Thermo Scientific LTQ XL User manual

For Research Use Only
Not for use in Diagnostic Procedures
LTQ XL ®
Getting Started
97355-97042 Revision A June 2006

Technical information contained in this publication is for reference purposes only and is subject to change without
notice. Every effort has been made to supply complete and accurate information; however, Thermo Electron
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result from any use of this manual or the information contained therein (even if this information is properly
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This publication is not part of the Agreement of Sale between Thermo Electron Corporation and the purchaser of
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System Configurations and Specifications supersede all previous information and are subject to change
without notice.
© 2004 Thermo Electron Corporation. All rights reserved.
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All other trademarks are the property of Thermo Electron Corporation and its subsidiaries.
Printing History: Revision A printed June 2006.
Software Revision: LTQ 2.2, Xcalibur 2.2

Regulatory Compliance
Thermo Electron San Jose performs complete testing and evaluation of its products to ensure full compliance
with applicable domestic and international regulations. When the system is delivered to you, it meets all
pertinent electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC
• EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with Low Voltage Directive EN 61010-1:2001.
Changes that you make to your system may void compliance with one or more of these EMC and safety
standards. Changes to your system include replacing a part or adding components, options, or peripherals not
specifically authorized and qualified by Thermo Electron. To ensure continued compliance with EMC and
safety standards, replacement parts and additional components, options, and peripherals must be ordered
from Thermo Electron or one of its authorized representatives.
EN 55011 1999 EN 61000-4-3 2002 EN 55011 1998
IEC 61000-4-3 A1-1998
EN 61000-3-2 1995, A1; 1998,
A2; 1998, A14;
2000
EN 61000-4-4
IEC 61000-4-4
1995, A1; 2001, A2;
2001;
A2-1995
EN 61000-3-2 1995, A1; 1998,
A2; 1998, A14;
2000
EN 61000-3-3 1998 EN 61000-4-5 1995, A1; 2001 EN 61000-3-3 1998
IEC 61000-4-5 2005
EN 61326-1 1998, A3 EN 61000-4-6 1996, A1; 2001 EN 61326-1 1998
IEC 61000-4-6 2004
EN 61000-4-2 2000 EN 61000-4-11 1994, A1; 2001 EN 61000-4-2 2000
IEC 61000-4-2 2001 IEC 61000-4-11 2001-03
FCC Class A,
CFR 47 Part 18
2005 CISPR 11 1999, A1; 1999, A2;
2002

FCC Compliance Statement
Notice on Lifting and Handling of
Thermo Electron San Jose Instruments
For your safety, and in compliance with international regulations, the physical handling of this
Thermo Electron San Jose 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 Electron San Jose Instruments
In compliance with international regulations: If this instrument is used in a manner not specified by
Thermo Electron San Jose, the protection provided by the instrument could be impaired.
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.

WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie
2002/96/EC erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet:
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WEEE Compliance
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Electronic Equipment (WEEE) Directive 2002/96/EC. It is marked with the following
symbol:
Thermo Electron has contracted with one or more recycling/disposal companies in each
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Thermo Electron Corporation LTQ XL Getting Started vii
Preface .............................................................................................xi
About This Guide ......................................................................xi
Related Documentation .............................................................xi
Safety and Special Notices..........................................................xi
Contacting Us...........................................................................xii
Assistance...............................................................................xii
Changes to the Manual and Online Help...............................xii
Chapter 1 Introduction..........................................................................................1
Why Use the LTQ XL MS Detector?..........................................2
Which MS Detector Technique—ESI or APCI—Is Better for
Analyzing My Samples?............................................................4
Using ESI/MS..........................................................................4
Using APCI/MS.......................................................................5
Should I Use Sheath, Auxiliary, and/or Sweep Gases?..................7
How Can I Introduce My Samples into the MS Detector?..........8
What Types of Buffers Should I Use? What Types Should I
Avoid?....................................................................................10
How Should I Set Up the MS Detector for Various LC Flow
Rates?.....................................................................................11
What is Tuning and Calibration of the MS Detector All About?...
13
What Types of Experiments Can I Perform with the LTQ XL MS
Detector?................................................................................16
General MS or MSn Experiments ..........................................16
Data-Dependent Experiments................................................17
Ion Mapping Experiments .....................................................20
Ion Tree Experiments.............................................................23
Chapter 2 Setting Up the Ion Source for Tuning and Calibrating the MS
Detector27
Placing the LC/MS System in Standby......................................28
Removing the APCI Probe........................................................29
Removing the Ion Max Ion Source Housing .............................33
Installing the Ion Sweep Cone...................................................34
Installing the Ion Max Ion Source Housing ..............................36
Installing the ESI Probe ............................................................39
Contents

Contents
viii LTQ XL Getting Started Thermo Electron Corporation
Chapter 3 Tuning and Calibrating Automatically in the ESI/MS Mode .... 43
Setting Up the Syringe Pump for Tuning and Calibration ........45
Setting Up the MS Detector in the Xcalibur Data System for
Tuning and Calibration .........................................................47
Testing the Operation of the MS Detector in the ESI/MS Mode..
52
Tuning the MS Detector Automatically in the ESI/MS Mode ..56
Saving Your ESI/MS Tune Method ..........................................60
Calibrating the MS Detector Automatically ..............................62
Cleaning the MS Detector after Tuning and Calibrating...........65
Chapter 4 Tuning with Your Analyte in LC/ESI/MS Mode........................... 69
Setting Up to Introduce Sample by Syringe Pump into Solvent
Flow from an LC ...................................................................71
Setting Up to Tune the MS Detector with Your Analyte...........74
Optimizing the MS Detector Tune Automatically with Your
Analyte...................................................................................77
Saving the ESI/MS Tune Method.............................................81
Chapter 5 Acquiring ESI Sample Data Using the Tune Plus Window ...... 83
Setting Up to Acquire MS/MS Data in the Full Scan Type.......84
Optimizing the Isolation Width and Setting Up to Optimize
the Collision Energy............................................................84
Optimizing the Collision Energy Automatically for an MS/MS
Experiment .........................................................................89
Setting Up to Introduce Sample by Loop Injection into Solvent
Flow from an LC ...................................................................92
Acquiring MS Data in the SIM Scan.........................................94
Chapter 6 Setting Up the Ion Source for Acquiring Data in APCI/MS/MS
Mode101
Removing the ESI Probe .........................................................102
Removing the Ion Max Ion Source Housing ...........................105
Removing the Ion Sweep Cone ...............................................106
Installing the Corona Needle ..................................................107
Installing the Ion Max Ion Source Housing ............................108
Installing the APCI Probe .......................................................111
Chapter 7 Optimizing the MS Detector with Your Analyte in APCI/MS
Mode115
Setting Up the Inlet for Tuning Using High-Flow Infusion....116
Setting Up the MS Detector for APCI/MS Operation ............119

Contents
Thermo Electron Corporation LTQ XL Getting Started ix
Optimizing the Tune of the MS Detector Automatically in
APCI/MS Mode...................................................................123
Saving the APCI/MS Tune Method........................................126
Cleaning the MS Detector after Tuning in APCI Mode..........128
Chapter 8 Acquiring APCI Sample Data Using the Tune Plus Window..131
Setting Up to Introduce Sample by Loop Injection into Solvent
Flow from an LC .................................................................132
Acquiring APCI Data in the SIM Scan Mode .........................134
Appendix A Sample Formulations......................................................................139
Caffeine, MRFA, and Ultramark 1621 Stock Solutions ..........140
Stock Solution: Caffeine.......................................................141
Stock Solution: MRFA.........................................................142
Stock Solution: Ultramark 1621 ..........................................142
ESI Calibration Solution: Caffeine, MRFA, Ultramark 1621..143
Reserpine ................................................................................144
Stock Solution: Reserpine ....................................................144
Reserpine Tuning Solution and Reserpine APCI Sample
Solution ............................................................................144
Appendix B LTQ XL High Mass Range Calibration .........................................147
High Mass Range Calibration Solution...................................148
Normal Mass Range Calibration .............................................149
Enter Normal Mass Range Data into Tune Plus .....................150
Tune on m/z 524.3 .................................................................152
High Mass Range Calibration Procedure.................................154
Notes ......................................................................................159
Index..................................................................................................161