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
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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
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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
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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,
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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
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Notice on Lifting and Handling of
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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.
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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.

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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

Thermo Electron Corporation LTQ XL Getting Started xi
Preface
About This Guide Welcome to the Thermo Electron, LTQ XL™ system. The LTQ XL is a
member of the Thermo family of MS detectors.
This LTQ XL Getting Started manual provides information on how to set up,
calibrate, and tune the LTQ XL MS detector,and how to acquire LC/MS
data. All of these procedures can be performed from the Xcalibur®Tune Plus
window.
To perform analyses in ESI mode, see Chapters 2, 3, 4, and 5. To perform
analyses in APCI mode, see Chapters 2, 3, 6, 7, and 8.
Related
Documentation
In addition to this guide, Thermo Electron provides the following
documents for the LTQ XL system:
• LTQ XL Preinstallation Guide
• LTQ XL Getting Connected
• LTQ XL Hardware Manual
Help is also available from within the software.
Safety and Special
Notices
Make sure you follow the precautionary statements presented in this guide.
The safety and other special notices appear in boxes.
Safety and special notices include the following:
CAUTION Highlights laser-related hazards to human beings. It includes
information specific to the class of laser involved. Each DANGER notice
is accompanied by the international laser radiation symbol.
CAUTION Highlights hazards to humans, property, or the environment.
Each CAUTION notice is accompanied by an appropriate CAUTION
symbol.

Preface
Contacting Us
xii LTQ XL Getting Started Thermo Electron Corporation
Contacting Us There are several ways to contact Thermo Electron.
Assistance For new product updates, technical support, and ordering information,
contact us in one of the following ways:
Visit Us on the Web
www.thermo.com/finnigan
Contact Technical Support
Phone: [phone]
Fax: [phone]
[email protected]
Contact Customer Service
In the US and Canada for ordering information:
Phone: [phone]
Fax: [phone]
International contacts for ordering information:
Visit www.thermo.com/finnigan for the current listing,
Changes to the Manual
and Online Help
To suggest changes to this guide or to the Help, use either of the following
methods:
• Fill out a reader survey online at www.thermo.com/lcms-techpubs
• Send an e-mail message to the Technical Publications Editor at
[email protected]
IMPORTANT Highlights information necessary to avoid damage to
software, loss of data, invalid test results, or information critical for
optimal performance of the system.
Note Highlights information of general interest.
Note Helpful information that can make a task easier.

Thermo Electron Corporation LTQ XL Getting Started 1
Chapter 1 Introduction
The LTQ XL™ is a member of the Thermo family of MS detectors. The
LTQ XL MS detector is an advanced analytical instrument that includes a
syringe pump, a divert/inject valve, an atmospheric pressure ionization
(API) source, an MS detector, and the Xcalibur data system. In a typical
analysis, a sample can be introduced in any one of the following ways:
• Using the syringe pump (direct infusion)
• Using the inject valve fitted with a loop and an LC pump (flow injection
analysis)
• Using a valve and an LC system fitted with a column (LC/MS)
In analysis by LC/MS, a sample is injected onto an LC column. The sample
is then separated into its various components. The components elute from
the LC column and pass into the MS detector where they are analyzed.
Analysis by direct infusion or flow injection provides no chromatographic
separation of components in the sample before it passes into the MS
detector. The data from the MS detector is then stored and processed by the
Xcalibur data system.
This introduction answers the following questions:
•Why Use the LTQ XL MS Detector?
•Which MS Detector Technique—ESI or APCI—Is Better for Analyzing
My Samples?
•How Can I Introduce My Samples into the MS Detector?
•What Types of Buffers Should I Use? What Types Should I Avoid?
•How Should I Set Up the MS Detector for Various LC Flow Rates?
•What is Tuning and Calibration of the MS Detector All About?
•What Types of Experiments Can I Perform with the LTQ XL MS
Detector?

1Introduction
Why Use the LTQ XL MS Detector?
2LTQ XL Getting Started Thermo Electron Corporation
Why Use the LTQ XL
MS Detector?
The attribute that sets the LTQ XL MS detector apart from other LC
detectors is the high level of analytical specificity that it provides. The LTQ
XL MS detector can provide multiple levels of analysis. Each level of analysis
adds a new dimension of specificity for positive compound identification.
The various levels of analysis are as follows:
• Chromatographic separation and compound detection (non MS
technique utilizing chromatographic retention time)
• Mass analysis (molecular mass information)
• Two-stage mass analysis, MS/MS (structural information)
• Multiple MS-MS mass analysis, MSn(structural information)
• ZoomScan™ analysis (charge state information)
Chromatographic separation and compound detection can be obtained by
all LC/detector systems. Retention time alone, however, does not positively
identify a compound because many compounds can have the same retention
time under the same experimental conditions. In addition, even if a
compound is identified correctly by retention time, quantitation results can
be in error because other compounds in the sample might co-elute with the
compound of interest.
Single stage mass analysis allows for the identification of analytes of interest.
Atmospheric pressure ionization typically produces mass spectra that
provide molecular mass information.
Two-stage mass analysis allows for even more positive compound
identification. MS/MS analysis monitors how a parent ion fragments when
exposed to an additional stage of ionization. There are two types of MS/MS
analysis: Full Scan MS/MS and Selective Reaction Monitoring (SRM). Full
Scan MS/MS monitors the production of all product ion from a specific
parent ion. SRM MS/MS analysis monitors a specific reaction path: the
production of a specific product ion from a specific parent ion. Using
MS/MS analysis, you can easily quantitate target analytes in complex
matrices such as plant or animal tissue, plasma, urine, groundwater, or soil.
Because of the specificity of MS/MS measurements and the ability to
eliminate interferences by an initial mass selection stage, quantitative target
compound analysis is easily accomplished using the LTQ XL MS detector.
Multiple MS/MS mass analysis provides a unique capability to obtain
structural information that can be useful in structure elucidation of
metabolites, natural products, and sugars. MSntechniques on the LTQ XL
MS detector allow for stepwise fragmentation pathways, making
interpretation of MSnspectra relatively straightforward. The LTQ XL MS

1 Introduction
Why Use the LTQ XL MS Detector?
Thermo Electron Corporation LTQ XL Getting Started 3
detector has several advanced features that make its MSncapabilities
extremely powerful for qualitative analysis. (See “What Types of
Experiments Can I Perform with the LTQ XL MS Detector?” on page 16.)
ZoomScan analysis provides information about the charge state of one or
more mass ions of interest. ZoomScan data is collected by using slower scans
at higher resolution. This allows for unambiguous determination of charge
state, which in turn allows for the correct determination of molecular mass.
In addition to the aforementioned levels of analysis, there is an additional
technique called Wideband Activation. The Wideband Activation option
allows the LTQ XL MS detector to apply collision energy to ions during
MS/MS fragmentation over a fixed mass range of 20 u. This option allows
the LTQ XL MS detector to apply collision energy to both the parent ion, as
well as to product ions created as a result of non-specific losses of water
(18 u) or ammonia (17 u), for example, or to product ions formed from the
loss of fragments less than 20 u. When you want enhanced structural
information and you do not want to perform MS3analysis with the LTQ XL
MS detector, choose the Wideband Activation option for qualitative
MS/MS. Because the collision energy is applied to a broad mass range,
signal sensitivity is somewhat reduced when you choose this option.
Therefore, increase the value of the collision energy (Activation Amplitude)
to compensate somewhat for the reduction of sensitivity.

1Introduction
Which MS Detector Technique—ESI or APCI—Is Better for Analyzing My Samples?
4LTQ XL Getting Started Thermo Electron Corporation
Which MS Detector
Technique—ESI or
APCI—Is Better for
Analyzing My
Samples?
The LTQ XL MS detector includes two standard atmospheric pressure
ionization source probes:1
• Electrospray ionization (ESI) probe
• Atmospheric pressure chemical ionization (APCI) probe
Typically, more polar compounds such as amines, peptides, and proteins are
best analyzed by ESI, and nonpolar compounds such as steroids are best
analyzed by APCI.
Sample ions can carry a single charge or multiple charges. The number of
charges carried by the sample ions depends on the structure of the analyte of
interest, the mobile phase, and the ionization mode.
Using ESI/MS The ESI mode typically produces mass spectra consisting of multiply
charged ions (for proteins and peptides) depending on the structure of the
analyte and the solvent. For example, the resulting mass spectrum of a
higher molecular mass protein or peptide typically consists of a distribution
of multiply charged analyte ions. The resulting mass spectrum can be
mathematically manipulated to determine the molecular mass of the sample.
The ESI mode transfers ions in solution into the gas phase. Many samples
that previously were not suitable for mass analysis (for example, heat-labile
compounds or high molecular mass compounds) can be analyzed by ESI.
ESI can be used to analyze any polar compound that makes a preformed ion
in solution. The term preformed ion can include adduct ions. For example,
polyethylene glycols can be analyzed from a solution containing ammonium
acetate, because of adduct formation between the NH4+ions in the solution
and oxygen atoms in the polymer. With ESI, the range of molecular masses
that can be analyzed by the LTQ XL MS detector is greater than 100,000 u,
due to multiple charging. ESI is especially useful for the mass analysis of
polar compounds, which include: biological polymers (for example,
proteins, peptides, glycoproteins, and nucleotides); pharmaceuticals and
their metabolites; and industrial polymers.
You can use the ESI mode in either positive or negative ion polarity mode.
The ion polarity mode is determined by the polarity of the preformed ions
in solution: Acidic molecules form negative ions in high pH solution, and
basic molecules form positive ions in low pH solution. A positively charged
ESI needle is used to generate positive ions and a negatively charged needle
is used to generate negative ions.
1Optional ionization sources [atmospheric photo ionization (APPI), atmospheric pressure matrix
assisted laser desorption ionization (AP MALDI), and nanospray] are also available.

1 Introduction
Which MS Detector Technique—ESI or APCI—Is Better for Analyzing My Samples?
Thermo Electron Corporation LTQ XL Getting Started 5
You can vary the flow rate from the LC into the MS detector over a range
from 1 μL/min to 1000 μL/min. See Tabl e 3 . (In ESI, the buffer and the
buffer strength both have a noticeable effect on sensitivity. Therefore, it is
important to choose these variables correctly.) In the case of higher
molecular mass proteins or peptides, the resulting mass spectrum consists
typically of a series of peaks corresponding to a distribution of multiply
charged analyte ions.
The ESI process is affected by droplet size, surface charge, liquid surface
tension, solvent volatility, and ion solvation strength. Large droplets with
high surface tension, low volatility, strong ion solvation, low surface charge,
and high conductivity prevent good electrospray.
Mixed organic/aqueous solvent systems that include organic solvents such as
methanol, acetonitrile, and isopropyl alcohol are superior to water alone for
ESI. Volatile acids and bases are good, but salts above 10 mM are not
recommended. Strong mineral acids and bases are extremely detrimental to
the instrument.
The rules for a good electrospray are as follows:
• Keep non-volatile salts and buffers out of the solvent system. For
example, avoid the use of salts containing sodium or potassium and
avoid the use of phosphates. If necessary, use ammonium salts instead.
• Use organic/aqueous solvent systems and volatile acids and bases.
• If possible, optimize the pH of the solvent system for your analyte of
interest. For example, if your analyte of interest contains a primary or
secondary amine, your mobile phase should be slightly acidic
(pH 2 to 5). The acid pH tends to keep positive ions in solution.
Using APCI/MS Like ESI, APCI is a soft ionization technique. APCI provides molecular
mass information for compounds of medium polarity that have some
volatility. APCI is typically used to analyze small molecules with molecular
masses up to about 2000 Da.
APCI is a gas phase ionization technique. Therefore, the gas phase acidities
and basicities of the analyte and solvent vapor play an important role in the
APCI process.
APCI is a very robust ionization technique. It is not affected by minor
changes in most variables such as changes in buffer or buffer strength. The
rate of solvent flowing from the LC into the MS detector in APCI mode is
typically high (between 0.2 and 2 mL/min). See Table 3.

1Introduction
Which MS Detector Technique—ESI or APCI—Is Better for Analyzing My Samples?
6LTQ XL Getting Started Thermo Electron Corporation
You can use APCI in positive or negative ion polarity mode. For most
molecules, the positive-ion mode produces a stronger ion current. This is
especially true for molecules with one or more basic nitrogen (or other basic)
atoms. Molecules which generally produce strong negative ions, with acidic
sites such as carboxylic acids and acid alcohols, are an exception to this
general rule.
Although, in general, fewer negative ions are produced than positive ions,
negative ion polarity can be more specific. This is because the negative ion
polarity mode sometimes generates less chemical noise than does the
positive mode. Thus, the signal-to-noise ratio might be better in the
negative ion mode than in the positive ion mode.

1 Introduction
Should I Use Sheath, Auxiliary, and/or Sweep Gases?
Thermo Electron Corporation LTQ XL Getting Started 7
Should I Use Sheath,
Auxiliary, and/or
Sweep Gases?
Nitrogen gas can be applied to the system using any combination of the
three gas sources: Auxiliary gas, Sweep gas, and/or Sheath gas. When Sheath
gas is used, nitrogen is applied as an inner coaxial gas (when used in tandem
with Auxiliary gas), helping to nebulize the sample solution into a fine mist
as the sample solution exits the ESI or APCI nozzle. (Sheath gas is not used
with the NSI source.) When Auxiliary gas is being used, nitrogen flows
through the ion source nozzle, the vapor plume is affected; the spray is
focused and desolvation is improved. When Sweep gas is used, the nitrogen
flows out from behind the sweep cone and can result in solvent declustering
and adduct reduction.
When you are analyzing complex matrices such as plasma or nonvolatile salt
buffers, Sweep gas is required for ruggedness. In full-scan MS or data
dependent scan experiments, the signal-to-noise ratio can be improved by
application of Sweep gas. In some cases, signal intensity can be increased by
using Auxiliary gas, particularly for higher LC flow rates.
All analyses are analyte dependent and require separate optimization with
Sheath gas, Sweep gas, and Auxiliary gas to determine which combination
will yield optimum performance. It is especially important to optimize with
each gas independently before you perform experiments using MSn
techniques and before you perform any quantitative analysis experiments
because optimum results could be achieved with any combination of
Sheath, Sweep, and/or Auxiliary gas. See Tabl e 2 and Table 3 for additional
information on using supplemental gas flows.

1Introduction
How Can I Introduce My Samples into the MS Detector?
8LTQ XL Getting Started Thermo Electron Corporation
How Can I Introduce
My Samples into the
MS Detector?
You can introduce your samples into the MS detector in a variety of ways.
Refer to Tab l e 1.
The syringe pump is often used to introduce calibration solution for
automatic tuning and calibrating in ESI mode. You can also use this
technique to introduce a solution of pure analyte at a steady rate in ESI
mode, for example, for determining the structure of an unknown
compound.
You can also use a Tee union to direct samples from the syringe pump into
an LC flow (without a column), which then enters the MS detector. This
technique is used to introduce sample at a steady rate and at higher solvent
flow rates; it is used especially for tuning in ESI or APCI on an analyte of
interest. You can also use this technique to introduce a solution of pure
analyte at a steady rate in ESI or APCI.
You can introduce samples from a syringe into the loop of the injector valve.
You can then use the divert valve to introduce the sample into an LC flow,
which then enters the MS detector. This technique is used in ESI or APCI
to introduce pure analytes into the MS detector in a slug. It is useful when
you have a limited quantity of pure analyte.
You can also use an LC autosampler to introduce samples into an LC flow.
This technique is also used in ESI or APCI to introduce a slug of pure
analyte into the LC flow and then into the MS detector.
Finally, you can perform LC/MS experiments by using an LC autosampler
to introduce a mixture onto an LC column. This technique is used with ESI
or APCI to separate the analytes before they are introduced sequentially into
the MS detector.
You can refer to subsequent chapters in this manual and to LTQ XL Getting
Connected for plumbing diagrams and methods of sample introduction.
Table 1. Sample introduction techniques
Sample Introduction
Technique
Analytical
Technique Figure Reference
Syringe Pump
Flow
(no LC Flow)
Syringe pump* ESI automatic tuning
and calibrating
ESI analysis of a
pure analyte solution
LTQ XL Getting
Started
Figure 2-5