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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The contents of this document are subject to change without notice. All technical information in this
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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.

Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
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.
For manufacturing location, see the label on the instrument.

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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