Orbitrap Velos Pro Hardware Manual

Orbitrap Velos Pro Hardware Manual
Thermo Fisher Scientific
Orbitrap Velos Pro
Hardware Manual
Revision A - 1288290
Part of Thermo Fisher Scientific
© 2011 Thermo Fisher Scientific Inc. All rights reserved.
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Release History: Revision A released in June 2011.
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 section or 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.
Velos Pro Mass Spectrometer (April 2011)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-3: 2006
EN 55011: 2007, A2: 2007
EN 61000-4-4: 2004
CFR 47, FCC Part 15, Subpart B, Class A: 2009
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 1995, A1: 2001, A2: 2005
EN 61000-4-11: 2004
EN 61000-4-2: 1995, A1: 1999, A2: 2001
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
Velos Pro/ETD System (April 2011)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-3: 2006
EN 55011: 2007, A2: 2007
EN 61000-4-4: 2004
CFR 47, FCC Part 15, Subpart B, Class A: 2009
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 1995, A1: 2001, A2: 2005
EN 61000-4-11: 2004
EN 61000-4-2: 1995, A1: 1999, A2: 2001
Low Voltage Safety Compliance
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.
WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic
Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling/disposal companies in each EU
Member State, and this product should be disposed of or recycled through them. Further information
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information on Thermo Fisher Scientific products which may assist the detection of substances
subject to the RoHS Directive are available at www.thermo.com/WEEERoHS.
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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 Orbitrap Velos Pro system! The
Orbitrap Velos Pro is a member of the family of LTQ™ mass
spectrometer (MS) hybrid instruments.
All information in this guide concerning the Orbitrap Velos Pro mass
spectrometer also applies to the Orbitrap Velos Pro ETD system where
the ETD Module is physically coupled to the back of the Orbitrap Velos
Pro mass spectrometer.
About This Guide
This Orbitrap Velos Pro Hardware Manual contains a description of the
modes of operation and principle hardware components of your
Orbitrap Velos Pro instrument. In addition, this manual provides
step-by-step instructions for cleaning and maintaining your instrument.
Who Uses This Guide
This Orbitrap Velos Pro 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 Orbitrap Velos Pro mass spectrometer.
•
Chapter 2: “Basic System Operations” provides procedures for
shutting down and starting up the Orbitrap Velos Pro mass
spectrometer.
•
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 mass
spectrometer and data system.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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Read This First
About This Guide
•
ii
Appendix A: “Fluoranthene” describes properties of the reagent that
is used in the ETD Module portion of the Orbitrap Velos Pro ETD
mass spectrometer.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Read This First
Related Documentation
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the
following documents for Orbitrap Velos Pro mass spectrometer and
Orbitrap Velos Pro ETD mass spectrometer:
•
LTQ Orbitrap Series Preinstallation Requirements Guide
•
Orbitrap Velos Pro Getting Started Guide
•
Velos Pro manual set
You can access PDF files of the documents listed above and of this guide
from the data system computer. The software also provides Help.
❖
To view product manuals
1. From the Microsoft™ Windows™ taskbar, choose Start > Programs
> Thermo Instruments > LTQ > Manuals > model.
2. Click the PDF file that you want to view.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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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.thermoscientific.com/ms
Service contact details for customers in Europe are available under:
www.thermoscientific.com/euservicecontact
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
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.
iv
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
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 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
Thermo Fisher Scientific
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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. ▲
vi
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Thermo Fisher Scientific
Read This First
Safety and EMC Information
Identifying Safety Information
This guide 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 that appear in Thermo Fisher Scientific manuals are
shown below.
In addition, every instrument has specific hazards. So, be sure to read
and comply with all precautions described in this guide. They will help
to ensure the safe and long-term use of your system.
Warning General Hazard. 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 Electric Shock Hazard. 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 Burn Hazard. 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 Corrosive Material. Wear gloves when handling toxic,
carcinogenic, mutagenic, or corrosive/irritant chemicals. Use approved
containers and procedures for disposal of waste solution. ▲
General Safety Precautions
Observe the following safety precautions when you operate or perform
service on your instrument:
Thermo Fisher Scientific
•
The system should be operated by trained personnel only. Read the
manuals before starting the system and make sure that you are
familiar to the warnings and safety precautions!
•
Accurate results can be obtained only, if the system is in good
condition and properly calibrated.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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Safety and EMC Information
viii
•
Service by the customer should be performed by trained qualified
personnel only and should be restricted to servicing mechanical
parts! Service on electronic parts should be performed by Thermo
Fisher Scientific field service engineers only!
•
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.
•
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. When leaving the system, make sure that all protective
covers and doors are properly connected and closed, and that heated
areas are separated and marked to protect for unqualified personnel!
•
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 Thermo Fisher Scientific field service engineer 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 (for example, 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 Thermo
Fisher Scientific field service engineer.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Read This First
Safety and EMC Information
•
Do not place any objects upon the instrument—especially not
containers with liquids—unless it is requested by the user
documentation. Leaking liquids might get into contact with
electronic components and cause a short circuit.
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 that due to their
structure and the applied concentration might be toxic or that are
reported in publications 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 Health and Safety Form confirms that the
returned parts have been decontaminated and are free of hazardous
materials. Download the form from decon.thermo-bremen.com or
order it from the Thermo Fisher Scientific field service engineer.
Parts contaminated by radioisotopes should not be returned to Thermo
Fisher Scientific—neither under warranty nor within the exchange part
program. If unsure about parts of the system possibly being
contaminated by hazardous material, please make sure the Thermo
Fisher Scientific field service engineer is informed before the engineer
starts working on the system.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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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
Curved Linear Trap ........................................................ 1-13
Orbitrap Analyzer ........................................................... 1-14
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 on 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
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Contents
Placing the MS in Standby Condition............................ 2-6
Shutting Down the Orbitrap Velos Pro Mass
Spectrometer 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 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 Turbomolecular Pumps ................ 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 .............................. 3-45
Replacing the Reagent Vials ......................................... 3-48
Cleaning the Fan Filters of the ETD Module............... 3-57
Maintenance of the Cooling Circuit................................ 3-58
Maintenance for the Recirculating Chiller.................... 3-58
Replacing the Water Filter Cartridge............................ 3-58
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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Figures
Orbitrap Velos Pro MS front view ........................................................ 1-2
Schematic of the Orbitrap Velos Pro MS .............................................. 1-3
Top lid of MS portion opened .............................................................. 1-4
System status LEDs ............................................................................... 1-5
Right side of the Orbitrap Velos Pro MS ............................................... 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 Orbitrap Velos Pro MS ............................ 1-10
Layout of the Orbitrap Velos Pro MS, also showing the applied
voltages ............................................................................................... 1-13
Schematic of Orbitrap cell and example of stable ion trajectory ........... 1-14
Principle of electrodynamic squeezing of ions in the Orbitrap
analyzer as the field strength is increased ............................................. 1-15
Approximate shape of ion packets of different m/z after
stabilization of voltages ........................................................................ 1-16
Schematic of the Orbitrap Velos Pro ETD MS ................................... 1-20
Orbitrap Velos Pro ETD MS, 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 Orbitrap Velos Pro ETD MS ................................... 1-24
ETD Power Module panel .................................................................. 1-24
Reagent Ion Source dialog box ............................................................ 1-27
Reagent ion source schematics ............................................................. 1-29
Schematic of Orbitrap analyzer 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
Schematic of gas supply for Orbitrap Velos Pro ETD MS ................... 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
Schematic of cooling water circuit ....................................................... 1-42
Electronic connections to linear trap ................................................... 1-45
Electronic boards on the right side of the instrument .......................... 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
Data Acquisition Analog board ........................................................... 1-51
Instrument Control board ................................................................... 1-52
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Figures
Power Distribution board ................................................................... 1-54
Power Supply 1 board ......................................................................... 1-58
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 (Orbitrap Velos Pro ETD), 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 (Orbitrap Velos Pro ETD) .................................... 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 ................. 3-35
Removing the foreline hose from its connection .................................. 3-35
Unscrewing the vacuum manifold probe plate ..................................... 3-36
Removing the vacuum manifold probe plate ....................................... 3-36
Interior of vacuum manifold ............................................................... 3-37
Removing the ion source assembly from the vacuum manifold ........... 3-38
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Thermo Fisher Scientific
Figures
Ion source assembly ............................................................................. 3-39
Ion source assembly exploded view ...................................................... 3-39
Ion source, exploded view ................................................................... 3-41
Ion source lens assembly and ion source .............................................. 3-43
Filament wire as seen from the bottom of the filament through
the electron lens hole ........................................................................... 3-44
Inlet valve components ........................................................................ 3-45
Inlet valve seal tool .............................................................................. 3-46
Inlet valve seal tool inserted in the inlet valve ...................................... 3-46
Inlet valve seal on the inlet valve seal tool ............................................ 3-47
Inlet valve seal disengaged from tool .................................................... 3-47
Reagent Ion Source dialog box ............................................................ 3-50
ETD Module with back panel removed .............................................. 3-52
Reagent vials with holders ................................................................... 3-53
ETD Module with vial heater cover removed ...................................... 3-53
Reagent inlet assembly ........................................................................ 3-56
ETD Module, top panel ...................................................................... 3-57
Installed water filter ............................................................................. 3-59
Removing the filter cartridge ............................................................... 3-60
Filter cartridge with Quick couplers .................................................... 3-60
ETD Reagent (fluoranthene radical anion) generation from
fluoranthene ..........................................................................................A-1
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Tables
System status LEDs of the Orbitrap Velos Pro MS ................................ 1-5
Circuit breakers of the Orbitrap Velos Pro MS ..................................... 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 ................ 1-68
User maintenance procedures ................................................................ 3-2
Indications requiring maintenance of the ETD system ........................ 3-13
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xvii
Procedures
To view product manuals..........................................................................iii
To suggest changes to this manual.............................................................iv
To connect the nitrogen source to the Orbitrap Velos Pro mass
spectrometer......................................................................................... 1-38
To connect the helium source to the Orbitrap Velos Pro mass
spectrometer......................................................................................... 1-38
To place the ETD Module in Standby condition ................................... 2-4
To place the Orbitrap Velos Pro system in Standby condition ............... 2-6
To shut down the instrument completely............................................... 2-7
To shut down the Orbitrap Velos Pro system......................................... 2-7
To start up the Orbitrap Velos Pro mass spectrometer ........................... 2-9
To set up your Orbitrap Velos Pro mass spectrometer for
operation.............................................................................................. 2-10
To start up the ETD Module after a complete shutdown ..................... 2-11
To reset the Orbitrap Velos Pro MS tune and calibration
parameters............................................................................................ 2-13
To perform a system bakeout ................................................................. 3-4
To remove the panel .............................................................................. 3-8
To add oil to the ETD forepump........................................................... 3-8
To purge the rotary-vane pump oil......................................................... 3-9
To change the ETD forepump oil ........................................................ 3-10
To clean reagent ion source stainless steel parts .................................... 3-15
To clean the non-stainless-steel portions of hybrid parts....................... 3-17
To remove the ETD main access panel ................................................ 3-18
To remove the ETD side access panel .................................................. 3-19
To clean the ion volume with an inlet valve ......................................... 3-22
To reinsert the ion volume ................................................................... 3-29
To clean the ion source lens assembly................................................... 3-33
To clean the ion source block............................................................... 3-40
To replace the ion source filament........................................................ 3-43
To replace inlet valve components........................................................ 3-45
To place the Orbitrap Velos Pro ETD mass spectrometer in Off
Condition and Service mode and to verify that the vials are safe
to handle .............................................................................................. 3-49
To install or exchange the reagent vials................................................. 3-51
To change the reagent ion source flow restrictors ................................. 3-54
To clean the fan filters of the ETD Module ......................................... 3-57
To replace the water filter cartridge ...................................................... 3-59
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Chapter 1
Functional Description
This chapter provides an overview of the functional elements of the
Orbitrap Velos Pro mass spectrometer. 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
•
“Curved Linear Trap” on page 1-13
•
“Orbitrap Analyzer” on page 1-14
•
“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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-1
Functional Description
General Description
General Description
The Orbitrap Velos Pro mass spectrometer is a hybrid mass spectrometer
incorporating the Velos Pro™ 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 Orbitrap Velos Pro MS
Orbitrap Analyzer
Linear Trap
Forepumps cabinet
Figure 1-1.
Orbitrap Velos Pro MS front view
The Orbitrap Velos Pro mass spectrometer consists of four main
components (See Figure 1-2 on page 1-3.), which are described in the
following topics:
•
Dual cell linear ion trap (Thermo Scientific Velos Pro) for sample
ionization, selection, fragmentation, and AGC™.
•
Intermediate storage device (curved linear trap) that is required for
short pulse injection.
•
An Orbitrap analyzer for Fourier transformation based analysis.
•
Collision cell for performing higher energy CID experiments.
The Orbitrap Velos Pro ETD mass spectrometer 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
Velos Pro MS
Electrospray Ion Source
S-Lens
Square Quadrupole
with beam blocker
Octopole
Orbitrap analyzer
High Pressure Cell
Low Pressure Cell
Multipole
C-Trap
HCD Collision Cell
Orbitrap Mass Analyzer
Figure 1-2.
Schematic of the Orbitrap Velos Pro MS
Mechanical Characteristics
Wheels at the bottom side of the instrument facilitate positioning the
Orbitrap Velos Pro mass spectrometer 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 analyzer 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 Thermo Fisher
Scientific field service engineers from the top. See Figure 1-3.
In the Orbitrap Velos Pro ETD mass spectrometer, after removing the
cables the top lid of the ETD Module is also removable to allow
accessing its electronic components.
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-3
Functional Description
General Description
Figure 1-3.
Top lid of MS portion opened
A stand-alone recirculating water chiller is shipped with the instrument.
It is connected to the right side of the instrument.
Specifications
The Orbitrap Velos Pro mass spectrometer 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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Functional Description
Control Elements
Control Elements
The Orbitrap Velos Pro mass spectrometer 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 Orbitrap Velos Pro MS
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
Orbitrap analyzer is scanning
Off
Orbitrap analyzer is not scanning
Vacuum
a
Communication
Systema
Detect
a
Thermo Fisher Scientific
These LEDs are flashing when a system bakeout is performed. See “Baking Out the System” on
page 3-4.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-5
Functional Description
Control Elements
Control Panels
Figure 1-5 shows the right side of the Orbitrap Velos Pro mass
spectrometer. 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 Orbitrap Velos Pro MS
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 Orbitrap Velos Pro mass spectrometer
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 Orbitrap Velos Pro MS
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 Orbitrap Velos Pro mass spectrometer 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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1-7
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 Orbitrap Velos Pro
mass spectrometer, the linear ion trap, and the vacuum pumps. In the
Orbitrap Velos Pro ETD mass spectrometer, 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
Orbitrap Velos Pro mass spectrometer 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 Orbitrap Velos Pro mass spectrometer, the outlet provides
the mains supply for the data system. In the Orbitrap Velos Pro ETD
mass spectrometer, 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
Orbitrap Velos Pro mass spectrometer 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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1-9
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
Cooling water inlet port
Collision gas inlet1
Nitrogen gas inlet
Figure 1-9.
Cooling water outlet port
External connections to the Orbitrap Velos Pro MS
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.
Caution Do not connect other gases than nitrogen or helium to the
Orbitrap Velos Pro mass spectrometer! 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). ▲
1
1-10
The port named Collision Gas is not used in the Orbitrap Velos Pro MS.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Functional Description
Control Elements
In the Orbitrap Velos Pro ETD mass spectrometer, 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-11
Functional Description
Linear Ion Trap
Linear Ion Trap
The Orbitrap Velos Pro 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
Velos Pro), which can store, isolate, and fragment ions and then send
them either to the Orbitrap analyzer 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 analyzer. 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 1-25 on page 1-33. The Orbitrap Velos Pro mass
spectrometer provides power for the linear ion trap. The Orbitrap Velos
Pro ETD mass spectrometer 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 Velos Pro 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 analyzer are fixed to the transfer chamber.
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Functional Description
Curved Linear Trap
Curved Linear Trap
On their way from the linear trap to the Orbitrap analyzer, ions move
through the gas-free RF-only octapole into the gas-filled curved linear
trap (C-Trap). See Figure 1-10 on page 1-13. Ions entering the C-Trap
loose their kinetic energy in collisions with nitrogen bath gas emanating
from the HCD cell and get collected near the middle part of the C-Trap.
The nitrogen 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 (entrance and exit
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.) Entrance and exit DC voltages as
well as RF voltages to the octapole are all provided by the ion optic
supply board. (See page 1-60.) High voltages to the lenses are provided
by the high voltage power supply board. (See page 1-66.)
Octapole
Entrance C-Trap Exit
Collision Cell
TMP 1
TMP 2
Static
Pulsing from LTQ
Squeezing in C-Trap
TMP 3
Figure 1-10. Layout of the Orbitrap Velos Pro MS, also showing the applied voltages
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-13
Functional Description
Orbitrap Analyzer
Orbitrap Analyzer
The heart of the Orbitrap™ analyzer 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 1-11. The Orbitrap
analyzer employs electric fields to capture and confine ions.
r
z
Figure 1-11. Schematic of Orbitrap cell and example of stable ion trajectory
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 electrode.
Because of the initial curvature of the C-Trap and the subsequent lenses,
the ion beam converges on the entrance into the Orbitrap analyzer. The
lenses that follow the C-Trap (Z-lens) form also differential pumping
slots and cause spatial focusing of the ion beam into the entrance of the
Orbitrap analyzer. Ions are electrostatically deflected away from the gas
jet, thereby eliminating gas carryover into the Orbitrap analyzer.
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 analyzer 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 analyzer 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
analyzer 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/z)
to enter the C-Trap as well. After ions of all m/z have entered the
Orbitrap analyzer 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 1-11 on page 1-14, 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/z and the instrumental constant k:
w =
z
--m- × k
Two split halves of the outer electrode of the Orbitrap analyzer 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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1-15
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.
Lower m/z
Higher m/z
Figure 1-13. Approximate shape of ion packets of different m/z after
stabilization of voltages
As mentioned above, stable ion trajectories within the Orbitrap analyzer
combine axial oscillations along the z-axis with rotation around the
central electrode and vibrations in the radial direction. (See Figure 1-11
on page 1-14.) For any given m/z, 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-to-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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Thermo Fisher Scientific
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 analyzer 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 1-42 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 Orbitrap Velos Pro mass
spectrometer. See “Cooling Water Circuit” on page 1-42 for further
information.
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1-17
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 analyzer show a fragmentation pattern comparable to
the pattern of typical triple quadrupole spectra. See the Orbitrap Velos
Pro Getting Started manual for more information.
HCD and ETD
In the Orbitrap Velos Pro ETD mass spectrometer, 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 (that is,
scan to scan) between HCD and ETD fragmentation, thus making
comparative measurements possible. When compared with the standard
Orbitrap Velos Pro mass spectrometer, 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 Orbitrap Velos Pro ETD mass spectrometer, an ETD Module is
physically coupled to the back of the Orbitrap Velos Pro mass
spectrometer. A quadrupole mass filter replaces the octapole of the
Orbitrap Velos Pro MS. 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 1-22 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 1-34 on page 1-47.
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 Among otehrs, the ETD system is also available as an upgrade on
new and existing Velos Pro and Orbitrap Velos Pro systems. ▲
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-19
Velos Pro MS
Electrospray Ion Source
S-Lens
Square Quadrupole
Octopole
Orbitrap
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
Reagent 2
Heated Inlet
Figure 1-14. Schematic of the Orbitrap Velos Pro ETD MS
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
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 1-14 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 analyzer (if mass
resolution and accuracy are important).
ETD Module
Figure 1-15 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-21
Functional Description
ETD System
Fan filter
Control elements
of inlet valve
Inlet port for ETD reagent
carrier gas
Cabinet for
ETD forepump
Figure 1-15. Orbitrap Velos Pro ETD MS, 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=TMP,
14=Convectron™ gauge, 15=vacuum manifold (contains ion source and ion
volume)
Figure 1-16. Rear view of the ETD Module, with major component locations
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Thermo Fisher Scientific
Functional Description
ETD System
ETD Ion Optic
Supply Board
Peripherals
Power Outlet
Orbitrap Vacuum System,
see Figure 1-22 on page 1-30
Orbitrap Instrument
Control Board
Orbitrap Velos Pro
ETD Module
Heater Control PCB
Interface
Board
Ion Gauge
Power Module
ETD Control PCB
4
H1
Ion Source
H2
Reagent
Heaters
3
ETD TMP
DC HV Supply PCB
Flow
Control
ETD Forepump
ETD Reagent
Carrier Gas
Convectron Gauge
3 = Transfer line
4 = Ion volume
Figure 1-17. ETD Module functional block diagram
The following sections describe the major ETD Module components
that are shown in Figure 1-16 on page 1-22 and Figure 1-17.
ETD Power Module
The ETD power module (item #1 in Figure 1-16) 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 1-18.
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1-23
Functional Description
ETD System
ETD Module
ETD Module
power panel
Figure 1-18. Right side of the Orbitrap Velos Pro ETD MS
Figure 1-19 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 1-19. 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
Orbitrap Velos Pro ETD system (the mass spectrometer and the
ETD Module) are shut down with one set of switches, the mass
spectrometer 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 mass spectrometer’s service switch to
the Service position. The service switch turns On or Off power to all
ETD Module components except turbomolecular pump and forepump.
ETD Module Interface Board
The ETD Module Interface board (item #2 in Figure 1-16 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
Orbitrap Velos Pro ETD mass spectrometer 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 1-16) 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-25
Functional Description
ETD System
The DC HV Supply PCB (item #3 in Figure 1-16 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 1-16)
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 1-17 on page 1-23, and items #9 and #10 in
Figure 1-16), the transfer line heater (#3 in Figure 1-16), and the
restrictor oven heater (not shown in Figure 1-16). 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 1-16 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 1-30 on page 1-40.
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Functional Description
ETD System
Reagent Heaters
The reagent heaters (items #9 and #10 in Figure 1-16 on page 1-22, H1
and H2 in Figure 1-17 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 1-20.
Figure 1-20. 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-27
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 “Replacing the Reagent Vials” on page 3-48.
Note The rushing or hissing noise of the nitrogen coming from the back
of the ETD Module will stop when the cooling nitrogen turns off. ▲
Warning 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 “Replacing the Reagent Vials” on page 3-48 if it is
necessary to install or replace the reagent vials. ▲
When the reagent heaters are in Standby mode, they are immediately
turned on by selecting the Reagent Ion Source On check box
(Figure 1-20 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 1-20 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 1-16 on page 1-22 and inside of the vacuum
manifold, see item #14 in Figure 1-16) 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 1-21. 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 1-21. 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-29
Functional Description
Vacuum System
Vacuum System
Figure 1-22 shows a schematical overview of the Orbitrap analyzer
vacuum system.
UHV Chamber
HCD Housing
Vacuum Chamber
Linear Trap
ETD Module
Vacuum System,
see Figure 1-17 on
page 1-23
TMP 4
Cold Ion Gauge
Pirani Gauge
TMP 2
Forepump
TMP 3
TMP 1
Forepump
Figure 1-22. Schematic of Orbitrap analyzer vacuum system (CLT compartment and Orbitrap chamber not shown)a
a
For an abridged version of the parts list, see page 4-3.
The Orbitrap Velos Pro mass spectrometer has the following vacuum
compartments:
1-30
•
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 HiPace™ 80, TMP 1, manufacturer:
Pfeiffer)
•
Ultra high vacuum chamber (UHV chamber, pumped by a
water-cooled 60 L/s turbomolecular pump HiPace 80, TMP 2,
manufacturer: Pfeiffer)
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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Functional Description
Vacuum System
•
Orbitrap chamber (pumped by a 260 L/s—for N2—water-cooled
turbomolecular pump HiPace 300, TMP 3, manufacturer: Pfeiffer)
•
HCD housing (pumped by a water-cooled 60 L/s turbomolecular
pump HiPace 80, 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 1-23). 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 analyzer, lenses, and corresponding
electrical connections.
TMP 4
Gas Regulator
for Vent Valve
TMP 1
Pirani Gauge
Figure 1-23. 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 1-24 on
page 1-32). The Orbitrap analyzer itself is separated from the UHV
chamber by differential apertures and is evacuated down to 10-10 mbar
by a 260 L/s turbomolecular pump (TMP 3, see Figure 1-24). The
HCD housing is evacuated by a 60 L/s UHV turbomolecular pump
(TMP 4, see Figure 1-23) 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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Functional Description
Vacuum System
In the Orbitrap Velos Pro ETD mass spectrometer, 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 1-24. Vacuum components on the right instrument side
All turbomolecular pumps are equipped with TC 110 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 Orbitrap Velos Pro ETD mass spectrometer, a separate
turbomolecular pump (Edwards EXT75DX) provides the high vacuum
for the ETD reagent ion source. See Figure 1-16 on page 1-22. It is
backed up by a dedicated rotary vane pump at the bottom of the
ETD Module. See Figure 1-26 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 1-25.
Oil mist filters
Forepumps
Figure 1-25. 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 Health Hazard. 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.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Orbitrap Velos Pro ETD mass spectrometer, a rotary vane pump
(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 1-26 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 1-19 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 1-26. Forepump for ETD Module
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Functional Description
Vacuum System
Vacuum System Controls
The power distribution board controls all turbomolecular pumps via
voltage levels. See “Power Distribution Board” on page 1-53. An
interface for RS485 data via the instrument control board connects the
turbomolecular pumps 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 Orbitrap Velos Pro mass spectrometer is
monitored by an Active Pirani gauge (TPR 280, manufacturer:
Pfeiffer) connected to the forevacuum line. See Figure 1-23 on
page 1-31.
•
The high vacuum of the Orbitrap Velos Pro mass spectrometer is
monitored by a Cold Ion Gauge (IKR 270, manufacturer: Pfeiffer)
connected to the UHV chamber. See Figure 1-24 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 Orbitrap Velos Pro ETD mass spectrometer, two dedicated
vacuum gauges monitor the vacuum in the ETD Module. A
Convectron gauge (see Figure 1-16 on page 1-22 and Figure 1-17
on page 1-23) monitors the pressure in the ETD forevacuum line
and an ion gauge (see Figure 1-16) 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 Orbitrap Velos Pro mass spectrometer 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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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 Orbitrap Velos Pro mass spectrometer are run
up. The Pirani gauge (see above) controls the Orbitrap Velos Pro
MS 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 turbomolecular pumps (for example,
80% after 15 minutes).
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
analyzer region.
Vacuum Failure
In case the pressure in the Orbitrap Velos Pro mass spectrometer 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 turbomolecular pumps on the
Orbitrap analyzer 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 (for example, 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
Orbitrap Velos Pro mass spectrometer and the reagent ion source of the
Orbitrap Velos Pro ETD mass spectrometer.
Gas Supply for the Mass Analyzers
Figure 1-27 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
Collision gas1
Helium (He)
ETD Module
Linear Trap
Regulator with
manometer
Analyzer
TMP 2
TMP 3
C-Trap
TMP 1
Cooling Gas
N2 venting
TMP 4
Collision Cell
Vent valve
Figure 1-27. Schematic of gas supply for Orbitrap Velos Pro ETD MSa
a
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:
•
1
Thermo Fisher Scientific
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).
The port named Collision Gas is not used in the Orbitrap Velos Pro MS.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-37
Functional Description
Gas Supply
In the Orbitrap Velos Pro ETD mass spectrometer, 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 Orbitrap Velos Pro mass
spectrometer
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 Orbitrap Velos Pro mass
spectrometer
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 1-28
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 1-28. Proper orientation of the Swagelok-type nut and two-piece
ferrule
1-38
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 1-27 on page 1-37.
High purity nitrogen gas is led from the nitrogen port via Teflon tubing
to the right side of the Orbitrap Velos Pro mass spectrometer. 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 1-29 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 1-29, 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 1-29. Gas regulators
In the Orbitrap Velos Pro ETD mass spectrometer, 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.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-39
Functional Description
Gas Supply
The instrument is vented with high purity nitrogen from the same
tubing that supplies the Velos Pro MS sheath gas. See Figure 1-27 on
page 1-37. The vent valve of the Velos Pro mass spectrometer 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 Orbitrap Velos Pro
mass spectrometer. (See Figure 1-29, front.)
Gas Supply of the Reagent Ion Source
In addition to high purity nitrogen for cooling, the reagent ion source of
the Orbitrap Velos Pro ETD mass spectrometer 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 1-30.
Figure 1-30. 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. ▲
1-40
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-41
Functional Description
Cooling Water Circuit
Cooling Water Circuit
Figure 1-31 on page 1-42 shows a schematical view of the cooling water
circuit in the Orbitrap Velos Pro mass spectrometer. For a parts list of
the cooling water circuit, see page 4-4. 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.
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. An inline filter, which is installed upstream, protects the
sensor. It must be replaced annually, see page 3-58 for instructions.
Input
Output
Recirculating
chiller
Power Distribution Board
Linear Trap
Preamplifier cooling
Heating element
(Peltier element)
Water filter
TMP 3
Analyzer
Flow control sensor
TMP 1
Peltier element Central Electrode
Power Supply Box
TMP 4
TMP 2
Water cooler for TMP
Figure 1-31. Schematic of cooling water circuit
1-42
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Functional Description
Cooling Water Circuit
Recirculating Chiller
A recirculating chiller (Thermo Scientific NESLAB ThermoFlex™ 900)
is shipped with the instrument, making the mass spectrometer
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
shipped with the instrument.
For instruction about performing maintenance for the chiller, see
“Maintenance of the Cooling Circuit” on page 3-58. 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! ▲
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-43
Functional Description
Printed Circuit Boards
Printed Circuit Boards
The Orbitrap Velos Pro mass spectrometer 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 analyzer.
The following pages contain a short overview of the electronic boards in
the MS portion of the Orbitrap Velos Pro mass spectrometer. 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 Orbitrap Velos Pro mass spectrometer contains
complicated and numerous circuits. Therefore, only qualified and
skilled electronics engineers should perform servicing.
A Thermo Fisher Scientific field 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 personnel. ▲
Note Many of the electronic components can be tested by the Orbitrap
Velos Pro MS diagnostics, which is accessible from the Tune Plus
window. ▲
1-44
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Linear Ion Trap Electronics
The linear ion trap is connected to the Orbitrap Velos Pro MS main
power switch. The linear ion trap has a sheet metal back cover.
Figure 1-32 shows the electronic connections at the rear side of the
linear trap.
Cold Ion Gauge
Figure 1-32. Electronic connections to linear trap
The linear ion trap electronics has two connections with the Orbitrap
Velos Pro MS electronics:
•
Data communication with the internal computer of the Orbitrap
Velos Pro mass spectrometer. See “Electronic Boards on 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-45
Functional Description
Printed Circuit Boards
Electronic Boards on the Right Side of the Instrument
Figure 1-33 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 1-33. Electronic boards on the right side of the instrument
The side panel is connected to the instrument frame by two
green/yellow ground wires. See bottom of Figure 1-33. 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 1-34. It supplies the voltages for the
HCD collision cell. In the Orbitrap Velos Pro ETD mass spectrometer,
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.
1-46
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Functional Description
Printed Circuit Boards
Figure 1-34. 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 1-35.
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-47
Functional Description
Printed Circuit Boards
Preamplifier
The preamplifier is located in a housing next to the Cold Ion Gauge. See
Figure 1-35. 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 1-35. 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 1-35.
Table 1-5. Diagnostic LEDs on the Preamplifier board
1-48
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Internal Computer
Figure 1-36 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 1-36. 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.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-49
Functional Description
Printed Circuit Boards
Data Acquisition Digital PCI Board
Figure 1-37 shows the data acquisition digital PCI board. It is an add-on
board to the internal computer. (See Figure 1-36 on page 1-49.)
Figure 1-37. 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 Orbitrap Velos Pro 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 1-37.
Table 1-6. Diagnostic LEDs of the Data Acquisition Digital PCI board
1-50
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Functional Description
Printed Circuit Boards
Data Acquisition Analog Board
Figure 1-38 shows the data acquisition analog board. This board is an
add-on board to the mainboard of the internal computer. See
Figure 1-36 on page 1-49. It is used to convert analog to digital signals
for Orbitrap analyzer 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 1-38. 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 1-38.
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 1-36 on page 1-49.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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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 1-39 shows the instrument control board. The instrument
control board is located in a housing next to the internal computer. It is
connected to the Orbitrap Velos Pro MS main power.
Diagnostic LEDs
Status LEDs
Figure 1-39. Instrument Control board
The instrument control board is used to interface the Velos Pro MS
control electronics to the Orbitrap analyzer control electronics. Three
signal lines are passed from the Velos Pro: 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.
1-52
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Thermo Fisher Scientific
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.) Turbomolecular pumps
(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 1-39 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 1-39 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 Velos
Pro SPI bus enabled
On
6.4
Orbitrap analyzer SPI bus enabled
On
Flashing on error
Power Distribution Board
Figure 1-40 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 turbomolecular 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.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-53
Functional Description
Printed Circuit Boards
Figure 1-40. 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 1-40.
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 1-40.
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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
Electr. On
Service mode
FT Electronics switch off
Vac. Units OK
Vacuum measurement
failure
Vacuum gauge defective
Pirani Orbitrap
analyzer OK
No function, at present
Pirani LT OK
Pirani Velos Pro MS failure
Control signal < 0.5 V
Ion Gauge On
Penning Orbitrap Velos Pro
MS Off
Forevacuum > 10-2 mbar
Ion Gauge OK
Penning Orbitrap Velos Pro
MS failure
Control signal < 0.5 V
LT Vacuum Work
Velos Pro MS vacuum
failure
Vacuum forepump Velos Pro MS
>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
TMP defective/errora
Rotation 1 OK
TMP 1 failure
80% rotation speed of TMP not
reached
Turbo P. 2 On
TMP 2 failure
TMP defective/errora
Rotation 2 OK
TMP 2 failure
80% rotation speed of TMP 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
a
Instrument is not scanning
System reset has occurred
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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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
• Velos Pro MS (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 Orbitrap Velos
Pro MS forevacuum pumps:
If not ok: switch off system and light
error LEDa; 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 TMPs reach 80% rotation speed
Switch on Penning gauge
5.
Vacuum and 80% rotation speed of
TMPs 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 Orbitrap Velos Pro MS
>10-1 mbar
Rebooting of the system by switching
off/on of the main switch.
• Penning gauge Orbitrap Velos Pro MS
>10-3 mbar
• Pirani gauge Velos Pro MS 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 TMP 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.
Orbitrap Velos Pro MS without data
link, keeps on running
10.
FT Electronics switch Orbitrap Velos Pro
MS off
Orbitrap Velos Pro MS electronics
switched off, pumps keep on running;
Orbitrap Velos Pro MS without data
link, keeps on running
a
Thermo Fisher Scientific
11.
Failure of linear ion trap or Orbitrap
Velos Pro MS (for example, 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.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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Functional Description
Printed Circuit Boards
Power Supply 1 Board
Figure 1-41 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 1-60.) and the
instrument control board. (See “Instrument Control Board” on
page 1-52.)
Figure 1-41. Power Supply 1 board
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 1-41.
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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Functional Description
Printed Circuit Boards
Table 1-14. Diagnostic LEDs of the Power Supply 1 board, continued
Name
Color
Description
Normal Operating
Condition
+18 V
Green
+18 V Output voltage present
On
-18 V
Green
-18 V Output voltage present
On
+8.5 V
Green
+8.5 V Output voltage present
On
Electronic Boards on the Left Side of the Instrument
Figure 1-42 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 analyzer 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 1-42. Electronic boards on the left side of the instrument
The main components on this side are described starting from the top.
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
1-59
Functional Description
Printed Circuit Boards
Ion Optic Supply Board
Figure 1-43 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 Orbitrap Velos Pro mass
spectrometer. It has an RF detector for the RF output control. The
board also provides the entrance voltage, the exit voltage, and the
reflector DC voltages as well as the RF voltages to the octapole of the
Orbitrap analyzer. See “Orbitrap Analyzer” on page 1-14 for further
information.
Figure 1-43. 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 1-43.
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
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
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Functional Description
Printed Circuit Boards
Table 1-15. Diagnostic LEDs of the Ion Optic Supply board, continued
No.
Name
Color
Description
Normal Operating
Condition
LD3
+29 V
Green
+29 V Input voltage present
On
LD5
+15 V
Green
+15 V Input voltage present
On
LD6
-15 V
Green
-15 V Input voltage present
On
LD7
RF1_ON
Blue
RF1 generator switched on
depending on application;
LED flashes during
scanning
LD8
RF2_ON
Blue
RF2 generator switched on
depending on application;
LED flashes during
scanning
Central Electrode Pulser Board
The central electrode pulser board is located in a housing that is
mounted to the flange of the UHV chamber. See Figure 1-44.
Figure 1-44. Central Electrode Pulser board
The board switches the injection and measurement voltages for the
central electrode and the detection electrodes of the Orbitrap analyzer.
Resistor-capacitor circuits on the board convert the switching pulse into
a smooth transition between the voltages.
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Functional Description
Printed Circuit Boards
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 1-44.
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 1-42 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 1-45. 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 1-45.
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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 1-42 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 1-14 for further information. The
board communicates with the instrument control board via an SPI bus.
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Functional Description
Printed Circuit Boards
CLT Offset Connector
RF Off & Feedback board
Figure 1-46. 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 1-46.
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 1-46 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 1-47.
Figure 1-47. Central Electrode Power Supply board
The board supplies four DC voltages to the Orbitrap analyzer:
•
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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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 1-47 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 1-42 on page 1-59. This
board provides five DC voltages for the ion optics of the Orbitrap Velos
Pro mass spectrometer. Two voltages supply the lenses of the
instrument. Three voltages are applied to the RF CLT main board to be
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Functional Description
Printed Circuit Boards
used as focusing potentials for the curved linear trap. See “Orbitrap
Analyzer” on page 1-14 for further information. The board
communicates via the SPI bus.
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 1-48. High Voltage Power Supply board (cover removed)
The diagnostic LEDs listed in Table 1-20 on page 1-68 show the
operating states of the board. The position of the LEDs on the board is
indicated by the white rectangles in Figure 1-48.
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1-67
Functional Description
Printed Circuit Boards
Table 1-20. Diagnostic LEDs of the High Voltage Power Supply board
No.
Name
Color
Description
Normal Operating
Condition
LD1
NO TERM
Red
SPI bus termination board
missing
Off
LD2
SEND
Yellow
Interface has been addressed
and sends/receives data
Flashing on SPI bus
data transfer
LD3
SEL
Green
Board has been addressed
Flashing on SPI bus
data transfer
LD4
HV ON
Green
High voltage is switched on
On
LD5
POLARITY
Green
Positive/negative ion mode
Off (positive mode)
SPI Bus Termination Board
Various boards communicate via the SPI bus, a serial RS485-based bus
system. The SPI Bus Termination board reduces unwanted signal
reflections. The boards indicate a missing termination (after
maintenance, for example) by LEDs.
The SPI Bus Termination board is located below the High Voltage
Power Supply board, at the bottom left side of the instrument. See
Figure 1-49.
SPI bus termination board
Figure 1-49. High Voltage Power Supply board with SPI Bus Termination
board
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Chapter 2
Basic System Operations
Many maintenance procedures for the Orbitrap Velos Pro system
require that the mass spectrometer be shut down. In addition, the
Orbitrap Velos Pro system can be placed in Standby condition if the
system is not to be used for 12 hours or more.
The following topics are described 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 Orbitrap Velos Pro Mass Spectrometer
Completely” on page 2-7
•
“Starting Up the System after a Shutdown” on page 2-9
•
“Resetting the System” on page 2-12
•
“Resetting 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 mass spectrometer in an emergency, place the
main power switch (located on the power panel at the right side of the
Orbitrap Velos Pro mass spectrometer) 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 seconds 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.
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Basic System Operations
Shutting Down the System in an Emergency
It is not possible to check whether the system was vented. The log file of
the data system indicates a reboot of the system. In case of frequent but
short power failures we recommend installing an uninterruptible power
supply (UPS). If main power failures occur frequently while the system
is not attended (for example, 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. ▲
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
2-3
Basic System Operations
Placing the Instrument in Standby Condition
Placing the Instrument in Standby Condition
The Orbitrap Velos Pro 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 Orbitrap Velos Pro ETD mass spectrometer, 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 (Orbitrap Velos Pro ETD), 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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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 Orbitrap Velos
Pro ETD mass spectrometer 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 “Replacing the Reagent Vials” on page 3-48.
The reagent vials will be too hot to touch after the cooling nitrogen
turns off at 70°C. Verify that the reagent vials are cool to the touch
before handling them. ▲
More information about turning on and off the reagent heaters is
given in “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 Orbitrap Velos Pro mass spectrometer is shut down (See “Shutting
Down the Orbitrap Velos Pro Mass Spectrometer Completely” on
page 2-7.) and these heaters have had sufficient time to cool down to
room temperature. ▲
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
2-5
Basic System Operations
Placing the Instrument in Standby Condition
Placing the MS in Standby Condition
❖
To place the Orbitrap Velos Pro 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
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 Pro mass
spectrometer turns 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 Orbitrap Velos Pro MS main power switch in the On
position.
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Thermo Fisher Scientific
Basic System Operations
Shutting Down the Orbitrap Velos Pro Mass Spectrometer Completely
Shutting Down the Orbitrap Velos Pro Mass Spectrometer Completely
The Orbitrap Velos Pro mass spectrometer 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 Orbitrap Velos Pro MS 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 Orbitrap Velos Pro 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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
2-7
Basic System Operations
Shutting Down the Orbitrap Velos Pro Mass Spectrometer Completely
6. Leave the main power switch of the Orbitrap Velos Pro mass
spectrometer in the On position.
7. During service or maintenance operations that require opening the
vacuum system of the LTQ Velos Pro MS or the Orbitrap Velos Pro
MS, 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 Orbitrap Velos Pro mass spectrometer 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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Thermo Fisher Scientific
Basic System Operations
Starting Up the System after a Shutdown
Starting Up the System after a Shutdown
To start up the Orbitrap Velos Pro mass spectrometer 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 Orbitrap Velos Pro mass spectrometer
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 Pro MS is
in the On position and the electronics service switch of the
LTQ Velos Pro MS is in the Operating position.
5. Place the main power switch at the right side of the Orbitrap Velos
Pro mass spectrometer 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 turns yellow to
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2-9
Basic System Operations
Starting Up the System after a Shutdown
indicate that the data system has started to establish a
communication link.
c. After several more seconds, the Communication LED turns
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 turns
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 Pro turns
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 S-lens 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 Pro to establish the
communication link between LTQ Velos Pro 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 Orbitrap Velos Pro mass spectrometer for operation
1. Before you begin data acquisition with your Orbitrap Velos Pro
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
•
Helium: 275 ± 70 kPa (2.75 ± 0.7 bar, 40 ±10 psi),
•
Nitrogen: 690 ± 140 kPa (6.9 ± 1.4 bar, 100 ± 20 psi).
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Basic System Operations
Starting Up the System after a Shutdown
In case of an Orbitrap Velos Pro ETD mass spectrometer, 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 Orbitrap Velos Pro ETD mass spectrometer, start up
the ETD Module as described in “Starting the ETD Module After a
Complete Shutdown“. In case of an Orbitrap Velos Pro mass
spectrometer, continue to set up for ESI or APCI operation as
described in Orbitrap Velos Pro Getting Started.
Starting the ETD Module After a Complete Shutdown
❖
To start up the ETD Module after a complete shutdown
1. Start the Orbitrap Velos Pro ETD mass spectrometer 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
Orbitrap Velos Pro Getting Started manual.
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
2-11
Basic System Operations
Resetting the System
Resetting the System
If the communication link between Orbitrap Velos Pro mass
spectrometer and data system computer is lost, it may be necessary to
reset the system using the Reset button of the LTQ Velos Pro mass
spectrometer.
The procedure given here assumes that the Orbitrap Velos Pro mass
spectrometer 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 Orbitrap Velos Pro mass spectrometer, press the Reset
button of the LTQ Velos Pro. 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 turns 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 turns 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
turns 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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Basic System Operations
Resetting Tune and Calibration Parameters to their Default Values
Resetting Tune and Calibration Parameters to their Default Values
You can reset the Orbitrap Velos Pro 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 Orbitrap Velos Pro MS 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Orbitrap Velos Pro ETD mass spectrometer, 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
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.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Orbitrap Velos Pro ETD mass spectrometer 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 Orbitrap
Velos Pro ETD mass spectrometer completes the Xcalibur Sequence
step in progress before going into Standby mode.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
2-15
Chapter 3
User Maintenance
This chapter describes routine maintenance procedures that must be
performed to ensure optimum performance of the Orbitrap Velos Pro
mass spectrometer.
For instructions on maintaining the LTQ Velos Pro 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 Cooling Circuit” on page 3-58
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 inTable 3-1.
Table 3-1. User maintenance procedures
MS 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
Replace operating fluid reservoir
and pump bearings
Every four years
Manufacturer’s documentation
Check cooling fluid level
See manufacturer’s documentation
Turbomolecular pumps
Cooling water circuit
page 3-5
page 3-11
Check cooling fluid filter
Manufacturer’s documentation
page 3-58
Check air inlet filter
ETD Module
a
Replace filter cartridge
Annually
page 3-58
Clean ion volume
As neededa
page 3-21
Replace inlet valve components
As needed
a
page 3-45
Clean ion source lenses
As neededa
page 3-33
Clean ion source
As needed
a
page 3-40
Replace ion source filament
As neededa
page 3-42
a
page 3-48
Replace reagent vials
As needed
Check rotary-vane pump oil and
add when needed
Every month
page 3-8
Change rotary-vane pump oil
Every four months
page 3-9
Clean rear cooling fans
Every four months
page 3-57
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
•
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.
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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
Orbitrap Velos Pro mass spectrometer.
•
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 ix for further information.
Cleaning the Surface of the Instrument
Clean the outside of the instrument with a dry cloth. For removing
stains or fingerprints on the surface of the instrument (panels, for
example), slightly dampen the cloth (preferably made of microfiber)
with distilled water.
Caution Prevent any liquids from entering the inside of the
instrument. ▲
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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.
3-4
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Orbitrap Velos Pro mass spectrometer 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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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.
3-6
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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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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 Orbitrap Velos Pro ETD mass
spectrometer.
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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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
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3-9
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 Orbitrap Velos Pro ETD mass
spectrometer.
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 23 kg (50 lb). ▲
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.
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User Maintenance
Maintenance of the Vacuum System
b. If the oil level goes above the MAX level mark, remove the drain
plug and drain the excess oil from the pump.
6. Reassemble the rotary-vane pump.
a. Replace the oil filler plug.
b. Return the rotary-vane pump to the floor.
c. Reconnect the foreline vacuum hose to the rotary-vane pump.
d. Reconnect the exhaust vacuum hose to the rotary-vane pump.
e. Plug in the rotary-vane pump.
7. Reattach the lower panel at the rear side of the ETD Module.
8. Plug in the instrument.
9. Restart the system.
Maintenance of the Turbomolecular Pumps
The turbomolecular pumps in the MS portion of the Orbitrap Velos Pro
mass spectrometer need maintenance work by the user that is briefly
outlined below. In contrast, the turbomolecular pump in the
ETD Module of the Orbitrap Velos Pro ETD mass spectrometer
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 cautions contained in these manuals! ▲
Replacing the Operating Fluid Reservoir of the Turbomolecular Pumps
The manufacturer recommends replacing the operating fluid reservoirs
of the turbomolecular pumps at least every four years. The storage
stability of the operating fluid is limited. The specification of durability
is given by the pump manufacturer. The disposal of used oil is subject to
the relevant regulations.
Replacements for the operating fluid reservoirs including Porex rods
(HiPace™ 80: P/N 1275740; HiPace™ 300: P/N 1275730) are available
from Thermo Fisher Scientific.
Note The pump bearings have also to be replaced at least every four
years. This maintenance operation requires special training and
additional equipment. Therefore, Thermo Fisher Scientific recommends
calling a Thermo Fisher Scientific field service engineer to replace both
the operating fluid reservoir and the pump bearings. ▲
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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.
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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 volume 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 3-42.
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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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:
3-14
•
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)
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•
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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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
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.
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•
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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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 3-48.
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Note In Service mode, all power to the Orbitrap Velos Pro ETD MS
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 3-48.
Note In Service mode, all power to the Orbitrap Velos Pro ETD MS
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, mechanical pump and
turbomolecular pump 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:
3-20
•
“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 3-40
•
“Replacing the Ion Source Filament” on page 3-42
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•
“Replacing Inlet Valve Components” on page 3-45
The ion source, the ion trap, and their components are shown in
Figure 3-9.
2
3
4
1
6
5
Labeled components: 1=ion source lenses, 2=filament assembly, 3=ion
source block, 4=magnet support, 5=magnets, 6=ion volume (inside the ion
source block, 3)
Figure 3-9.
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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❖
On
On/Standby button
Off
Standby
To clean the ion volume with an inlet valve
1. Click the On/Standby button in the Tune Plus window to place the
Orbitrap Velos Pro ETD mass spectrometer in Standby mode. See
Figure 3-10.
Reagent Ion Source instrument control icon
Status View
Figure 3-10. Tune Plus window (Orbitrap Velos Pro ETD)
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
7
13
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 openinga
a
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 completea
a
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 3-45. 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 3-45. 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 Orbitrap Velos Pro ETD mass
spectrometer 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.
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Caution It is good practice to keep the inlet valve lever in the down
(closed) position whenever it is not explicitly required to be in the up
position (open), even if the vacuum manifold is at atmospheric pressure.
This is to be consistent with maintenance procedures that rely on the
inlet valve lever being closed at the appropriate step to prevent the
accidental loss of vacuum. If the vacuum is accidently lost the system
may be damaged. At a minimum, the components that were under
vacuum might have to be cleaned. ▲
Labeled components: 1=inlet valve plug, 2=vacuum manifold, 3=inlet valve
lever, 4=guide bar, 5=entry housing, 6=inlet valve knob, 7=inlet valve block,
8=foreline hose connection, 9=12 pin feedthrough, 10=vacuum manifold
probe plate, 11=ball valve housing, 12= inlet valve solenoid
Figure 3-27. 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 1-16 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.
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1
Figure 3-28. Valve shield (1) covering the vacuum manifold probe plate
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).
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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).
Figure 3-31. Removing the vacuum manifold probe plate
g. Unplug the 12-pin feedthrough harness from the feedthrough
(Figure 3-32).
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1
4
2
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 3-38) 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
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 3-37) to disengage it
from the ion source assembly.
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1
3
2
Figure 3-33. Removing the ion source assembly from the vacuum manifolda
a
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 3-39). 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
10
1
2
3
5
9
8
7
Labeled components: 1=thumbscrew, 2=springs, 3=magnet yoke, 4=Ion
Source PCB, 5=magnets, 6=ion source block, 7=ceramic lens holder, 8=spring
clip, 9=spring clip thumb screw, 10=12 pin feedthrough harness, 11=finger
over front edge of ceramic lens holder to keep unsecured components from
falling out of the ion source assembly.
Figure 3-34. 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 Orbitrap Velos Pro ETD mass
spectrometer. (See “Shutting Down the Orbitrap Velos Pro Mass
Spectrometer Completely” on page 2-7.)
Caution Shut down and unplug the Orbitrap Velos Pro ETD mass
spectrometer 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 3-39 and
Figure 3-35 on page 3-39), 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
9
5
6
2
4
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 3-41).
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 3-43.
Supplies needed for replacing the ion source filament:
3-42
•
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 Orbitrap Velos Pro ETD mass
spectrometer. (See “Shutting Down the Orbitrap Velos Pro Mass
Spectrometer Completely” on page 2-7.)
Caution Shut down and unplug the Orbitrap Velos Pro ETD mass
spectrometer 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 3-39 and
Figure 3-35 on page 3-39), remove and disassemble the ion source
(Figure 3-36 on page 3-41).
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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in Figure 3-36) according to the procedure in step e of
“Cleaning the Ion Source Block“ on page 3-41 .
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 3-41).
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 3-43).
4. Reassemble ion source and ion source assembly.
5. Insert the ion source assembly into the vacuum manifold.
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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 3-47.
1
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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
Thermo Fisher Scientific
Item contained in Inlet Valve Seal Kit (P/N 119265-0003).
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Replacing 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 Orbitrap Velos Pro ETD
mass spectrometer 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 3-48
•
“Installing/Exchanging the Reagent Vials” on page 3-51
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 Orbitrap Velos Pro ETD mass
spectrometer (MS and ETD Module). The ETD Module power
switches control the power to the ETD Module only. When the
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Orbitrap Velos Pro ETD MS is fully operational (all systems On), the
MS Main Power switch is in the On position and the FT Electronics
switch is in the operating (On) position.
Normally, the ETD Module Power and Service switches remain On. Use
the FT Electronics switch on the MS unit to place the Orbitrap Velos
Pro ETD mass spectrometer 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 Orbitrap Velos Pro ETD mass spectrometer 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 mass spectrometer is in Off
condition, the Orbitrap Velos Pro ETD MS 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 turbomolecular pumps and the
forepumps in both the mass spectrometer and the ETD Module.
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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 Orbitrap Velos Pro ETD mass spectrometer 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 3-52).
Warning Burn Hazard. Follow the procedures described in “Placing the
Instrument in Off Condition and Service Mode” on page 3-48 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 3-48.) Verify that the vial heater
cover is safe to handle before attempting to remove the vial holders and
reagent vials. ▲
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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 Orbitrap Velos
Pro ETD mass spectrometer (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 3-53 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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User Maintenance
Maintenance of the ETD Module
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 Health Hazard. 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. ▲
Caution If no vial is placed in the Vial 2 heater, 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 3-50.)
The Orbitrap Velos Pro ETD mass spectrometer 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 Orbitrap Velos Pro Mass Spectrometer
Completely” on page 2-7.
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User Maintenance
Maintenance of the ETD Module
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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
3-55
User Maintenance
Maintenance of the ETD Module
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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Thermo Fisher Scientific
User Maintenance
Maintenance of the ETD Module
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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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
3-57
User Maintenance
Maintenance of the Cooling Circuit
Maintenance of the Cooling Circuit
The recirculating chiller and the water filter require maintenance on a
regular basis.
Maintenance for 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.
Replacing the Water Filter Cartridge
The filter removes particulate matter in the cooling system that might
damage the flow sensor. The filter cartridge should be replaced annually
or as necessary. A replacement is available from Thermo Fisher Scientific
(P/N 1284050).
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Thermo Fisher Scientific
User Maintenance
Maintenance of the Cooling Circuit
❖
To replace the water filter cartridge
1. Place the system in Standby condition as described on page 2-4.
2. Turn off the chiller.
3. The filter is installed on the left instrument side, in the cooling lines
of the Orbitrap system between the Peltier element and the flow
sensor. See Figure 3-50. Quick couplings connect the filter assembly
to the hoses of the cooling lines. Press the thumb latch of each quick
coupling to release it; valves in the couplings prevent the water from
leaking out. Then remove the complete filter assembly.
Thumb latch
Thumb latch
Figure 3-50. Installed water filter
4. Remove the filter from the assembly by using a 5/16 inch wrench
and pressing against the gray ring on the quick coupling, away from
the filter. See Figure 3-51.
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Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
3-59
User Maintenance
Maintenance of the Cooling Circuit
Gray ring
Figure 3-51. Removing the filter cartridge
5. Insert the new filter into the quick couplings. See Figure 3-52.
Figure 3-52. Filter cartridge with Quick couplers
Caution Pay special attention to the direction of flow. Reversing the flow
can damage both the flow sensor and the filter. ▲
6. Connect the filter assembly to the hoses of the cooling lines.
7. Switch on the chiller system. Check for leaks and check the water
level in the chiller. Refill as appropriate.
8. Set the instrument to operating condition.
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Thermo Fisher Scientific
Chapter 4
Replaceable Parts
This chapter contains part numbers for replaceable and consumable
parts for the mass spectrometer, data system, and kits. To ensure proper
results in servicing the Orbitrap Velos Pro 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.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
4-1
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 . . . . . . . . . . . . . . . . . . . . . .
4-2
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Analyzer 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 1-22 on
page 1-30.
T-piece 13 mm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0512360
Hose 13 × 3.5; PVC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0690720
Turbomolecular pump HiPace 300. . . . . . . . . . . . . . . . . . . . . . . . . . .1272910
Turbomolecular pump; HiPace 80 . . . . . . . . . . . . . . . . . . . . . . . . . . .1272920
UHV gauge IKR 270; short . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1181380
Compact Pirani Gauge TPR280. . . . . . . . . . . . . . . . . . . . . . . . . . . . .1156400
Water cooling for HiPace 300. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1272930
Water cooling for HiPace 80. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .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 TMPs, 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
4-3
Replaceable Parts
Parts for the Basic System
Water Supply
For a schematical overview of the cooling water circuit, see Figure 1-31
on page 1-42.
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
Filter cartridge; 50 μm DIF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1284050
Gas Supply
For a schematical overview of the gas supply, see Figure 1-27 on
page 1-37.
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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 Orbitrap Velos Pro ETD mass spectrometer.
Quadrupole Orbitrap analyzer, 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
PUMP, TURBO, EDWARDS EXT75DX ISO100, TNR . . 00108-01-00016
Splinter guard, DN_63_ISO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1198600
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
Clamping piece 8/16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .0370130
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
4-5
Replaceable Parts
Parts Lists for the ETD System
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
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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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
4-7
Appendix A
Fluoranthene
Fluoranthene is used as the Electron Transfer Dissociation (ETD)
reagent in the ETD Module portion of the Orbitrap Velos Pro ETD
mass spectrometer. 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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
A-1
Glossary
This section lists and defines terms used in this guide. 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; a device that converts
data from analog to digital form.
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).
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.
See also corona discharge and APCI corona discharge
voltage.
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.
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
M N
O
P
Q
R
S
T
U
V W X
Y
Z
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.
See also atmospheric pressure chemical ionization
(APCI), and API stack.
APCI source Contains the APCI probe assembly,
APCI manifold, and API stack.
See also atmospheric pressure chemical ionization
(APCI), APCI manifold, and API stack.
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.
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).
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G-1
Glossary: API–atmospheric pressure chemical ionization (APCI)
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.
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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.
AP-MALDI See atmospheric pressure matrix-assisted
laser desorption/ionization (AP-MALDI).
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)–consecutive reaction monitoring (CRM) scan type
atmospheric pressure ionization (API) Ionization
performed at atmospheric pressure by using
atmospheric pressure chemical ionization (APCI),
electrospray ionization (ESI), or nanospray ionization
(NSI).
B
atmospheric pressure matrix-assisted laser
desorption/ionization (AP-MALDI) Matrix-assisted
laser desorption/ionization in which the sample target
is at atmospheric pressure.
baud rate data transmission speed in events per second
See also matrix-assisted laser desorption/ionization
(MALDI).
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.
atomic mass unit Atomic Mass Unit (u) defined by
taking the mass of one atom of carbon12 as being
12u; unit of mass for expressing masses of atoms or
molecules.
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.
See also ion injection time.
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.
auxiliary gas flow rate The relative rate of flow of
auxiliary gas (nitrogen) into the API source reported
in arbitrary units.
auxiliary gas inlet An inlet in the API probe where
auxiliary gas is introduced into the probe.
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.
b bit
B byte (8 b)
BTU British thermal unit, a unit of energy
C
°C degrees Celsius
CE central electrode (of the Orbitrap analyzer);
European conformity. Mandatory European marking
for certain product groups to indicate conformity with
essential health and safety requirements set out in
European Directives.
cfm cubic feet per minute
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.
chemical ionization (CI) plasma The collection of
ions, electrons, and neutral species formed in the ion
source during chemical ionization.
See also chemical ionization (CI).
CI See chemical ionization (CI).
CID See collision-induced dissociation (CID).
cm centimeter
cm3 cubic centimeter
collision gas A neutral gas used to undergo collisions
with ions.
collision-induced dissociation (CID) An ion/neutral
process in which an ion is dissociated as a result of
interaction with a neutral target species.
auxiliary gas valve A valve that controls the flow of
auxiliary gas into the API source.
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.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
G-3
Glossary: Convectron™ gauge–ESI flange
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).
CPU central processing unit (of a computer)
CRM See consecutive reaction monitoring (CRM) scan
type.
C-Trap curved linear trap
<Ctrl> control key on the terminal keyboard
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.
DC direct current
divert/inject valve A valve on the mass spectrometer
that can be plumbed as a divert valve or as a loop
injector.
DS data system
DSP digital signal processor
E
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.
See also electron transfer dissociation (ETD) and
infrared multiphoton dissociation (IRMPD).
electron multiplier A device used for current
amplification through the secondary emission of
electrons. Electron multipliers can have a discrete
dynode or a continuous dynode.
electron transfer dissociation (ETD) A method of
fragmenting peptides and proteins. In electron
transfer dissociation (ETD), singly charged reagent
anions transfer an electron to multiply protonated
peptides within the ion trap mass analyzer. This leads
to a rich ladder of sequence ions derived from cleavage
at the amide groups along the peptide backbone.
Amino acid side chains and important modifications
such as phosphorylation are left intact.
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. Discharge of stored static
electricity that can damage electronic equipment and
impair electrical circuitry, resulting in complete or
intermittent failures.
ESI See electrospray ionization (ESI).
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.
ECD See electron capture dissociation (ECD).
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Thermo Fisher Scientific
Glossary: ESI probe–FWHM
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.
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.
ESI source Contains the ESI probe and the API stack.
FFT See Fast Fourier Transform (FFT).
See also electrospray ionization (ESI), ESI probe, and
API stack.
fluoranthene A reagent anion that is used in an
electron transfer dissociation (ETD) experiment.
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.
firmware Software routines stored in read-only
memory. Startup routines and low-level input/output
instructions are stored in firmware.
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.
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump.
See also ESI spray current.
ETD See electron transfer dissociation (ETD).
eV Electron Volt. The energy gained by an electron that
accelerates through a potential difference of one volt.
Extensible Markup Language See XML (Extensible
Markup Language).
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.
Fourier Transform - Ion Cyclotron Resonance Mass
Spectrometry (FT-ICR MS) A technique that
determines the mass-to-charge ratio of an ion by
measuring its cyclotron frequency in a strong
magnetic field.
fragment ion A charged dissociation product of an
ionic fragmentation. Such an ion can dissociate
further to form other charged molecular or atomic
species of successively lower formula weights.
fragmentation The dissociation of a molecule or ion to
form fragments, either ionic or neutral. When a
molecule or ion interacts with a particle (electron, ion,
or neutral species) the molecule or ion absorbs energy
and can subsequently fall apart into a series of charged
or neutral fragments. The mass spectrum of the
fragment ions is unique for the molecule or ion.
FT Fourier Transformation
F
FT-ICR MS See Fourier Transform - Ion Cyclotron
Resonance Mass Spectrometry (FT-ICR MS).
f femto (10-15)
FTMS Fourier Transformation Mass Spectroscopy
°F degrees Fahrenheit
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.
.fasta file extension of a SEQUEST™ search database
file
ft foot
FWHM Full Width at Half Maximum
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
G-5
Glossary: g–ion optics
G
Hz hertz (cycles per second)
g gram
I
G Gauss; giga (109)
ICR ion cyclotron resonance
GC gas chromatograph; gas chromatography
ID inside diameter
GC/MS gas chromatography / mass spectrometer
IEC International Electrotechnical Commission
GUI graphical user interface
IEEE Institute of Electrical and Electronics Engineers
H
in. inch
h hour
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.
h height
handshake A signal that acknowledges that
communication can take place.
HCD See higher energy collision-induced dissociation
(HCD).
header information Data stored in each data file that
summarizes the information contained in the file.
H-ESI probe 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.
higher energy collision-induced dissociation (HCD)
Collision-induced dissociation that occurs in the
HCD cell of the Orbitrap mass analyzer. The
HCD cell consists of a straight multipole mounted
inside a collision gas-filled tube. A voltage offset
between C-Trap and HCD cell accelerates parent ions
into the collision gas inside the HCD cell, which
causes the ions to fragment into product ions. The
product ions are then returned to the Orbitrap
analyzer for mass analysis. HCD produces triple
quadrupole-like product ion mass spectra.
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.
HPLC See high performance liquid chromatography
(HPLC).
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
ion gauge Measures the pressure in the mass analyzer
region (high vacuum region) of the vacuum manifold.
ion injection time The amount of time that ions are
allowed to accumulate in the ion trap mass analyzer
when AGC is off. With AGC on, the ion injection
time is set automatically (up to the set maximum ion
injection time) based on the AGC target value.
See also: Automatic Gain Control™ (AGC).
ion optics Focuses and transmits ions from the
API source to the mass analyzer.
HV high voltage
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Thermo Fisher Scientific
Glossary: ion source–min
ion source A device that converts samples to gas-phase
ions.
ion sweep cone A removable cone-shaped metal cover
that fits on top of the API ion transfer capillary and
acts as a physical barrier to protect the entrance of the
capillary.
ion sweep gas Extra nitrogen gas that flows along the
axis of the API ion transfer capillary (between the ion
sweep cone and the capillary block) towards the API
spray. The sweep gas flow is thus countercurrent to the
flow of the ions.
See also ion sweep gas pressure.
ion sweep gas pressure The rate of flow of the sweep
gas (nitrogen) into the API source. A measurement of
the relative flow rate (in arbitrary units) to provide the
required flow of nitrogen gas out from the Ion Sweep
cone towards the API spray.
See also ion sweep gas.
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
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.
log file A text file, with a .log file extension, that is used
to store lists of information.
IRMPD See infrared multiphoton dissociation
(IRMPD).
M
K
m meter; milli (10-3)
k kilo (103, 1000)
M mega (106)
K kilo (210, 1024)
M+ molecular ion
KEGG Kyoto Encyclopedia of Genes and Genomes
MALDI See matrix-assisted laser desorption/ionization
(MALDI).
kg kilogram
L
l length
L liter
LAN local area network
lb pound
μ micro (10-6)
matrix-assisted laser desorption/ionization
(MALDI) A method of ionizing proteins where a direct
laser beam is used to facilitate vaporization and
ionization while a matrix protects the biomolecule
from being destroyed by the laser.
MB Megabyte (1048576 bytes)
MH+ protonated molecular ion
LED light-emitting diode
microscan One mass analysis (ion injection and storage
or scan-out of ions) followed by ion detection.
Microscans are summed, to produce one scan, to
improve the signal-to-noise ratio of the mass spectral
data. The number of microscans per scan is an
important factor in determining the overall scan time.
LHe liquid helium
min minute
LC See liquid chromatography (LC).
LC/MS See liquid chromatography / mass spectrometry
(LC/MS).
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
G-7
Glossary: mL–Orbitrap mass analyzer
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
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.
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:
• 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
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)
NIST National Institute of Standards and Technology
(USA)
NMR Normal Mass Range
NSI See nanospray ionization (NSI).
O
octapole An octagonal array of cylindrical rods that acts
as an ion transmission device. An RF voltage and
DC offset voltage applied to the rods create an
electrostatic field that transmits the ions along the axis
of the octapole rods.
OD outside diameter
Orbitrap mass analyzer The Orbitrap™ mass analyzer
consists of a spindle-shape central electrode
surrounded by a pair of bell-shaped outer electrodes.
Ions inside the mass analyzer orbit in stable
trajectories around the central electrode with
harmonic oscillations along it.
r
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.
G-8
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
z
Two detection electrodes record an image current of
the ions as they undergo harmonic oscillations. A
Fourier transformation extracts different harmonic
frequencies from the image current. An ion's
Thermo Fisher Scientific
Glossary: OT–retention time (RT)
mass-to-charge ratio m/z is related to the frequency f
of its harmonic oscillations and to the instrumental
constant k by:
m/z = k/f 2
OT Orbitrap
See Orbitrap mass analyzer.
OVC outer vacuum case
precursor ion An electrically charged molecular species
that can dissociate to form fragments. The fragments
can be electrically charged or neutral species. A
precursor ion (PR) can be a molecular ion or an
electrically charged fragment of a molecular ion. Also
known as parent ion.
precursor mass Mass of the corresponding precursor
(or parent) ion or molecule.
psig pounds per square inch, gauge
Ω ohm
PTM posttranslational modification
P
-12
p pico (10 )
Pa pascal
parent ion An electrically charged molecular species
that can dissociate to form fragments. The fragments
can be electrically charged or neutral species. A parent
ion can be a molecular ion or an electrically charged
fragment of a molecular ion. Also called a precursor
ion.
parent mass The mass-to-charge ratio of a parent ion.
The location of the center of a target parent-ion peak
in mass-to-charge ratio (m/z) units. Also known as
precursor mass.
See also: parent ion.
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.
pulsed Q dissociation (PQD) Collision-induced
dissociation that involves precursor ion activation at
high Q, a time delay to allow the precursor to
fragment, and then a rapid pulse to low Q where all
fragment ions are trapped. The fragment ions can
then be scanned out of the ion trap mass analyzer and
detected. PQD eliminates the “1/3 Rule” low mass
cut-off for MS/MS data.
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.
R
PE protective earth
RAM random access memory
PID proportional / integral / differential
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.
P/N part number
p-p peak-to-peak voltage
ppm parts per million
resolution The ability to distinguish between two
points on the wavelength or mass axis.
PQD pulsed-Q dissociation
retention time (RT) The time after injection at which
a compound elutes. The total time that the compound
is retained on the chromatograph column.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
G-9
Glossary: RF–SIM
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.
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.)
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
scan mode and scan type combinations A function
that coordinates the three processes in the
MS detector: ionization, mass analysis, and ion
detection. You can combine the various scan modes
and scan types to perform a wide variety of
experiments.
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.
G-10
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
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
serial port An input/output location (channel) for
serial data transmission.
sheath gas The inner coaxial gas (nitrogen), which is
used in the API source to help nebulize the sample
solution into a fine mist as the sample solution exits
the ESI or APCI nozzle.
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.
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.
Thermo Fisher Scientific
Glossary: skimmer–vacuum manifold
skimmer A vacuum baffle between the higher pressure
capillary-skimmer region and the lower pressure
region. The aperture of the skimmer is offset with
respect to the bore of the ion transfer capillary.
source CID A technique for fragmenting ions in an
atmospheric pressure ionization (API) source.
Collisions occur between the ion and the background
gas, which increase the internal energy of the ion and
stimulate its dissociation.
SPI See Serial Peripheral Interface (SPI).
SRM See selected reaction monitoring (SRM) scan
type.
sweep gas Nitrogen gas that flows out from behind the
sweep cone in the API source. Sweep gas aids in
solvent declustering and adduct reduction.
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.
T
T Tesla
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 instrument
software’s tune window and saved as tune file.
A tune method stores tune parameters only.
(Calibration parameters are stored separately, not with
the tune method.)
tune parameters Instrument parameters whose values
vary with the type of experiment.
turbomolecular pump A vacuum pump that provides
a high vacuum for the mass spectrometer and detector
system.
TWA time weighted average
U
u atomic mass unit
UHV ultra high vacuum
ultra-high performance liquid chromatography
(U-HPLC) See high performance liquid
chromatography (HPLC).
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.
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.
UMR Universal Mass Range
TIC See total ion current (TIC).
V AC volts alternating current
TMP See turbomolecular pump.
V DC volts direct current
Torr A unit of pressure, equal to 1 mm of mercury and
133.32 Pa.
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.
total ion current (TIC) The sum of the ion current
intensities across the scan range in a mass spectrum.
V
V volt
tube lens offset The voltage offset from ground that is
applied to the tube lens to focus ions toward the
opening of the skimmer.
Thermo Fisher Scientific
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
G-11
Glossary: vacuum system–XML (Extensible Markup Language)
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 watt
WEEE European Union Waste Electrical and
Electronic Equipment Directive. Provides guidelines
for disposal of electronic waste.
X
XML (Extensible Markup Language) A
general-purpose markup language that is used to
facilitate the sharing of data across different
information systems, particularly via the Internet.
w width
G-12
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
Thermo Fisher Scientific
Index
Numerics
00101-08-00006 3-56
00101-08500 1-38
00101-15500 1-38
00101-2500 1-38
00109-02-00020 3-57
00301-01-0013 4-7
00301-15517 4-7
0690280 1-38
119265-0003 3-45
119283-0001 3-46
119683-0100 3-47
12 pin feedthrough
harness 3-39
location 3-34, 3-37
120320-0030 3-42
1275730 3-11
1275740 3-11
1284050 3-58
23827-0008 3-3
23827-0009 3-3
32000-60340 3-14
3814-6530 3-47
98000-20060 3-56
98000-62006 3-56–3-57
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 3-50
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
Thermo Fisher Scientific
axial ion ejection 1-12
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 3-41, 3-43
bath gas 1-13
bayonet guide 3-30
bayonet lock 3-30
bayonet pin 3-30
buck/boost transformer 1-10
burnout, of filament 3-54
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 3-41
central electrode
location 1-14
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 3-39
ceramic spacer 3-41
charge-sign independent trapping (CSIT) 1-12, 1-21
circuit breakers 1-6–1-7
cleaning
instrument surface 3-3
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A) I-1
Index: D–E
ion source block 3-40
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 3-58
connector, to ETD Interface board 1-22
control elements
inlet valve 1-22
instrument 1-5
control panel 1-6
control unit, for TMPs 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
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
data system
communication 1-5, 2-12
I-2
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
connection 1-9
log file 2-3
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 3-39
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 1-60
left side 1-59
power distribution 1-53
right side 1-46
electronic connections, to linear trap 1-45
emergency shutdown 2-2
entrance voltage 1-60
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
weight 3-10
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
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
panel 1-23, 1-25
Thermo Fisher Scientific
Index: F–H
ETD Reagent Kit 4-7
ETD side access panel
interlocks 3-55
removing 3-19
ETD turbomolecular pump
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 shutdown 3-4
Exactive Installation Kit 1-38
exhaust
hose 1-11, 1-34
system 1-11, 1-33–1-34
exit voltage 1-60
external calibration 1-4
external connections 1-10
extracting voltage 1-14
extraction, of ion packets 1-14
F
fan filters 1-22, 3-57
ferrules, tightening 3-56
filament
assembly 3-21, 3-42
burnout 3-54
emission current 3-42
function 1-26, 1-28
wire 3-44
filter, for cooling water 1-42
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 3-58
fluoranthene 4-7, A-1
focusing potentials 1-67
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 3-56
from upper oven 3-56
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 3-56
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 3-45
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 3-41
heating element 1-42
helium
gas capillary 1-39
gas pressure 1-38
inlet 1-10, 1-37
purging the line 2-11
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
I-3
Index: I–L
supply 1-10
high voltage power supply board
diagnostic LEDs 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, 3-45
lever 1-22, 3-23–3-24, 3-34, 3-45
plug 3-24, 3-34, 3-45
seal kit 3-45
seal tool 3-46
solenoid 1-22, 3-34
installation kit, for the reagent inlet module 3-56
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 1-59–1-60
ion optics 1-12
ion oscillation 1-14
ion packets 1-14
shape 1-16
ion source
assembly 3-37
block 3-21, 3-39, 3-41, 3-43
I-4
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
filament 3-41, 3-43
filament assembly 3-42
lens assembly 3-39, 3-43
lenses 3-21
PCB 3-39, 3-41, 3-43
schematics 1-23
springs 3-39
ion trajectory 1-14
ion volume
alignment arrow 3-30
cleaning 3-21
key thumbscrew 3-41
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
maintenance 3-1
Power LED 2-9, 2-12
power panel 1-6, 1-33
Reset button 2-12
System LED 2-10, 2-12
Thermo Fisher Scientific
Index: M–P
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 2-3
lower oven 3-56
M
magnet support 3-21
magnet yoke 3-39
magnets, in ion source 3-21, 3-39
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 ETD Module 1-9
for instrument 1-9
mains supply, for the ETD Module 1-9
maintenance
API source 1-12
cooling circuit 3-58
linear trap 3-1
procedures 3-2
reagent ion source 3-20
recirculating chiller 3-58
vacuum system 3-4
mass accuracy 1-4
mass range 1-4
Material Safety Data Sheet 3-48
micro controller 1-52–1-53
MS/MS 1-4
MSDS 3-48
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 1-13
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 1-13
lenses 1-14
measuring principle 1-14–1-15
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 3-34
power
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
I-5
Index: Q–S
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 1-58
location 1-46, 1-58
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
quadrupole mass filter 1-21
quality, of vacuum 1-53
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 2-3
recirculating chiller
condenser filter 3-58
connections 1-4
description 1-43
fluid bag filter 3-58
maintenance 3-58
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
chiller operating fluid 3-58
filter cartridge 3-58
inlet valve components 3-45
ion source filament 3-42
operating fluid reservoir of turbopumps 3-11
reagent vials 3-48
turbopump operating fluid 3-11
reservoir, of recirculating chiller 3-58
resetting
instrument 2-12
system parameters 2-13
tune and calibration parameters 2-13
resolution, of instrument 1-4
restrictor
oven cover 3-55
oven heater 1-26
RF CLT main board 1-66
RF off & feedback board 1-59, 1-64
RF output control 1-60
RF voltage supply 1-63
right side panel, of instrument 1-3
R
S
Q
reagent heaters 1-22–1-23, 1-26–1-28
reagent inlet cover 3-55
reagent inlet source
heating unit 3-51
location 3-52
reagent ion source
cleaning frequency 3-13
description 1-28–1-29
flow restrictors 3-54
maintenance 3-20
I-6
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
safety
features 1-25
interlock switch 2-10
problem 3-54
sample inlet aperture 3-41
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
Thermo Fisher Scientific
Index: T–U
sheath gas 1-37
shutdown 1-57, 2-7, 2-9
signal communication 1-45
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 3-39, 3-41
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 2-3
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
Orbitrap Elite 1-2
T
temperature
analyzer chamber 1-62
control 1-17
differential 1-17
monitoring 3-51
Thermo Fisher Scientific
sensor 3-41
temperature controller board
diagnostic LEDs 1-63
function 1-17
layout 1-62
location 1-59, 1-62
thermoelectric elements 1-17
thumbscrews 3-37, 3-39
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 3-37
heater 1-26
inlet 3-56
location 1-23
transfer multipole 1-19–1-21, 1-32
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
HiPace 300 1-30, 1-37, 1-42
HiPace 80 1-30, 1-37, 1-42
linear trap 1-32, 1-35
maintenance 3-11
TMP 1 1-30–1-31
TMP 2 1-30–1-32
TMP 3 1-31–1-32
TMP 4 1-31
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) 2-3
upper control panel 1-6–1-7
user maintenance 3-1–3-2, A-1
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
I-7
Index: V–X
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
right instrument side 1-32
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
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
Orbitrap Velos Pro Hardware Manual (P/N 1288290, Revision A)
ventilation, in the laboratory 1-38
venting pressure 1-40
venting, the system 2-3, 3-19
vial heaters
cover 3-51–3-52
location 3-53, 3-56
ribs 3-53
vial holder 3-52–3-53
vial temperature 1-28
voltage sags 1-10
W
water
chiller 1-4, 3-58
filter 1-42, 3-58
hoses 1-43
ports 1-10
temperature 1-43
water cooler, for TMP 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.thermoscientific.com
Part of Thermo Fisher Scientific
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