Thermo Scientific ETD User manual

ETD Module
Getting Started Guide
for the LTQ XL and LTQ Velos MS Detectors
(compatible with LTQ Orbitrap XL and LTQ Orbitrap Velos)
98000-97003 Revision C December 2010

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Release history: Revision A, March 2008; Revision B, January 2009; Revision C, December 2010
Software version: Xcalibur 2.1.0 or earlier, LTQ Series 2.6.0 SP2 or earlier
For Research Use Only. Not for use in diagnostic procedures.

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.
LTQ XL/ETD System (January 2007)
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
EN 61000-3-2: 1995, A1: 1998, A2: 1998, A14: 2000 EN 61000-4-4:1995, A1: 2000, A2:2001
EN 61000-3-3: 1995, A1:2001 EN 61000-4-5: 1995, A1: 2001
EN 61326-1: 1997, A1:1998, A2:2001, A3:2003 EN 61000-4-6: 2003
EN 61000-4-2: 2001 EN 61000-4-11: 1994, A1: 2001
EN 61000-4-3: 2002 CISPR 11: 1999, A1: 1999, A2: 2002
FCC Class A, CFR 47 Part 15: 2005

LTQ Velos/ETD System (November 2008)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
FCC Compliance Statement
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.
EN 61326-1: 2006 EN 61000-4-4: 2004
EN 55011: 2007 EN 61000-4-5: 2005
EN 61000-3-2: 2006 EN 61000-4-6: 2007
EN 61000-3-3: 2005 EN 61000-4-11: 2004
EN 61000-4-2: 2001 FCC Part 15: 2007
EN 61000-4-3: 2006
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.

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Notice on the Susceptibility
to Electromagnetic Transmissions
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For manufacturing location, see the label on the instrument.

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disponibles sur www.thermo.com/WEEERoHS.

Thermo Scientific MS/ETD System Getting Started Guide ix
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Electron Transfer Dissociation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Types of Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
LTQ XL and LTQ Velos Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ETD Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Tuning and Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Chapter 2 Setting Up the Xcalibur Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . . . .7
Adding the MS Detector to the Xcalibur Instrument Configuration . . . . . . . . . . 7
Specifying the Reagent Ion Source for the MS Detector . . . . . . . . . . . . . . . . . . 10
Chapter 3 Tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Opening the Tune Plus Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Tuning the Reagent Ion Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Automatic Tuning of the Reagent Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . 15
Manually Tuning the Reagent Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Semi-Automatically Tuning the Reagent Ion Optics . . . . . . . . . . . . . . . . . . . 22
Viewing the Reagent Ion Optics Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Saving the ETD Tune Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 4 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Before Operating the LTQ XL/ETD or LTQ Velos/ETD System. . . . . . . . . . . 25
Checking the System Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Checking the Vacuum Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Turning On the Reagent Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
After Operating the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Purging the Oil in the Fore Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Contents

Contents
xMS/ETD System Getting Started Guide Thermo Scientific
Chapter 5 Performing an ETD Infusion Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Viewing the Injection Reagent Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Troubleshooting an AGC Target Error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Obtaining an ETD Spectrum for Angiotensin I. . . . . . . . . . . . . . . . . . . . . . . . . 35
Optimizing the Reagent Ion Reaction Time . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Chapter 6 Running an Xcalibur Experiment by Using ETD. . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Nth Order Double Play (ETD) Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Data Dependent NL MS3Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Appendix A Fluoranthene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Appendix B Angiotensin I Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Thermo Fisher Scientific MS/ETD System Getting Started Guide xi
F
Figure 1. LTQ XL/ETD system New Method page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Figure 2. Thermo Foundation Instrument Configuration window . . . . . . . . . . . . . . . . . . 8
Figure 3. Thermo Foundation Instrument Configuration window with configured
devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Figure 4. LTQ XL Configuration dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure 5. LTQ Velos Configuration dialog box with the reagent ion source
configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Figure 6. LTQ Velos Configuration dialog box with the low vial temperature option
selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Figure 7. Tune Plus window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Figure 8. Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Figure 9. Spectrum displayed in Tune Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Figure 10. Automatic page in the Tune dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 11. Reagent Ion Optics dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 12. Manual page in the Tune dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 13. Graph view of the reagent ion source tuning in the Tune Plus window
for the LTQ XL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Figure 14. Semi-Automatic page in the Tune dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 15. Reagent Ion Optics dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 16. Ion Trap page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Figure 17. Reagent page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Figure 18. Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Figure 19. Fluoranthene radical anion mass spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Figure 20. Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Figure 21. Ion Trap page in the Injection Control dialog box . . . . . . . . . . . . . . . . . . . . . . 33
Figure 22. Reagent page in the Injection Control dialog box . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 23. Define Scan dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Figure 24. Activation Type list in the Define Scan dialog box . . . . . . . . . . . . . . . . . . . . . . 36
Figure 25. ETD MS/MS spectrum of Angiotensin I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Figure 26. Tune dialog box for ETD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Figure 27. Reagent Ion Reaction Time page in the Tune dialog box . . . . . . . . . . . . . . . . . 39
Figure 28. Xcalibur Roadmap view of the Home Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Figure 29. Instrument Setup window for Thermo EASY-nLC. . . . . . . . . . . . . . . . . . . . . . 43
Figure 30. New Method page for the LTQ XL/ETD system . . . . . . . . . . . . . . . . . . . . . . . 44
Figure 31. Nth Order Double Play dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Figure 32. Nth Order Double Play with ETD template. . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Figure 33. Data Dependent Settings dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Figure 34. Activation parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Figures

Figures
xii MS/ETD System Getting Started Guide Thermo Fisher Scientific
Figure 35. Data Dependent NL MS3 dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Figure 36. Neutral loss masses table example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Figure 37. Data Dependent NL MS3 template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Figure 38. ETD Reagent (fluoranthene radical anion) generation from fluoranthene . . . . . 53

Thermo Scientific MS/ETD System Getting Started Guide xiii
P
Preface
The ETD Module Getting Started Guide provides information about how to set up, calibrate,
and tune the LTQ XL™/ETD or LTQ Velos™/ETD system and how to acquire electron
transfer dissociation (ETD) data.
This guide uses a shorter description for navigating Microsoft™ Windows™ and the Xcalibur™
data system. For example:
• Long method is “On the To o l s menu, click Options.”
• Short method is “Choose Tools > Options.”
To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the link below.
Thank you in advance for your help.
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the following documentation for
the LTQ XL/ETD and LTQ Velos/ETD systems:
• A printed copy of the Safety and Regulatory Guide
The Safety and Regulatory Guide contains important safety information about Thermo
Scientific mass spectrometry and liquid chromatography systems. This document is
shipped with every Thermo Scientific mass spectrometer and liquid chromatography
device.
• PDF files of the documents in Table 1 that you can access from the data system computer.

Preface
xiv MS/ETD System Getting Started Guide Thermo Scientific
To access the manuals for the mass spectrometer, from the Microsoft Windows taskbar,
choose Start > Programs > Thermo Instruments > LTQ > Manuals > model, where model is
your specific LTQ Series model, and then click the PDF you want to view.
The software also provides Help. To access the Help, choose Help from the menu bar or click
the Help ( ) button on the toolbar.
Safety and Special Notices
Ensure that you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes, as follows:
Safety and special notices include the following:
Table 2 lists the Caution statements that appear in the MS/ETD System Getting Started Guide.
Table 1. LTQ XL/ETD and LTQ Velos/ETD system documentation
Model Related documents
LTQ XL and LTQ Velos LTQ Series Preinstallation Requirements Guide
LTQ Series Getting Connected Guide
LTQ Series Quick Reference Guides
ETD module ETD Module Hardware Manual
Note For Xcalibur data system version 2.0.7 or earlier, choose Start > Programs >
Xcalibur > Manuals > LTQ > model.
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION
notice is accompanied by an appropriate CAUTION symbol.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.

Preface
Thermo Scientific MS/ETD System Getting Started Guide xv
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
To contact Technical Support
Find software updates and utilities to download at mssupport.thermo.com.
To contact Customer Service for ordering information
To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
Table 2. Caution symbols and their meanings
Symbol Meaning
General Hazard: A hazard is present that is not included in the
following categories. This symbol also appears on the instrument.
Refer to the instructions in the instrument manual for details on the
hazard.
Chemical: Hazardous chemicals might be present in the instrument.
Wear gloves when handling carcinogenic, corrosive, irritant,
mutagenic, or toxic chemicals. Use only approved containers and
procedures for disposing of waste oil.
Eye Hazard: Eye damage could occur from splattered chemicals or
airborne particles. Wear safety glasses when handling chemicals or
servicing the instrument.
Phone [phone]
Fax [phone]
E-mail [e-mail]
Knowledge base www.thermokb.com
Phone [phone]
Fax [phone]
E-mail [e-mail]
Web site www.thermo.com/ms

Preface
xvi MS/ETD System Getting Started Guide Thermo Scientific
To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[e-mail].

Thermo Scientific MS/ETD System Getting Started Guide 1
1
Introduction
The LTQ XL/ETD and LTQ Velos/ETD systems are members of the Thermo Scientific
family of mass spectrometer (MS) detectors, and consist of an ETD module installed at the
back of an LTQ XL or LTQ Velos MS detector. With the LTQ XL/ETD or LTQ Velos/ETD
system you can perform electron transfer dissociation (ETD) mass spectroscopy on analytes.
The LTQ XL and LTQ Velos MS detectors are advanced analytical instruments that include
an atmospheric pressure ionization (API) source, a divert/inject valve, a linear ion trap, a
syringe pump, and the Xcalibur data system.
The MS/ETD System is a source of fluoranthene reagent ions that react with analyte
molecules in the linear ion trap of the LTQ XL or LTQ Velos MS detector. The ETD module
contains two reagent vials, chemical ionization (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
which prevents the contents of the reagent vials from being expelled into the laboratory
atmosphere.
The nitrogen gas serves two functions in the ETD process. It is both a carrier gas and a CI
vehicle. As a carrier gas, the nitrogen sweeps the reagent from the vial to the ion source where
reagent radical anions are formed.
As a CI vehicle, the nitrogen gas collides with 70eV electrons from the filament in the ion
volume. These 70eV electrons from the filament knock electrons from the nitrogen
molecules, creating nitrogen ions. The secondary electrons resulting from these collisions have
near thermal kinetic energies. The fluoranthene captures these thermal electrons to form
reagent radical anions. The ETD optics transport the reagent radical anions to the linear ion
trap where they react with the analyte.
•Electron Transfer Dissociation
•Types of Experiments
•Tuning and Calibration
•Diagnostics

1Introduction
Electron Transfer Dissociation
2MS/ETD System Getting Started Guide Thermo Scientific
Electron Transfer Dissociation
ETD provides peptide dissociation by transferring electrons to positively charged peptides,
leading 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.
Types of Experiments
The New Method page of the Instrument Setup window for the LTQ XL (Figure 1) or
LTQ Velos MS detector has buttons for the various types of experiment templates. Open the
template for a particular experiment type, enter the parameters for the experiment, and then
save the entries as part of an Xcalibur instrument method.
The New Method page has two experiment categories:
•LTQ XL and LTQ Velos Experiment Types
•ETD Experiment Types

1 Introduction
Types of Experiments
Thermo Scientific MS/ETD System Getting Started Guide 3
Figure 1. LTQ XL/ETD system New Method page

1Introduction
Types of Experiments
4MS/ETD System Getting Started Guide Thermo Scientific
LTQ XL and LTQ Velos Experiment Types
As described in the LTQ Series Getting Started Guide, the experiment templates available on all
LTQ XL and LTQ Velos mass spectrometers are as follows:
• General MS or MSnexperiment
• Data-dependent experiments:
– Data Dependent MS/MS
– Data Dependent Triple Play
–NthOrderDoublePlay
–FAIMSNthOrderDoublePlay
–NthOrderTriplePlay
– Data Dependent NL MS3
– Data Dependent product MS3
– Data Dependent Zoom Map
• Data Dependent Ion Tree
• Ion Mapping
ETD Experiment Types
With the addition of the ETD module to the LTQ XL or LTQ Velos MS detector, two other
experiment templates are available:
• Nth Order Double Play (ETD)—This experiment is useful as a survey experiment when
you cannot determine whether the CID or ETD mode of dissociation works best. For
example, CID works best for dissociating doubly-charged ions while ETD works best for
ions of a higher charge state.
• Data Dependent NL MS3 (ETD)—Repeating the MS/MS experiment by using ETD
dissociation might make it easier to identify sites of the neutral loss (modification). ETD
dissociation is also useful when there are multiple sites of modification.
For additional information, see Chapter 6, “Running an Xcalibur Experiment by Using
ETD.”