pulled forward when the inlet valve is evacuated.
d. Tighten the inlet valve knob (Figure 3-16) to ensure that a
leak-tight seal is made.
e. Click Open Probe Interlock in the Reagent Ion Source dialog
box (Figure 3-17). 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 “Replacing Inlet Valve
Components” on page 3-44. When the target pressure is
achieved, a message appears stating that the ball valve can be
opened (Figure 3-18).
Open Probe Interlock
Figure 3-17. Reagent Ion Source dialog box, Open Probe Interlock button.
Figure 3-18. Instrument Message box: The Ball Valve can now be opened
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f. Once evacuation is complete, push up the inlet valve lever to
open the inlet valve (Figure 3-19).
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 3-19.
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 3-19. Ion volume tool inserted into the inlet valve
second mark
second stop
first mark
Guide Ball
Figure 3-20. Detail of ion volume tool fully inserted into the inlet valve
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You will know that the ion volume tool is fully inserted into the
ion volume holder because the guide ball (item #11, Figure 3-11
on page 3-23) will be just past the first mark on the guide bar as
shown in Figure 3-20 on page 3-27.
b. Turn the ion volume tool handle counterclockwise to the lock
position, See Figure 3-21. Listen for a click indicating that the
handle is fully engaged in the lock position and is holding the
ion volume.
Figure 3-21. 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 3-11 on
page 3-23 and Figure 3-16 on page 3-25 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
that are under vacuum will be required. ▲
e. Loosen the inlet valve knob (Figure 3-19 on page 3-27).
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 Burn Hazard. The ion volume will be too hot to touch. Let it
cool to room temperature before handling it. ▲
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10. Clean the ion volume:
a. Turn the ion volume tool handle to the unlock position
(Figure 3-15 on page 3-25). 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.
Pull the ion volume out of the ion volume tool, as illustrated in
Figure 3-22.
Bayonet Pin Guide
Bayonet Pin
Ion Volume Tool
Ion Volume
Ion Volume Holder
Spring Washer
Figure 3-22. Ion volume assembly
c. Press the ion volume into the ion volume holder and rotate the
ion volume to remove it from the ion volume holder See
Figure 3-23.
Figure 3-23. Separating ion volume and ion volume holder
d. Clean ion volume and ion volume holder according to the
instructions in “Cleaning Stainless Steel Parts” on page 3-14.
❖
To reinsert the ion volume
1. Press the ion volume into the ion volume holder and rotate the ion
volume to secure it to the ion volume holder.
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2. 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 3-24.
Caution To avoid damage to the ion source, ensure that the arrows on
the ion volume tool and ion volume are aligned. ▲
4
2
3
1
5
6
7
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 3-24. Placing the ion volume on the ion volume tool
Note Wear clean, lint-free, and powder-free gloves when you handle
parts inside the vacuum manifold. ▲
b. Turn the ion volume tool handle to the lock position. (See
Figure 3-21 on page 3-28.)
3. 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 3-11 on page 3-23 and
Figure 3-16 on page 3-25).
b. Turn the ion volume tool so that the guide ball is in the groove
at the first stop (Figure 3-16 on page 3-25). This prevents the
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probe from being pulled forward when the inlet valve is
evacuated.
c. Tighten the inlet valve knob to ensure a leak-tight seal
(Figure 3-19 on page 3-27).
d. Click Open Probe Interlock in the Reagent Ion Source dialog
box (Figure 3-17 on page 3-26). 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 “Replacing Inlet Valve Components” on page 3-44. When the
target pressure is achieved, a message will appear stating that the
ball valve can be opened. See Figure 3-18 on page 3-26.
e. Once evacuation is complete, push the inlet valve lever up to
open the inlet valve. See Figure 3-19 on page 3-27.
4. Reinsert the ion volume:
a. Slide the ion volume tool into the vacuum manifold, as
illustrated in Figure 3-19.
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 3-20 on page 3-27.
c. Turn the ion volume tool handle to the unlock position. See
Figure 3-25.
Figure 3-25. 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 3-26 on page 3-32.
ii. Slide the ion volume tool back into the vacuum manifold
until the end of the ion volume tool just touches the ion
volume.
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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 3-11 on page 3-23 and Figure 3-16 on
page 3-25).
Figure 3-26. Ion volume tool handle in the locked position
e. Close the inlet valve by pushing down on the inlet valve lever
(Figure 3-14 on page 3-24).
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. ▲
f. Loosen the inlet valve knob (item 6 in Figure 3-19 on
page 3-27).
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.
5. Remove the ion volume tool and guide bar from the vacuum
manifold:
a. Remove the guide bar by rotating it 90 degrees
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 3-19 on page 3-27).
c. Click Close in the message stating that the ball valve can be
opened. (See Figure 3-18 on page 3-26.)
6. Re-tune the MS detector.
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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. ▲
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
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 Velos 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 Burn Hazard. 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:
a. Remove the main access panel of the ETD Module (item 1 in
Figure 3-8 on page 3-18). Follow the procedures in “Removing
the ETD Main Access Panel” on page 3-18.
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. ▲
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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 3-27. Inlet valve components (ion volume tool not shown)
b. Remove all connectors between the components on the vacuum
manifold probe plate (item #10, Figure 3-27 on page 3-34) and
the ETD Control PCB (Figure 1-17 on page 1-22).
c. Remove the valve shield from the vacuum manifold probe plate
(Figure 3-28) by loosening the four screws at the corners of the
shield.
1
Figure 3-28. Valve shield (1) covering the vacuum manifold probe plate
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d. Remove the foreline hose on the source from its connection
(Figure 3-29 and item 8 in Figure 3-27).
Figure 3-29. Removing the foreline hose from its connection
e. Remove the four screws holding the vacuum manifold probe
plate (Figure 3-30 and item 10 in Figure 3-27 on page 3-34).
Support the plate with your hand as shown in Figure 3-30.
Arrows point to the four hex screw locations (items 1–4).
1
2
4 (at lower left corner of 3
manifold probe plate)
Figure 3-30. Unscrewing the vacuum manifold probe plate
f. Remove the vacuum manifold probe plate (Figure 3-31 on
page 3-36).
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Figure 3-31. Removing the vacuum manifold probe plate
g. Unplug the 12-pin feedthrough harness from the feedthrough
(Figure 3-32).
1
2
4
3
2
Labeled components: 1=unplugged 12 pin feedthrough, 2=thumbscrews,
3=transfer line bellows, 4=ion source assembly
Figure 3-32. Interior of vacuum manifold
h. Remove the ion source assembly from the vacuum manifold
(Figure 3-33 on page 3-37) by first loosening the ion source
thumbscrews (item 2 in Figure 3-32).
i. Second, as you remove the ion source assembly (item 1 in
Figure 3-33) gently shift it to the left (arrow 2 in Figure 3-33)
before and while pulling it out. This will allow the ion source
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assembly to disengage from the transfer line bellows (item 3 in
Figure 3-33) as it is removed. Alternatively, gently depress the
transfer line bellows (Figure 3-32 on page 3-36) to disengage it
from the ion source assembly.
1
3
2
Figure 3-33. 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.
The ion source assembly is held together with a clip (item 8 in
Figure 3-34 on page 3-38). 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 3-34) and the back of the magnet yoke (item 3 in
Figure 3-34) 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
3
4
5
6
11
1
10
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 3-34. Ion source assembly
An exploded view of the ion source assembly is shown in Figure 3-35.
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 3-35. 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 3-35).
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5. Clean the ion source lens assembly according to the procedure in
“Cleaning Stainless Steel Parts” on page 3-14. 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 “Starting Up the
System after a Shutdown” on page 2-9.
Cleaning the Ion Source Block
If cleaning the ion volume and ion source lens assembly does not restore
system performance, you might need to clean the ion source block.
Generally, you need to clean the ion source block 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
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 Velos ETD. (See
“Shutting Down the LTQ Orbitrap Velos Completely” on
page 2-7.)
Caution Shut down and unplug the LTQ Orbitrap Velos ETD before
proceeding with the next steps of this procedure. ▲
c. Remove the ion source assembly by following the procedures in
step 2 in “Cleaning the Ion Source Lens Assembly” on
page 3-33.
Note Wear clean, lint- and powder-free gloves when you handle parts
inside the vacuum manifold. ▲
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2. Disassemble the ion source assembly (Figure 3-34 on page 3-38 and
Figure 3-35 on page 3-38), remove and disassemble the ion source
(Figure 3-36).
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.
1
3
2
14
12
13
5
9
4
6
2
8
10
7
11
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 3-36. Ion source, exploded view
d. Remove the three base studs (item 3 in Figure 3-36). Be careful
not to damage the leads on the Ion Source PCB (item 4 in
Figure 3-36).
e. Gently remove the Ion Source PCB (item 4 in Figure 3-36) from
the ion source by loosening the spring clip thumbscrew (item 11
in Figure 3-36) and the spring clip (item 10 in Figure 3-36) and
sliding the three cartridge heaters and the temperature sensor
(items 2 and 5 in Figure 3-36) off the ion source and pulling the
filament (item 1 in Figure 3-36) straight away from the three
filament connectors on the Ion Source PCB. Do not bend or
twist the cartridge heaters or temperature sensor.
f. Remove the filament and ceramic spacer (items 15 and 1 in
Figure 3-36) from the ion source block (item 6 in Figure 3-36).
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g. Remove the ion volume key thumbscrew (item 7 in Figure 3-36
on page 3-40).
Note It is not necessary to remove the ion volume pin (item 8 in
Figure 3-36). If you remove it, you should reinsert it just far enough so
the ball will keep an ion volume (item 9 in Figure 3-36) from falling
out. If the ball extends too far, the ion volume will be difficult to
remove. ▲
3. Clean the ion source parts and replace the ion source assembly:
a. Clean each component of the ion source, as described in
“Cleaning Stainless Steel Parts” on page 3-14 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 “Cleaning the Ion Source Lens Assembly” on
page 3-33 in reverse order.
4. Restore the ETD Module to operational status. See “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 3-37 on page 3-42.
Supplies needed for replacing the ion source filament:
Thermo Fisher Scientific
•
Filament Assembly DSQ II (P/N 120320-0030)
•
Gloves, clean, lint-free, and powder-free
•
Protective eyewear
•
Lint-free cloth
•
Forceps or dental pick
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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 3-37. Ion source lens assembly and ion source
❖
To replace the ion source filament
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 Velos ETD. (See
“Shutting Down the LTQ Orbitrap Velos Completely” on
page 2-7.)
Caution Shut down and unplug the LTQ Orbitrap Velos ETD before
proceeding with the next steps of this procedure. ▲
c. Remove the ion source assembly by following the procedures in
step 2 in “Cleaning the Ion Source Lens Assembly” on
page 3-33.
Note Wear clean, lint- and powder-free gloves when you handle parts
inside the vacuum manifold. ▲
2. Disassemble the ion source assembly (Figure 3-34 on page 3-38 and
Figure 3-35 on page 3-38), remove and disassemble the ion source
(Figure 3-36 on page 3-40).
a. Remove the ion source lens assembly (item 1 in Figure 3-37).
b. Remove the three base-studs (item 3 in Figure 3-36, item 4 in
Figure 3-37).
c. Remove the filament assembly (items 1 and 15 in Figure 3-36,
item 5 in Figure 3-37) and ion source block (item 2 in
Figure 3-37) from the three filament connectors and cartridge
heaters (item 2 in Figure 3-36) on the Ion Source PCB (item 4
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User Maintenance
Maintenance of the ETD Module
in Figure 3-36) according to the procedure in step e of
“Cleaning the Ion Source Block“ on page 3-40 .
Note Now is a good time to clean the ion volume and ion source
lenses. ▲
3. Inspect and install a new filament assembly:
a. Turn the filament assembly over and, using a strong light and a
magnifying glass, verify that the filament wire is centered in the
electron lens hole. If necessary, carefully use forceps (or a dental
pick) to adjust the filament wire. Figure 3-38 shows the centered
filament wire as seen from the bottom of the filament through
the electron lens hole.
Note A bent filament can lead to a low or absent anion signal. If the
filament wire is bent, not centered, or otherwise damaged, you must
replace the filament assembly. ▲
Centered wire
Direction of light source
Figure 3-38. 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 3-36 on page 3-40).
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 3-36, item 4 in
Figure 3-37 on page 3-42).
4. Reassemble ion source and ion source assembly.
5. Insert the ion source assembly into the vacuum manifold.
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Maintenance of the ETD Module
6. Restore the ETD Module to operational status. See “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. ▲
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:
•
Inlet Valve Seal Kit (P/N 119265-0003)
•
Lint-free cloth
•
Wrench, open-ended, 5/16-in
•
Wrench, Allen, 4 mm
❖
To replace inlet valve components
1. Pull down the inlet valve lever to close the inlet valve. See
Figure 3-39.
Inlet valve knob
Inlet valve plug
Inlet valve lever in the
down (closed) position
Guide bar opening
Figure 3-39. Inlet valve components
2. Rotate the inlet valve knob counter-clockwise until you can easily
remove the inlet valve plug.
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3. Continue to rotate the valve knob until you can remove it.
The inlet valve knob has a stainless-steel ferrule inside. Keep the
inlet valve knob and ferrule together.
4. Pull out the knob on the inlet valve seal tool (P/N 119283-0001)1,
so that the knob is loose. See Figure 3-40.
Knob
Figure 3-40. Inlet valve seal tool
5. Insert the tool straight into the inlet valve. See Figure 3-41.
Figure 3-41. Inlet valve seal tool inserted in the inlet valve
Caution Do not scratch the surface of the seal. Use only the inlet valve
seal tool to remove or install an inlet valve seal. ▲
6. Press in the knob on the tool until it stops.
7. Remove the tool. The inlet valve seal should be on the tool. See
Figure 3-42 on page 3-46.
1
Item contained in Inlet Valve Seal Kit (P/N 119265-0003).
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Figure 3-42. Inlet valve seal on the inlet valve seal tool
8. Loosen the knob to disengage the seal. See Figure 3-43.
Inlet valve seal with O-rings
Inlet valve seal
Figure 3-43. Inlet valve seal disengaged from tool
9. Discard the seal with its O-rings in place.
10. Place one O-ring (P/N 3814-6530)1 into each of the two slots on
the inlet valve seal (P/N 119683-0100)1.
11. Place the new inlet valve seal onto the inlet valve seal tool.
12. Insert the inlet valve seal tool into the inlet valve into it stops.
13. Remove the tool. The O-rings on the valve seal secure the inlet valve
seal in the opening.
14. Reinstall the ferrule, knob, and plug into the inlet valve opening.
1
Item contained in Inlet Valve Seal Kit (P/N 119265-0003).
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Maintenance of the ETD Module
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 Velos ETD
be placed in Service mode after the vials have cooled. (Vial cooling is
done in Off condition.) See the following sections for procedures to be
used to change the reagent vials:
•
“Placing the Instrument in Off Condition and Service Mode” on
page 3-47
•
“Installing/Exchanging the Reagent Vials” on page 3-50
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
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”.
Placing the Instrument in Off Condition and Service Mode
The power switches control power to the LTQ Orbitrap Velos ETD
(MS and ETD Module). The ETD Module power switches control the
power to the ETD Module only. When the LTQ Orbitrap Velos ETD is
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User Maintenance
Maintenance of the ETD Module
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
Velos ETD in Service mode. Turn On and Off the instrument (both
ETD Module and MS) with the MS Main Power switch.
Warning Burn Hazard. 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. ▲
Note The instructions that follow assume that no analyte is flowing into
the API source. ▲
❖
To place the LTQ Orbitrap Velos ETD in Off Condition and Service mode
and to verify that the vials are safe to handle
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 3-10 on
page 3-22.)
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
condition, the LTQ Orbitrap Velos 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 3-44).
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Observe the temperature of Vial 1 in the Actual column of the
Reagent Ion Source dialog box (Figure 3-44). Nitrogen cooling gas
will flow until the vial reaches 70 °C. (See “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 3-44. Reagent Ion Source dialog box
Warning Burn Hazard. 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.
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User Maintenance
Maintenance of 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 Burn Hazard. 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 Velos ETD is now in Service mode and the vials are
at a safe temperature for handling.
Installing/Exchanging 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
1. Remove the back panel from the ETD Module. (See “Removing the
ETD Main Access Panel” on page 3-18.) This exposes the reagent
inlet source heating unit, which has its own cover (Figure 3-45 on
page 3-51).
Warning Burn Hazard. Follow the procedures described in “Placing the
Instrument in Off Condition and Service Mode” on page 3-47 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 Burn Hazard. 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 “Placing the Instrument in Off
Condition and Service Mode” on page 3-47.) Verify that the vial heater
cover is safe to handle before attempting to remove the vial holders and
reagent vials. ▲
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User Maintenance
Maintenance of the ETD Module
Reagent Inlet
Source Unit
Vial Heater Cover
Figure 3-45. ETD Module with back panel removed
3. Put on a pair of new, white nitrile clean room gloves and protective
eye wear.
4. Using a Phillips screwdriver, remove the screws in the vial heater
cover. 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
Velos ETD (Figure 3-45).
5. Remove the vial holder by gently pulling it out of the vial heater.
6. 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 3-46. These ribs prevent the vial holder from rotating once it
is placed into the vial heater. Figure 3-47 on page 3-52 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. ▲
Warning Avoid exposure to potentially harmful materials.
Always wear protective gloves and safety glasses when you handle
solvents or corrosives. Also contain waste streams and use proper
ventilation. Refer to your supplier's Material Safety Data Sheet (MSDS)
for proper handling of a particular compound. ▲
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Figure 3-46. Reagent vials with holders
7. Take a vial containing the ETD reagent (fluoranthene) from its box
and remove the aluminum tab from the top of the vial’s crimp seal.
8. Put the vial into a vial holder.
Vial Heater ribs
Vial 1 Heater
Vial Holder Knob
Vial 2 Heater
Figure 3-47. ETD Module with vial heater cover removed
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9. 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.
10. Place the empty vial from the box into the other vial holder if an
empty vial is not already installed.
11. 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:
•
The carrier/CI gas containing the reagent might escape to the
laboratory causing a safety problem.
•
The ETD Module will not operate correctly and the filament will
burn out. ▲
12. Reinstall the vial heater cover over the vial heaters.
13. Reinstall the back panel of the ETD Module. See “Removing the
ETD Main Access Panel” on page 3-18. The ETD Module will not
turn on unless the back panel is installed.
14. 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 3-10 on page 3-22.) 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 3-44 on page 3-49.)
The LTQ Orbitrap Velos ETD is now ready for use.
Changing the Reagent Ion Source Flow Restrictors
❖
To change the reagent ion source flow restrictors
1. Shut down completely the instrument according to the procedures
in “Shutting Down the LTQ Orbitrap Velos Completely” on
page 2-7.
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Warning Burn Hazard. 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
“Removing the ETD Side Access Panel” on page 3-19.
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. ▲
3. Remove the four screws that hold the reagent inlet cover in place.
Warning Burn Hazard. 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 Burn Hazard. 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 3-48.
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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 3-48. Reagent inlet assembly
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 3-48) 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 3-48) 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.
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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 3-48) to the Tee below the reagent inlet assembly (item 9
in Figure 3-48) and from the gas valves (item 10 in Figure 3-48).
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 “Starting Up the System after a Shutdown” on
page 2-9.
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 3-49.
Fan filters
Figure 3-49. ETD Module, top panel
❖
To clean the fan filters of the ETD Module
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 Burn Hazard. 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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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 Velos system, order only the parts listed
or their equivalent.
Note Not all parts are available for purchase separately. Some parts may
only be available for purchase as part of a kit or assembly. ▲
For information on how to order parts, see “Contacting Us” in the
front section of this guide.
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Replaceable Parts
Ion Sources
Ion Sources
ESI probe, for Ion Max source. . . . . . . . . . . . . . . . . . . . . . . .
Low flow metal needle for API 2 probes . . . . . . . . . . . . . . . .
Nanospray II Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Static Nanospray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Dynamic Nanospray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
APCI probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
APPI probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
HESI-II Probe Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
High-flow needle insert assembly. . . . . . . . . . . . . . . . . . . . . .
Low-flow needle insert assembly . . . . . . . . . . . . . . . . . . . . . .
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LTQ Orbitrap Velos Hardware Manual
OPTON-20011
OPTON-30004
OPTON-20050
OPTON-20051
OPTON-97017
OPTON-20012
OPTON-20026
OPTON 20037
OPTON-53010
OPTON-53011
Thermo Fisher Scientific
Replaceable Parts
Parts for the Basic System
Parts for the Basic System
Orbitrap Installation Kit
Tube, 1/8” × 2.1- 1.4301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0261000
Ferrule, stainless steel; R. 1/8” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0520950
Ferrule, stainless steel; V. 1/8” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0522520
Cap nut, stainless steel; 1/8“. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0520890
Fitting KJH06-00. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1221620
Pumping System
For a schematical overview of the pumping system, see Figure 1-23 on
page 1-30.
T-piece 13 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0512360
Hose 13 × 3.5; PVC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0690720
Turbomolecular pump TMU262; modified . . . . . . . . . . . . . . . . . . . .1184340
Turbomolecular pump; TMH 071 P . . . . . . . . . . . . . . . . . . . . . . . . .1141500
UHV gauge IKR 270; short . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181380
Compact Pirani Gauge TPR280. . . . . . . . . . . . . . . . . . . . . . . . . . . . .1156400
Water cooling for TMH 262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1149140
Water cooling for TMH 071 P. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0794742
PVC hose, with steel helix; ID=45 mm, L=1.6 m . . . . . . . . . . . . . . . .1184330
Hose nipple, DN 40, ISO-KF-45. . . . . . . . . . . . . . . . . . . . . . . . . . . .1159230
Venting flange; DN 10, KF-G1/8” . . . . . . . . . . . . . . . . . . . . . . . . . . .1184400
Splinter shield for turbopumps, with DN 100 CF-F flange . . . . . . . .1198590
Centering ring, with integrated splinter shield; DN 63 ISO . . . . . . . .1198600
Anti-magnetic cover for IKR 270 . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181390
Gasket; NW 100 CF, copper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0552440
Hose, metal; KF16-KF25 - 250mm . . . . . . . . . . . . . . . . . . . . . . . . . .1154130
Gasket; copper, NW 35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0550480
Metal tube, KF NW16×250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0524260
KF Tee piece; NW 16 KF, stainless steel . . . . . . . . . . . . . . . . . . . . . . .0524230
Centering ring with o-ring; DN 16, Viton . . . . . . . . . . . . . . . . . . . . .0522140
Centering ring with o-ring; DN 25, Viton . . . . . . . . . . . . . . . . . . . . .0522150
Centering ring; NW 16/10, aluminum-Viton . . . . . . . . . . . . . . . . . .0522200
Clamping ring; NW 10/16, KF . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0521830
Clamping ring; NW 20/25, KF . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0521560
Reducing cross piece; DN40/DN16 KF . . . . . . . . . . . . . . . . . . . . . . .1184310
Metal tube; DN40x500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1184350
Metal tube; DN40x750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181290
Hose clamp; NW 40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181320
Centering ring; NW 40 KF, aluminum-Viton . . . . . . . . . . . . . . . . . .0522260
Tension ring; NW 32/40 KF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181250
Clamping screw; DN63-100 ISO, aluminum. . . . . . . . . . . . . . . . . . .1042670
Flexible metal hose KF NW 16x500. . . . . . . . . . . . . . . . . . . . . . . . . .0534500
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
4-3
Replaceable Parts
Parts for the Basic System
Water Supply
For a schematical overview of the gas supply, see Figure 1-28 on
page 1-37.
Quick coupling insert; 9.6 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1141640
Quick coupling body; 9.6 mm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1138960
Hose; 9 x 3, black, PVC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1049540
Hose; 6 x 1, Teflon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1042660
Quick coupling insert; Delrin Acetal, NW 6.4 . . . . . . . . . . . . . . . . . 1185030
Quick coupling body; Delrin Acetal, NW 6.4 . . . . . . . . . . . . . . . . . . 1185020
Clamping piece 8/16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0370130
Adaptor hose nipple; male, 1/2 x 10 . . . . . . . . . . . . . . . . . . . . . . . . . 1185840
Flow control sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1191740
Gas Supply
For a schematical overview of the cooling water circuit, see Figure 1-32
on page 1-42.
Bulkhead union; 1/16”, for hose 4 x 1 (for P/N 069 1130) . . . . . . . . 1153660
Bulkhead union; 1/8”×1/8” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0523450
Hose; 4 x 1, Teflon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0690280
Hose; 4 x 1, polyurethane, blue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0691130
Capillary 1/16” ID-SS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0605470
Plug-in T-piece; 3 x 6mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1128140
Regulator + manometer f. Orbitrap . . . . . . . . . . . . . . . . . . . . . . . . . . 1257670
Capillary; 1/16”x0.13x400mm (red), PEEK . . . . . . . . . . . . . . . . . . . 1253830
Coupling; 1/16”, SS-100-6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0524340
Ferrule; 1/16” GVF 16-000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1121110
Reducer Swagelok; 1/8” × 1/16”, stainless steel . . . . . . . . . . . . . . . . . 0662880
Ferrule; 1/16” GVF/16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0674800
Connector 1/8”, for hose OD 4 mm . . . . . . . . . . . . . . . . . . . . . . . . . 1128680
Cap nut; 1/16”, stainless steel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0520880
Hose; 2 x 1, PTFE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1091650
Sleeve; Ø 6 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1047320
Capillary; PEEKsil, 1/16”, 0.1 × 500 mm . . . . . . . . . . . . . . . . . . . . . 1223420
Plug, KQ2P-06 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1185620
Cap, KQ2C-06 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1258220
4-4
LTQ Orbitrap Velos Hardware Manual
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 Velos ETD.
Quadrupole Orbitrap, complete . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1239200
Housing HCD/ETD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1231740
Separating plate HCD/ETD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1231770
Screw M 4 x 8 DIN912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1044420
O-ring 129 X 4 A Viton. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1240520
Lid HCD/ETD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1231760
Screw-in connector; 1/16” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1186150
Gasket; NW 63 ISO, aluminum/Viton . . . . . . . . . . . . . . . . . . . . . . .0554060
Blank flange; stainless steel, NW 63 . . . . . . . . . . . . . . . . . . . . . . . . . .0652620
Clamping screw; DN63-100, aluminum . . . . . . . . . . . . . . . . . . . . . .1028380
Washer 8.4; stainless steel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0470070
Screw, hexagonal; M 8 x 35, stainless steel . . . . . . . . . . . . . . . . . . . . .0454400
Washer 8.4 x 11 x 1.5, stainless steel. . . . . . . . . . . . . . . . . . . . . . . . . .0470860
Screw M8 x 35; stainless steel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0454250
Centering ring NW 16 Viton. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0522140
Feedthrough; 8-fold 1,5kV DN16KF. . . . . . . . . . . . . . . . . . . . . . . . .1231750
O-ring; 118 X 5 A, Viton. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1168240
Box f. feedthrough; KF16 / Sub-D9 . . . . . . . . . . . . . . . . . . . . . . . . . .1231800
Cylindrical Screw ISO4762-M6X12-A4. . . . . . . . . . . . . . . . . . . . . . .0453300
Vacuum system ETD
Flange clamp; KF16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1145860
Turbopump TMH 071 P . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1141500
Splinter guard, DN_63_ISO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1198600
Water cooling, for TMH 071 P . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0794742
Metal hose, DN 16 ISO-KF x500 . . . . . . . . . . . . . . . . . . . . . . . . . . .1181410
Centering ring with o-ring; DN 16, Viton . . . . . . . . . . . . . . . . . . . . .0522140
Clamping ring; NW 10/16, KF . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0521830
Hose flange; NW 25 KF. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1042330
Centering ring, with o ring; DN 25, Viton . . . . . . . . . . . . . . . . . . . .0522150
Clamping ring, DN 25. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0521560
Flange, KF16 - hose OD 19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1239340
Reducer; DN 16/DN 25, aluminum . . . . . . . . . . . . . . . . . . . . . . . . .0522160
PUMP, ROTARY VANE, EDWARDS RV3. . . . . . . . . . . . . . 00108-01-0008
KIT, ACCESSORY, MECHANICAL PUMP, RV3 . . . . . . . . . 98000-620007
Gas Supply ETD
Plug-in T-piece; 3 x 6mm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1128140
Sleeve 6 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1047320
Reducing hose connector, 3.2−>6 . . . . . . . . . . . . . . . . . . . . . . . . . . .1239220
Hose cutter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1239280
T-piece 13 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0512360
Hose 9 X 3; PVC, black . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1049540
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
4-5
Replaceable Parts
Parts Lists for the ETD System
Clamping piece 8/16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0370130
Hose; 4 X 1, Teflon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0690280
Clamping ring; stainless steel, NW10/16. . . . . . . . . . . . . . . . . . . . . . 1149200
PEEK capillary; 1/16” x 0.040. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1245940
Ferrule, 1/16”, for GVF/16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0674800
Ferrule 1/16” - CTFE, collapsible . . . . . . . . . . . . . . . . . . . . . . . . . . . 1224700
Electronic Parts ETD
Cable Y-ADAPTER/T.PUMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2108630
Coupling; RJ45 BU/2BU . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2075210
Patch cable; 0.51MT RJ45 gray SFTP . . . . . . . . . . . . . . . . . . . . . . . 2080870
Cable POWER DIS./T-PUMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2081200
Cable CLT-OFFSET-A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2108710
Cable IOS ETD/ION OPTIC-S . . . . . . . . . . . . . . . . . . . . . . . . . . . 2108820
UNIT_ION OPTIC SUPPLY ETD . . . . . . . . . . . . . . . . . . . . . . . . 2108920
PCB LTQ CABLE DRIVER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2097780
PCB ORBITRAP CABLE RECEIVER. . . . . . . . . . . . . . . . . . . . . . 2097830
PCB ETD CABLE RECEIVER . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2097800
Cable ETD/LTQ/ORBITRAP-INTERCONNECT 60 . . . . . . . . . . 2108940
Cable ETD/LTQ/ORBITRAP-INTERCONNECT 36 . . . . . . . . . . 2108950
Cable ETD/LTQ/ORBITRAP-INTERCON SUPPLY . . . . . . . . . . 2108960
Coaxial cable; ETD IOS/ANALOG CTRL, J5554 . . . . . . . . . . . . . 2108990
Coaxial cable; ETD IOS/ANALOG CTRL, J5555 . . . . . . . . . . . . . 2109000
Coaxial cable; ETD IOS/ANALOG CTRL, J5556 . . . . . . . . . . . . . 2109010
Cable ANALOG CTRL / ETD IOS . . . . . . . . . . . . . . . . . . . . . . . . 2108970
Cable ETD IOS/HCD multipole . . . . . . . . . . . . . . . . . . . . . . . . . . . 2108980
Extension cable; 16A C20-C19 2M . . . . . . . . . . . . . . . . . . . . . . . . . 2097050
ADAPTER_IOS/MULTIPOLE-HCD . . . . . . . . . . . . . . . . . . . . . . 2100410
Reagent Inlet Module
ASSY, TOOL, ION VOLUME INSERTION/REMOVAL . . . 98000-60028
TUBING, PEEKsil, 1/16” OD, 100mm LONG, RoHS. . . .00109-02-00020
FRLE, 1HOLE, 1/16 OD, 0.4mm ID, VESP/GRPHT, RO .00101-08-00005
FRLE, 2HOLS, 1/16 OD, 0.4mm ID, VESP/GRPHT, RO .00101-08-00006
Inlet Valve Seal Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119265-0003
Inlet valve seal removal tool. . . . . . . . . . . . . . . . . . . . . . . . . 119283-0001
Spool inlet valve seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119683-0100
O-ring Viton, 0530 ID × 0.082 W . . . . . . . . . . . . . . . . . . . . . 3814-6530
4-6
LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Replaceable Parts
Parts Lists for the ETD System
ETD Reagent Kit
ETD Reagent Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98000-62008
Angiotensin I, 1mg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-15517
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 Velos Hardware Manual
4-7
Appendix A
Fluoranthene
Fluoranthene is used as the Electron Transfer Dissociation (ETD)
reagent in the ETD Module portion of the LTQ Orbitrap Velos 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 4-7) 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 Velos 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
B
C
D
E
F
G
H
I
J
K
L
A
A ampere
ac alternating current
ADC analog-to-digital converter
adduct ion An ion formed by the joining together of
two species, usually an ion and a molecule, and often
within the ion source, to form an ion containing all
the constituent atoms of both species.
AGC™ See Automatic Gain Control™ (AGC).
APCI See atmospheric pressure chemical ionization
(APCI).
M N
O
P
Q
R
S
T
U
V W X
Y
APCI needle, corona discharge A needle to which a
sufficiently high voltage (typically ±3 to ±5 kV) is
applied to produce a chemical ionization plasma by
the corona discharge mechanism.
See also chemical ionization (CI), chemical ionization
(CI) plasma, atmospheric pressure chemical ionization
(APCI), and corona discharge.
APCI nozzle The nozzle in the APCI probe that sprays
the sample solution into a fine mist.
See also atmospheric pressure chemical ionization
(APCI).
APCI sample tube A fused silica tube that delivers
sample solution to the APCI nozzle. The APCI
sample tube extends from the sample inlet to the
APCI nozzle.
APCI corona discharge current The ion current
carried by the charged particles in the APCI source.
The voltage on the APCI corona discharge needle
supplies the potential required to ionize the particles.
The APCI corona discharge current is set; the APCI
corona discharge voltage varies, as required, to
maintain the set discharge current.
APCI source Contains the APCI probe assembly,
APCI manifold, and API stack.
See also corona discharge and APCI corona discharge
voltage.
See also atmospheric pressure chemical ionization
(APCI), APCI manifold, and API stack.
APCI corona discharge voltage The high voltage that
is applied to the corona discharge needle in the APCI
source to produce the APCI corona discharge. The
corona discharge voltage varies, as required, to
maintain the set APCI spray current.
APCI spray current The ion current carried by the
charged particles in the APCI source. The APCI
corona discharge voltage varies, as required, to
maintain the set spray current.
See also APCI spray current.
APCI manifold The manifold that houses the APCI
sample tube and nozzle, and contains the plumbing
for the sheath and auxiliary gas.
Thermo Fisher Scientific
Z
See also atmospheric pressure chemical ionization
(APCI), and API stack.
APCI vaporizer A heated tube that vaporizes the
sample solution as the solution exits the sample tube
and enters the atmospheric pressure region of the
APCI source.
See also atmospheric pressure chemical ionization
(APCI).
LTQ Orbitrap Velos Hardware Manual
G-1
Glossary: API
API See atmospheric pressure ionization (API).
API atmospheric pressure region The first of two
chambers in the API source. Also referred to as the
spray chamber.
API capillary-skimmer region The area between the
capillary and the skimmer, which is surrounded by the
tube lens. It is also the area of first-stage evacuation in
the API source.
API heated capillary A tube assembly that assists in
desolvating ions that are produced by the ESI or APCI
probe.
See also API heated capillary voltage.
API heated capillary voltage The dc voltage applied to
the heated capillary. The voltage is positive for positive
ions and negative for negative ions.
See also API source and API heated capillary.
API ion transfer capillary A tube assembly that assists
in desolvating ions that are produced by the ESI, NSI,
or APCI probe.
See also API ion transfer capillary offset voltage and
API ion transfer capillary temperature.
API ion transfer capillary offset voltage A dc voltage
applied to the ion transfer capillary. The voltage is
positive for positive ions and negative for negative
ions.
See also API source and API ion transfer capillary.
API ion transfer capillary temperature The
temperature of the ion transfer capillary, which should
be adjusted for different flow rates.
See also API source and API ion transfer capillary.
API source The sample interface between the LC and
the mass spectrometer. It consists of the API probe
(ESI or APCI) and API stack.
See also atmospheric pressure ionization (API), ESI
source, APCI source, ESI probe, and API stack.
API spray chamber The first of two chambers in the
API source. In this chamber the sample liquid exits
the probe and is sprayed into a fine mist (ESI or NSI)
or is vaporized (APCI) as it is transported to the
entrance end of the ion transfer capillary.
G-2
LTQ Orbitrap Velos Hardware Manual
API spray shield A stainless steel, cylindrical vessel
that, in combination with the ESI or APCI flange,
forms the atmospheric pressure region of the API
source.
See also atmospheric pressure ionization (API).
API stack Consists of the components of the API
source that are held under vacuum and includes the
API spray shield, API ion transfer capillary, API tube
lens, skimmer, the ion transfer capillary mount, and
the tube lens and skimmer mount.
See also atmospheric pressure ionization (API) and
API source.
API tube lens A lens in the API source that separates
ions from neutral particles as they leave the ion
transfer capillary. A potential applied to the tube lens
focuses the ions toward the opening of the skimmer
and helps to dissociate adduct ions.
See also API tube lens offset voltage, API source, API
ion transfer capillary, and adduct ion.
API tube lens and skimmer mount A mount that
attaches to the heated capillary mount. The tube lens
and skimmer attach to the tube lens and skimmer
mount.
API tube lens offset voltage A DC voltage applied to
the tube lens. The value is normally tuned for a
specific compound.
See also API tube lens, adduct ion, and source CID.
APPI See Atmospheric Pressure Photoionization
(APPI).
ASCII American Standard Code for Information
Interchange
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.
See also electrospray ionization (ESI).
Thermo Fisher Scientific
Glossary: atmospheric pressure ionization (API)
atmospheric pressure ionization (API) Ionization
performed at atmospheric pressure by using
atmospheric pressure chemical ionization (APCI),
electrospray ionization (ESI), or nanospray ionization
(NSI).
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.
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.
chemical ionization (CI) plasma The collection of
ions, electrons, and neutral species formed in the ion
source during chemical ionization.
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.
See also chemical ionization (CI).
CI See chemical ionization (CI).
CID See collision-induced dissociation (CID).
CLT curved linear trap
cm centimeter
cm3 cubic centimeter
auxiliary gas flow rate The relative rate of flow of
auxiliary gas (nitrogen) into the API source reported
in arbitrary units.
collision gas A neutral gas used to undergo collisions
with ions.
auxiliary gas inlet An inlet in the API probe where
auxiliary gas is introduced into the probe.
collision-induced dissociation (CID) An ion/neutral
process in which an ion is dissociated as a result of
interaction with a neutral target species.
See also auxiliary gas and atmospheric pressure
ionization (API).
auxiliary gas plumbing The gas plumbing that delivers
outer coaxial nitrogen gas to the ESI or APCI nozzle.
auxiliary gas valve A valve that controls the flow of
auxiliary gas into the API source.
B
b bit
B byte (8 b)
baud rate data transmission speed in events per second
BTU British thermal unit, a unit of energy
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.
corona discharge In the APCI source, an electrical
discharge in the region around the corona discharge
needle that ionizes gas molecules to form a chemical
ionization (CI) plasma, which contains CI reagent
ions.
See also chemical ionization (CI) plasma and
atmospheric pressure chemical ionization (APCI).
C
CPU central processing unit (of a computer)
°C degrees Celsius
CRM See consecutive reaction monitoring (CRM) scan
type.
CE central electrode (of the Orbitrap)
C-Trap curved linear trap
cfm cubic feet per minute
<Ctrl> control key on the terminal keyboard
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
G-3
Glossary: d
D
d depth
Da dalton
DAC digital-to-analog converter
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.
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.
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.
See also fluoranthene.
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.
EMBL European Molecular Biology Laboratory
<Enter> Enter key on the terminal keyboard
ESD electrostatic discharge
dc direct current
ESI See electrospray ionization (ESI).
divert/inject valve A valve on the mass spectrometer
that can be plumbed as a divert valve or as a loop
injector.
ESI flange A flange that holds the ESI probe in
position next to the entrance of the heated capillary,
which is part of the API stack. The ESI flange also
seals the atmospheric pressure region of the API
source and, when it is in the engaged position against
the spray shield, compresses the high-voltage
safety-interlock switch.
DS data system
DSP digital signal processor
E
ECD See electron capture dissociation (ECD).
EI electron ionization
electron capture dissociation (ECD) A method of
fragmenting gas phase ions for tandem mass
spectrometric analysis. ECD involves the direct
introduction of low energy electrons to trapped gas
phase ions.
ESI probe A probe that produces charged aerosol
droplets that contain sample ions. The ESI probe is
typically operated at liquid flows of 1 μL/min to
1 mL/min without splitting. The ESI probe includes
the ESI manifold, sample tube, nozzle, and needle.
ESI source Contains the ESI probe and the API stack.
See also electrospray ionization (ESI), ESI probe, and
API stack.
See also electron transfer dissociation (ETD) and
infrared multiphoton dissociation (IRMPD).
ESI spray current The flow of charged particles in the
ESI source. The voltage on the ESI spray needle
supplies the potential required to ionize the particles.
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.
ESI spray voltage The high voltage that is applied to
the spray needle in the ESI source to produce the ESI
spray current. In ESI, the voltage is applied to the
spray liquid as it emerges from the nozzle.
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
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LTQ Orbitrap Velos Hardware Manual
See also ESI spray current.
ETD See electron transfer dissociation (ETD).
eV electron volt
Thermo Fisher Scientific
Glossary: external lock mass
external lock mass A lock that is analyzed in a separate
MS experiment from your sample. If you need to run
a large number of samples, or if accurate mass samples
will be intermingled with standard samples, you might
want to use external lock masses. These allow more
rapid data acquisition by eliminating the need to scan
lock masses during each scan.
See also internal lock mass.
F
f femto (10-15)
°F degrees Fahrenheit
.fasta file extension of a SEQUEST® search database
file
ft foot
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.
FT Fourier Transformation
FT-ICR MS See Fourier Transform - Ion Cyclotron
Resonance Mass Spectrometry (FT-ICR MS).
FTMS Fourier Transformation Mass Spectroscopy
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.
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 into a
frequency-domain function and the converse.
FWHM Full Width at Half Maximum
FFT See Fast Fourier Transform (FFT).
G Gauss; giga (109)
fluoranthene A reagent anion that is used in an
electron transfer dissociation (ETD) experiment.
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.
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump.
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.
Thermo Fisher Scientific
G
g gram
GC/MS gas chromatography / mass spectrometer
GUI graphical user interface
H
h hour
h height
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.
LTQ Orbitrap Velos Hardware Manual
G-5
Glossary: high performance liquid chromatography (HPLC)
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.
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.
HPLC See high performance liquid chromatography
(HPLC).
ion source A device that converts samples to gas-phase
ions.
HV high voltage
IRMPD See infrared multiphoton dissociation
(IRMPD).
Hz hertz (cycles per second)
K
I
ICR ion cyclotron resonance
ID inside diameter
IEC International Electrotechnical Commission
IEEE Institute of Electrical and Electronics Engineers
in inch
infrared multiphoton dissociation (IRMPD) In
infrared multiphoton dissociation (IRMPD), multiply
charged ions consecutively absorb photons emitted by
a infrared laser until the vibrational excitation is
sufficient for their fragmentation. The fragments
continue to pick up energy from the laser pulse and
fall apart further to ions of lower mass.
k kilo (103, 1000)
K kilo (210, 1024)
KEGG Kyoto Encyclopedia of Genes and Genomes
kg kilogram
L
l length
L liter
LAN local area network
lb pound
LC See liquid chromatography (LC).
See also electron capture dissociation (ECD).
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.
internal lock mass A lock that is analyzed during the
same MS experiment as your sample and is contained
within the sample solution or infused into the
LC flow during the experiment. Internal lock masses
provide the most accurate corrections to the data.
See also external lock mass.
I/O input/output
LC/MS See liquid chromatography / mass spectrometry
(LC/MS).
LED light-emitting diode
LHe liquid helium
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
high-performance liquid chromatograph (LC) and a
mass spectrometer (MS) are combined.
LN2 liquid nitrogen
G-6
LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Glossary: lock mass
lock mass A known reference mass in the sample that is
used to correct the mass spectral data in an accurate
mass experiment and used to perform a real-time
secondary mass calibration that corrects the masses of
other peaks in a scan. Lock masses with well-defined,
symmetrical peaks work best. You can choose to use
internal lock mass or external lock mass.
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.
log file A text file, with a .log file extension, that is used
to store lists of information.
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:
M
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 type and selected ion
monitoring (SIM) scan type.
MSDS Material Safety Data Sheet
Thermo Fisher Scientific
• 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 by the ion.
For example, for the ion C7H72+, m/z=45.5.
N
n nano (10-9)
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).
NCBI National Center for Biotechnology Information
(USA)
LTQ Orbitrap Velos Hardware Manual
G-7
Glossary: NIST
NIST National Institute of Standards and Technology
(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.
O
Q
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.
OD outside diameter
R
OT Orbitrap
RAM random access memory
OVC outer vacuum case
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.
Ω ohm
P
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.
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.
PE protective earth
PID proportional / integral / differential
P/N part number
p-p peak-to-peak voltage
ppm parts per million
PQD pulsed-Q dissociation
psig pounds per square inch, gauge
PTM posttranslational modification
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LTQ Orbitrap Velos Hardware Manual
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.
RMS root mean square
ROM read-only memory
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.)
Thermo Fisher Scientific
Glossary: RS-232
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
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
sheath gas plumbing The gas plumbing that delivers
sheath gas to the ESI or APCI nozzle.
sheath gas pressure The rate of flow of sheath gas
(nitrogen) into the API source. A measurement of the
relative flow rate (in arbitrary units) that needs to be
provided at the sheath gas inlet to provide the required
flow of inner coaxial nitrogen gas to the ESI or APCI
nozzle. A software-controlled proportional valve
regulates the flow rate.
See also sheath gas.
sheath gas valve A valve that controls the flow of
sheath gas into the API source. The sheath gas valve is
controlled by the data system.
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).
serial port An input/output location (channel) for
serial data transmission.
SRM See selected reaction monitoring (SRM) scan
type.
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.
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.
sheath gas flow rate The rate of flow of sheath gas into
the API source. A measurement of the relative flow
rate (in arbitrary units) that needs to be provided at
the sheath gas inlet to provide the required flow of
sheath gas to the ESI or APCI nozzle.
sheath gas inlet An inlet in the API probe where sheath
gas is introduced into the probe.
See also sweep gas flow rate.
sweep gas flow rate The rate of flow of sweep gas into
the API source. A measurement of the relative flow
rate (in arbitrary units) to provide the required flow of
nitrogen gas to the sweep cone of the API source.
See also sweep gas.
syringe pump A device that delivers a solution from a
syringe at a specified rate.
Thermo Fisher Scientific
LTQ Orbitrap Velos Hardware Manual
G-9
Glossary: T
T
U
T Tesla
u atomic mass unit
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.
UHV ultra high vacuum
TIC See total ion current (TIC).
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.
TMP See turbomolecular pump.
UMR Universal Mass Range
Torr A unit of pressure, equal to 1 mm of mercury and
133.32 Pa.
V
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 Exactive Tune, Tune
Plus (LCQ Series, LXQ, and LTQ), or Tune Master
(TSQ Quantum) window and saved as the file type
.mstune, .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.
V volt
V ac volts alternating current
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 system Components associated with lowering
the pressure within the mass spectrometer. A vacuum
system includes the vacuum manifold, pumps,
pressure gauges, and associated electronics.
vent valve A valve that allows the vacuum manifold to
be vented to air or other gases. A solenoid-operated
valve.
vol volume
W
w width
W watt
TWA time weighted average
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LTQ Orbitrap Velos Hardware Manual
Thermo Fisher Scientific
Index
Numerics
00101-08-00006 3-55
00101-08500 1-38
00101-15500 1-38
00101-2500 1-38
00109-02-00020 3-56
00301-01-0013 4-7
00301-15517 4-7
0172350 3-11
0690280 1-38
1050160 3-11
119265-0003 3-44
119283-0001 3-45
119683-0100 3-46
12 pin feedthrough
harness 3-38
location 3-34, 3-36
120320-0030 3-41
23827-0008 3-3
23827-0009 3-3
32000-60340 3-14
3814-6530 3-46
98000-20060 3-55
98000-62006 3-55–3-56
98000-62008 4-7, A-1
A
A0301-15101 3-5
Active Pirani gauge (APG) 1-35
active temperature control 1-17
actual vial temperature 3-49
aluminum oxide abrasive, number 600 3-14
analog signals 1-53
analyzer
chamber temperature 1-62
system 2-10
temperature 1-42
angiotensin I 4-7
anti-aliasing filters 1-51
API source
safety interlock switch 2-10
settings 2-13
applicators, cotton-tipped 3-14
Automatic Gain Control (AGC) 1-12, 2-15
autosampler 2-8–2-9
auxiliary gas 1-37
axial ion ejection 1-12
Thermo Fisher Scientific
axial oscillations
frequency 1-15–1-16
B
bakeout
controls 1-6–1-7
timer 1-7, 3-4–3-5
bakeout procedure
indication 1-7
starting 1-6, 3-5
stopping 1-6, 3-5
base studs 3-40, 3-42
bath gas 1-13
bayonet guide 3-30
bayonet lock 3-30
bayonet pin 3-30
buck/boost transformer 1-10
burnout, of filament 3-53
buttons
Display Status View 2-11
On/Standby 2-6
system bakeout 1-6
C
cable tie 1-9
calibration parameters 2-13
CAN bus 1-55
cartridge heaters 3-40
central electrode
location 1-13
power supply box 1-42
voltages 1-15, 1-65
central electrode power supply board
cooling 1-17
diagnostic LEDs 1-66
location 1-59, 1-65
central electrode pulser board
diagnostic LEDs 1-62
location 1-59, 1-61
ceramic lens holder 3-38
ceramic spacer 3-40
changing
chiller operating fluid 3-57
reagent vials 3-47
charge-sign independent trapping (CSIT) 1-12, 1-21
circuit breakers 1-6–1-7
LTQ Orbitrap Velos Hardware Manual I-1
Index: D
cleaning
instrument surface 3-3
ion source block 3-39
ion source lens assembly 3-33
ion volume 3-21
CLT compartment 1-30
CLT Offset connector 1-59, 1-64
CLT RF main board
diagnostic LEDs 1-64, 1-66
function 1-13
location 1-59, 1-63
CLT RF unit 1-63
CLT RF voltage 1-13
Cold Ion Gauge 1-30, 1-32, 1-35–1-36, 1-45, 1-48
collision cell 1-37
collision gas
C-Trap 1-13
HCD 1-13
inlet 1-10
linear trap 1-38
Communication LED 1-54
communication link 1-5
condenser filter, of recirculating chiller 3-57
connector, to ETD Interface board 1-22
control elements
inlet valve 1-22
instrument 1-5
control panel 1-6
control unit, for turbopumps 1-32
Convectron gauge
ETD Module 1-22–1-23, 1-25, 1-35
linear trap 1-35
cooling water
circuit 1-17, 1-42–1-43
flow control sensor 1-42
properties 1-43
temperature 1-42
cover lid, for bakeout controls 1-7
C-Trap
description 1-13
gas supply 1-39
cycle time 1-4
D
data acquisition analog board
diagnostic LEDs 1-51
layout 1-50
location 1-49, 1-51
data acquisition digital PCI board
diagnostic LEDs 1-50
layout 1-50
location 1-49–1-50
data acquisition unit 1-49
data communication 1-45
I-2
LTQ Orbitrap Velos Hardware Manual
data system
communication 1-5, 2-12
connection 1-9
log file 2-2
DC HV Supply PCB 1-22–1-23, 1-26
default values, of tune and calibration parameters 2-13
deflector electrode (DE) voltages 1-65
Display Status View button 2-11
distilled water 3-3
drip pan, of ETD forepump 1-34
dynamic range, of instrument 1-4
E
E-clips 3-38
electric power, for recirculating chiller 1-43
electrodynamic squeezing 1-15
electronic boards
data acquisition analog 1-51
data acquisition digital PCI 1-50
instrument control 1-52
ion optic supply 1-59
left side 1-59
power distribution 1-53
right side 1-46
electronic connections, to linear trap 1-45
emergency shutdown 2-2
entry housing 3-34
error messages 1-36, 1-54, 1-56
ETD
main access panel 3-24
maintenance 3-12
reagent carrier gas supply 1-11
ETD Control PCB 1-22–1-23, 1-25–1-27
ETD forepump
cabinet 1-22
connections 1-23, 1-34
electrical cord 1-34
power supply 1-24
ETD Ion Optic Supply board 1-18–1-19, 1-23, 1-46, 1-49
ETD Module
forepump receptacle 1-24
Heater Control PCB 1-26
Interface board 1-23, 1-25
ion gauge 1-23
location 1-19
maintenance 3-12
power panel 1-24
power receptacle 1-24
power supply 1-9
power switch 1-24
service switch 1-24
Standby condition 2-4
ETD power module
function 1-23
Thermo Fisher Scientific
Index: F
panel 1-23, 1-25
ETD Reagent Kit 4-7
ETD side access panel
interlocks 3-54
removing 3-19
ETD turbopump
connections 1-23, 1-34
controller 1-35
function 1-32
location 1-22
maintenance 3-11
Ethernet 1-9–1-10
evacuating, after a complete shut down 3-4
Exactive Installation Kit 1-38
exchanging, the lubricant reservoir of the turbopumps 3-11
exhaust
hose 1-11, 1-34
system 1-11, 1-33–1-34
external calibration 1-4
external connections 1-10
extracting voltage 1-14
extraction, of ion packets 1-14
F
fan filters 1-22, 3-56
ferrules, tightening 3-55
filament
assembly 3-21, 3-41
burnout 3-53
emission current 3-41
function 1-26, 1-28
wire 3-43
fingerprints, removing 3-3
flatapole 1-32
flow control
sensor 1-42
UHP nitrogen 1-23, 1-26
flow rates
cooling water 1-42
HCD collision gas 1-39
flow restrictors 1-29
fluid bag filter, of chiller 3-57
fluoranthene 4-7, A-1
focusing potentials 1-66
foreline hose connection 3-34
forepump electrical cord 1-34
forepumps
cabinet 1-2, 1-6, 1-33
effluent 1-33
linear trap 1-30–1-31, 1-33
location 1-6, 1-12, 1-33
oil level 1-33
oil mist filters 1-33, 3-11
power supply 1-33
Thermo Fisher Scientific
switches 1-33
forevacuum tube 1-34
front panel 1-3
front side, LEDs 1-5
FT Electronics switch
functions 1-56
location 1-8
fused silica tubing
from lower oven 3-55
from upper oven 3-55
in ETD Module 1-29
G
gas ballast 1-33
gas pressures 2-10
gas supply
C-Trap 1-39
helium 1-10
nitrogen 1-10
schematics 1-37
gas valves 3-55
gate voltage 1-60
gloves 3-2
ground wires 1-46
guide bar
function 1-22, 3-34
handle 3-23–3-24
opening 3-23–3-24
guide bar opening 3-44
H
handling, hot pump oil 3-10
harmonic oscillations, in Orbitrap 1-15
hazardous materials 1-33
HCD
collision gas port 1-37
flow rate, of collision gas 1-39
fragment spectra 1-18
housing 1-30, 1-32
HCD collision cell
description 1-18
supply voltages 1-46
heated dual restrictor enclosure 1-29
heated transfer line 1-29
heater control 1-56
Heater Control PCB 1-22–1-23, 1-27
heater ring 3-40
heating element 1-42
helium
gas capillary 1-39
gas pressure 1-38
inlet 1-10, 1-37
LTQ Orbitrap Velos Hardware Manual
I-3
Index: I
purging the line 2-11
supply 1-10
high voltage power supply board
diagnostic LEDs 1-67–1-68
function 1-13
layout 1-67
location 1-59, 1-66
voltages 1-67
high voltage, at PCBs 1-44
I
image current 1-15–1-16, 1-48
inlet port, for UHP nitrogen 1-22
inlet valve
block 3-34
knob 3-24, 3-34, 3-44
lever 1-22, 3-23–3-24, 3-33–3-34, 3-44
plug 3-24, 3-34, 3-44
seal kit 3-44
seal tool 3-45
solenoid 1-22, 3-34
installation kit, for the reagent inlet module 3-55
instrument
controls 1-6
diagnostics 1-44
forevacuum measurement 1-35
high vacuum measurement 1-35
operating voltage 1-9
parts 4-2
rear side 1-6
right side 1-9
shutdown 1-53
switching off 1-9, 2-2
instrument control board
diagnostic LEDs 1-53
location 1-46, 1-49, 1-52
software status LEDs 1-53
internal calibration 1-4
internal computer
add-ons 1-50–1-51
data communication 1-45
location 1-46, 1-49
rebooting 2-12
timer 1-50
ion dephasing 1-16
ion gauge, for ETD Module 1-22
ion optic supply board
diagnostic LEDs 1-60
location 1-59
ion optics 1-12
ion oscillation 1-14
ion packets 1-14
shape 1-16
ion source
assembly 3-36
I-4
LTQ Orbitrap Velos Hardware Manual
block 3-21, 3-38, 3-40, 3-42
filament 3-40, 3-42
filament assembly 3-41
lens assembly 3-38, 3-42
lenses 3-21
PCB 3-38, 3-40, 3-42
schematics 1-23
springs 3-38
ion trajectory 1-13
ion volume
alignment arrow 3-30
cleaning 3-21
key thumbscrew 3-40
location 1-23, 1-29
temperature 3-28
ion volume assembly, cleaning frequency 3-21
ion volume tool
alignment arrow 3-30
components 3-23
handle 1-22, 3-25
usage 3-21, 3-27
ionization techniques 1-12
ions
detection 1-16
electrodynamic squeezing 1-15
image current 1-16
packet shape 1-16–1-17
L
laboratory
exhaust system 1-33–1-34
gas supplies 1-10
ventilation 1-38
LC 2-6–2-7
leak checking 1-26, 1-40
LEDs
power control 1-7
system status 1-5, 1-7
vacuum 1-5
left side panel, of instrument 1-3
lens voltages 1-66
line power 1-9
linear trap
collision gas 1-38
Communication LED 2-9, 2-12
connections 1-53
description 1-12
electronics 1-45
forepumps 1-31, 1-33
LEDs 1-5
location 1-2, 1-19
maintenance 3-1
Power LED 2-9, 2-12
power panel 1-6, 1-33
Reset button 2-12
Thermo Fisher Scientific
Index: M
System LED 2-10, 2-12
turbopump 1-32
Vacuum LED 2-10
vacuum measurement 1-35
vent valve 1-36, 1-39, 2-2–2-3
Link Port Signal line 1-52
log file 2-2
lower oven 3-55
lubricant reservoir, of turbopumps 3-11
M
magnet support 3-21
magnet yoke 3-38
magnets, in ion source 3-21, 3-38
main circuit breaker 2-8
main power switch
function 1-9, 1-56
location 1-6
Off position 2-2
securing 1-9
status 1-5
main RF supply 1-63
mains failure 1-57, 2-2, 3-4
mains supply, for the ETD Module 1-9
maintenance
API source 1-12
linear trap 3-1
procedures 3-2
reagent ion source 3-20
recirculating chiller 3-57
vacuum system 3-4
mass accuracy 1-4
mass range 1-4
Material Safety Data Sheet 3-47
micro controller 1-52–1-53
MS/MS 1-4
MSDS 3-47
multiple socket outlets 1-7, 1-56, 2-2
N
nitrogen
CLT 1-37
connection to source 1-38
cooling gas 1-28
gas flow 1-39
inlet 1-10
pressure 1-39
pressure regulator 1-39–1-40
supply 1-10
tubing 1-39
venting 1-37
Thermo Fisher Scientific
O
octapole RF voltages 1-60
oil
level 1-33
mist filters 1-33–1-34, 3-11
On/Standby button 2-4, 2-6, 3-22
operating vacuum 1-5
Orbitrap
applied voltages 1-14
central electrode 1-61
chamber 1-31
control LEDs 1-6
detection electrodes 1-61
differential pumping 1-14
electrodes 1-15
Instrument Control board 1-23
ion extraction 1-14
ion trajectories 1-16
layout 1-14
lenses 1-14
measuring principle 1-13, 1-15
voltages 1-13, 1-16
output current, of preamplifier 1-48
P
padlock, for main power switch 1-9
parameters
calibration 2-13
default values 2-13
tune 2-13
part numbers 4-1
Peltier elements
function 1-17, 1-42, 1-62
location 1-42, 1-65
temperature 1-63
water supply 1-32, 1-48
Penning gauge 1-56
peripherals power outlet 1-23–1-24
Pirani gauge 1-30–1-31, 1-36, 1-56
position, of inlet valve lever 3-33
power 1-9
connector 1-6, 1-10
connector for linear trap 1-12
control LEDs 1-8
control panel 1-7–1-8
panel 1-6
supply for linear trap 1-12
power distribution
operating states 1-56
resetting 1-36
working modes 1-56
power distribution board
control 1-8
function 1-42
LTQ Orbitrap Velos Hardware Manual
I-5
Index: Q
layout 1-54
location 1-46, 1-53
power supply 1-7, 1-56
status LEDs 1-55
power fail detector 2-3
Power LED 1-5
power module 1-22
power outlet, for peripheral devices 1-9–1-10
power supply
data system 1-9
ETD Module 1-9
power supply 1 board
diagnostic LEDs 1-58
layout 1-57
location 1-46, 1-57
power supply 2 board
diagnostic LEDs 1-52
location 1-49
preamplifier
cooling 1-42
diagnostic LEDs 1-47–1-48
location 1-32, 1-46, 1-48
pressure readings, in ETD Module 1-35
pressure regulator
location 1-40
nitrogen 1-39–1-40
preventive maintenance 2-8, 3-2
printed circuit boards 1-44
proton transfer reactions 1-21
pumping, the system 2-9, 3-4
pumps
exhaust 1-11
forevacuum 1-33
manuals 3-5, 3-11
oil mist filters 1-33
purging, helium line 2-11
maintenance tools 3-14
Reagent Ion Source dialog box 1-27, 2-4
Reagent Ion Source instrument control icon 2-4, 3-22
Reagent Ion Source On check box 1-27–1-28
reagent vapor, in the carrier gas 1-27
reagent vials 1-29
rebooting, of instrument 2-2
recirculating chiller
condenser filter 3-57
connections 1-4
description 1-43
fluid bag filter 3-57
maintenance 3-57
reflector dc voltages 1-60
removing
ETD main access panel 3-18
ETD side access panel 3-19
gases 2-10, 3-4
stains 3-3
repair covering letter 3-3
replacing
inlet valve components 3-44
ion source filament 3-41
turbopump lubricant reservoirs 3-11
reservoir, of recirculating chiller 3-57
resetting
instrument 2-12
system parameters 2-13
tune and calibration parameters 2-13
resolution, of instrument 1-4
restrictor
oven cover 3-54
oven heater 1-26
RF CLT main board 1-66
RF off & feedback board 1-59, 1-64
RF output control 1-59
RF voltage supply 1-63
right side panel, of instrument 1-3
Q
quadrupole mass filter 1-21
quality, of vacuum 1-53
R
reagent heaters 1-22–1-23, 1-26–1-28
reagent inlet cover 3-54
reagent inlet source
heating unit 3-50
location 3-51
reagent ion source
cleaning frequency 3-13
description 1-28–1-29
flow restrictors 3-53
maintenance 3-20
I-6
LTQ Orbitrap Velos Hardware Manual
S
safety
features 1-25
interlock switch 2-10
problem 3-53
sample inlet aperture 3-40
secondary electrons 1-26
SEM detector 1-12
serial port connector 1-53
service switch, of linear trap 1-8
setting up, conditions for operation 2-10
sheath gas 1-37
shutdown 1-57, 2-7, 2-9
signal communication 1-45
Thermo Fisher Scientific
Index: T
software
debugging 1-53
function 1-42, 1-44
status LEDs of the instrument control board 1-53
Tune Plus window 2-6
specifications, of instrument 1-4
spectrum 1-17
SPI bus
function 1-45
termination board 1-63–1-64, 1-66–1-68
spring clip thumb screw 3-38, 3-40
stainless steel parts, cleaning 3-14
stains, removing 3-3
Standby condition 1-28, 2-4
starting up
ETD Module 2-11
instrument 2-9
status LEDs, of power distribution board 1-55
Status View 3-22
sweep gas 1-37
switches
forepumps 1-33
FT Electronics 1-8, 3-4
linear trap 1-8
main power 1-9
vacuum pumps 1-8
switching on, the vacuum system 1-36
system
bakeout 1-5–1-6, 1-36, 1-48, 2-9, 3-4
bakeout timer 1-6
buttons for bakeout 1-6
heating 1-36
pump down time 2-10
rebooting 2-2
resetting 2-12
shutdown 2-2
Standby 2-4
starting up 2-9
status LEDs 1-5, 1-54
timing 1-50
venting 1-39, 2-2
system status LEDs
linear trap 1-2
LTQ Orbitrap Velos 1-2
T
temperature
analyzer chamber 1-62
control 1-17
differential 1-17
monitoring 3-50
sensor 3-40
temperature controller board
Thermo Fisher Scientific
diagnostic LEDs 1-63
function 1-17
layout 1-62
location 1-59, 1-62
thermoelectric elements 1-17
thumbscrews 3-36, 3-38
tools
cleanliness 3-3
for cleaning stainless steel parts 3-14
for cleaning the ion volume 3-21
reagent ion source 3-14
top lids
ETD Module 1-3
MS 1-3–1-4
transfer chamber 1-12
transfer line
bellows 3-36–3-37
heater 1-26
inlet 3-55
location 1-23
transfer multipole 1-19–1-21, 1-32
trap voltage 1-60
triple gas filter 1-41
tune parameters 2-13
Tune Plus window
buttons 2-6, 2-11
diagnostics 1-44
turbopumps
connections 1-53
controllers 1-32, 1-35
error 1-55
linear trap 1-32, 1-35
maintenance 3-11
maintenance intervals 3-11
TMH 071 1-30, 1-37, 1-42
TMP 1 1-30–1-31
TMP 2 1-30–1-32
TMP 3 1-31–1-32
TMP 4 1-31
TMU 262 1-30, 1-37, 1-42
vent valves 1-36
U
UHP nitrogen
inlet port 1-11, 1-40
UHV chamber
components 1-31
location 1-30
temperature control 1-17
vacuum 1-31
uninterruptible power supply (UPS) 2-2–2-3
upper control panel 1-6–1-7
user maintenance 3-1–3-2, A-1
LTQ Orbitrap Velos Hardware Manual
I-7
Index: V
V
vacuum
compartments 1-30
deterioration 1-36
failure 1-36, 1-53
gauges 1-35, 1-53
quality 1-53
safety threshold 1-35–1-36
system 1-9, 1-30
vacuum chamber 1-30–1-31
vacuum components
left instrument side 1-31
Vacuum LED
instrument 1-5
linear trap 2-10
vacuum manifold
location 1-22
probe plate 3-34–3-35
Vacuum Pumps switch 1-5, 1-8, 1-56
vacuum system
controls 1-35
heating 1-36
maintenance 3-11
moisture 1-36
vent valve
control 1-39
function 2-2, 2-7
linear trap 1-39, 2-3
nitrogen supply 1-37
I-8
LTQ Orbitrap Velos Hardware Manual
ventilation, in the laboratory 1-38
venting pressure 1-40
venting, the system 2-3, 3-19
vial heaters
cover 3-50–3-51
location 3-52, 3-55
ribs 3-52
vial holder 3-51–3-52
vial temperature 1-28
voltage sags 1-10
W
water
chiller 1-4
hoses 1-43
ports 1-10
temperature 1-43
water cooler, for TMH 071 1-42
wheels, of instrument 1-3
working modes, of power distribution 1-56
working principle, of the Orbitrap 1-3, 1-20
X
Xcalibur 1-44, 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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