Table of Contents
Chapter 1. About This Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Conventions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Safety Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
How This Manual Is Organized . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
International Standards Certifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Federal Communications Commission Compliance. . . . . . . . . . . . . . . . . . . . . . . .4
Chapter 2. Introduction to the Q Trap LC/MS/MS System . . . . . . . . . . . . . . 5
Triple Quadrupole/Linear Ion Trap Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . .6
Principles of MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Principles of MS/MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Q Trap LC/MS/MS Enhanced Modes of Operation . . . . . . . . . . . . . . . . . . . . . . .10
Chapter 3. Hardware Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Data System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Sample Introduction System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
LC Pump or Syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Ion Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
TurboIonSpray Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Heated Nebulizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Source Exhaust System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Source Exhaust Venturi Gas Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Gas Connection Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Vacuum System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Vacuum Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
Vacuum Control System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
Ion Path Chamber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Mass Filter Rail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Quadrupoles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Mass Filters (Q1 and Q3). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Linear Ion Trap (LIT) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
RF-Only Quadrupoles (Q0 and Q2) and Stubbies . . . . . . . . . . . . . . . . . . . . . . . .36
Vacuum Feedthroughs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Collision Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
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Q Trap LC/MS/MS Hardware Manual
Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ion Detector and Signal Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Power Distribution Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
AC Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DC Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ARF Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The System Electronics Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
37
39
39
40
40
40
40
Chapter 4. Operating the Q Trap LC/MS/MS System. . . . . . . . . . . . . . . . . . 41
Work Process Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Setting Up Instrument-Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Setting Up Compound-Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Setting Up Source-Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Shutting Down and Powering Up the Q Trap LC/MS/MS System . . . . . . . . . . . . . .
Powering Up the Q Trap LC/MS/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . .
Instrument Warmup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Shutting Down the Q Trap LC/MS/MS System . . . . . . . . . . . . . . . . . . . . . . . . . .
Pumping Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Pump-Down Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Removing the Instrument Covers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Removing the Front Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Removing the Top Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Removing the Back Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Power Distribution Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Removing the TurboIonSpray Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Replacing the TurboIonSpray Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
41
42
42
43
43
44
44
44
46
46
48
48
49
50
51
51
52
Appendix A: Maintenance Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Q Trap LC/MS/MS System Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Appendix B: PPG Exact Mass Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Appendix C: Scan Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Appendix D: Consumables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Appendix E: Sample Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Small Molecules: EPI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Small Molecules: MS3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Large Molecules: Protein Identification—Tryptic Digest . . . . . . . . . . . . . . . . . . . . . 74
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
iv
1
About This Manual
The Q Trap LC/MS/MS Hardware Manual contains a description of the principles of mass
spectrometry and an overview of the Q Trap LC/MS/MS system. This manual provides
information about the hardware components included in the instrument. You will also find
instructions on how to start up and shut down the mass spectrometer, how to remove the
instrument covers, how to create sample experiments, and how to troubleshoot instrument
problems.
This manual is targeted to users who are familiar with mass spectrometry but are new to
the Q Trap LC/MS/MS system.
The Q Trap LC/MS/MS Hardware Manual is part of a set of manuals that includes a
standard set of service manuals (Schematics and BOMs, SQ/IQ/OQ, IPV), the
Q Trap LC/MS/MS Qualified Maintenance Person’s Manual, the Q Trap Site Planning
Guide, and related manuals (Safety Manual, Peripheral Devices Setup Manual, Analyst
1.3 Operator’s Manual).
Conventions
Within the scope of this manual, the following conventions are used:
WARNING! This symbol indicates a warning of potential injury or damage to the
instrument. You should read the warning and follow all precautions before
performing any operation described in the manual.
WARNING! This symbol indicates a warning of electrical shock hazard. You should
read the warning and follow all precautions before performing any operation
described in the manual. Failure to do so can result in serious injury.
WARNING! This symbol indicates a warning of biohazardous materials. You should
read the warning and follow all precautions before performing any operation
described in the manual.
1
About This Manual
Q Trap LC/MS/MS Hardware Manual
WARNING! This symbol indicates a warning of high temperatures. The probes and
source housing reach high temperatures. Do not remove the probe from the source
housing or the housing from the instrument while either is hot. Allow at least ten
minutes for it to cool.
CAUTION! Indicates an operation that may cause damage to the instrument if the
precautions are not followed.
Safety Considerations
There are a number of important safety considerations you need to review before using the
Q Trap LC/MS/MS system.
WARNING! All persons using the Q Trap LC/MS/MS ion source should be aware of
potential hazards.
Observe the following safety precautions when operating, maintaining, or servicing the
Q Trap LC/MS/MS system.
•
Do not override safety interlocks in the mass spectrometer.
•
The Q Trap LC/MS/MS system operates with high voltages. Please observe electrical
shock hazard safety precautions.
Additional operational information is available in the Analyst online Help or in the user
manuals. For detailed information relating to the Q Trap LC/MS/MS system, refer to the
following manuals:
•
Peripheral Devices Setup Manual
•
Q Trap LC/MS/MS TurboIonSpray Ion Source Manual
•
Q Trap APCI Heated Nebulizer Ion Source Manual
•
Q Trap Flow NanoSpray Ion Source Manual
•
Q Trap LC/MS/MS Qualified Maintenance Person’s Manual
Any person using an Applied Biosystems/MDS Sciex mass spectrometer should be fully
trained in its safe operation as well as in laboratory procedures. All warnings should be
followed implicitly as failure to do so could result in serious injury.
How This Manual Is Organized
The information provided in this manual is organized as follows:
Chapter 1: About This Manual
This chapter provides an explanation of the warning symbols in the manual, information
about where you can access additional technical support, and a list of international
standards the instrument complies with. Also included in the section is a description of the
information provided in each chapter of the manual.
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Q Trap LC/MS/MS Hardware Manual
About This Manual
Chapter 2: Introduction to the Q Trap LC/MS/MS System
This chapter provides an introduction to the Q Trap LC/MS/MS system. The section
includes an overview of liquid chromatography (LC), MS, MS/MS, and the linear ion trap
(LIT) functionality of the Q Trap LC/MS/MS system.
Chapter 3: Hardware Overview
This chapter provides information about the sample introduction system, gas and vacuum
panel, vacuum system, ion path chamber, and the electronics of the Q Trap LC/MS/MS
system.
Chapter 4: Operating the Q Trap LC/MS/MS system
This chapter provides procedures for powering up and shutting down the
Q Trap LC/MS/MS system.
Appendices
Appendix A: Maintenance Checklist
This section provides a list of the regular maintenance procedures you should complete.
Appendix B: PPG Exact Mass Table
This section provides the exact monoisotopic masses and charged species (positive and
negative) observed with the polypropylene glycol (PPG) calibration solutions.
Appendix C: Scan Parameters Settings
This section provides a list of the exact monoisotopic masses and charged species
(positive and negative) observed with the PPG calibration solutions and Agilent ES Mix.
Appendix D: Consumables
This section provides a list of consumable parts for the Q Trap LC/MS/MS system.
Appendix E: Sample Experiments
This section provides examples of experiments you can perform using the
Q Trap LC/MS/MS system.
Technical Support
Applied Biosystems/MDS Sciex and its representatives maintain a staff of fully-trained
service and technical specialists located throughout the world. They can answer questions
about the API instruments or any technical issues that may arise. For more information,
visit the Applied Biosystems/MDS Sciex Web site at:
http://www.appliedbiosystems.com
3
About This Manual
Q Trap LC/MS/MS Hardware Manual
International Standards Certifications
This instrument and its components have been certified by the following international
agencies. Applicable labels for these qualifications have been attached to the instrument.
Federal Communications Commission Compliance
This equipment has been tested and found to comply with the limits for a Class A digital
device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide
reasonable protection against harmful interference when the equipment is operated in a
commercial environment. This equipment generates, uses, and can radiate radio frequency
energy and, if not installed and used in accordance with the instruction manual, may cause
harmful interference to radio communications. Operation of this equipment in a residential
area is likely to cause harmful interference in which case the user will be required to
correct the interference at the user’s own expense. Changes or modifications not expressly
approved by the manufacturer could void your authority to operate the equipment.
International Compliance
The Q Trap LC/MS/MS system is in compliance with the following standards:
4
•
FCC Part 15, Subpart B, Class A
•
CISPR publication 11(1997) IEC Standard EN 55011 (1998) Class A
•
IEC EN61326-1: 1997
•
IEC EN61010-1: 1990
•
CE Certificate of Compliance is included with the instrument
2
Introduction to the
Q Trap LC/MS/MS System
The Q Trap LC/MS/MS system is a hybrid triple quadrupole linear ion trap (LIT) mass
spectrometer. The Q3 region can be operated as either a standard quadrupole mass
spectrometer or a linear ion trap mass spectrometer. The unique scan modes of both
configurations can be linked to provide more and higher quality data than either
instrument alone. For example, a precursor ion scan in Transmission mode can be used as
a survey scan in order to target specific ions to be used in an enhanced product ion scan (in
LIT mode). Conversion between the two modes of operation is rapid, since it involves
only the addition or removal of the resolving DC voltages.
The Q Trap LC/MS/MS system retains all of the traditional triple quadrupole scan types
such as:
•
Q1 MS (Q1)
•
Q1 Multiple Ion (Q1 MI)
•
Q3 MS (Q3)
•
Q3 Multiple Ion (Q3 MI)
•
Multiple Reaction Monitoring (MRM)
•
Precursor Ion (Prec) (This is not possible with a conventional ion trap.)
•
Product Ion (MS2)
•
Neutral Loss (NL)
When Q3 operates as an LIT mass spectrometer, a number of new advantages and
capabilities are available:
•
High sensitivity product ion scanning
•
Fast scanning (4000 amu per second)
•
High resolution capabilities at reduced scan speeds
•
MS/MS/MS capabilities
•
Reduced space charge effects
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Introduction to the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
In LIT mode, a pulse of ions is introduced into the ion trap. The main RF fields trap the
ions in the radial direction, while DC voltages applied to the lenses at both ends of Q3,
trap the ions axially. The trapped ions are allowed to cool for several milliseconds, then
the RF voltage is scanned in the presence of a low voltage auxiliary AC applied to the
rods. The ions ejected axially toward the detector are counted.
If you configure the mass spectrometer with Q1 operating as a standard quadrupole mass
spectrometer and Q3 operated as an LIT mass spectrometer, you can achieve the following
enhanced scan types:
•
Enhanced MS (EMS)
•
Enhanced Resolution (ER)
•
Enhanced Product Ion (EPI)
•
Enhanced Multi-Charge (EMC)
•
Time Delayed Fragmentation (TDF)
•
MS/MS/MS (MS3)
In LIT mode, a pulse of ions passes through Q1 operated as a conventional quadrupole
mass spectrometer to select the precursor ion of interest. The precursor ions are
accelerated into the pressurized Q2 to promote fragmentation. The fragment and residual
precursor ions are then trapped in the Q3 linear ion trap. The Q3 RF voltage is ramped and
the ions ejected toward the detector are reported. For more information about these
enhanced scans, see “Q Trap LC/MS/MS Enhanced Modes of Operation” on page 10.
Triple Quadrupole/Linear Ion Trap Mass
Spectrometer
The Q Trap LC/MS/MS system uses a TurboIonSpray, Heated Nebulizer, or Flow
Nanospray ion source to produce ions from liquid samples. The term LC/MS/MS, applied
to the triple quadrupole series, is a generic label for the combined analytical processes of
liquid separation and subsequent mass spectrometric analysis. The instrument is
configured to perform complex MS/MS and MS/MS/MS analysis. For less rigorous
analytical requirements, it can perform single MS (LC/MS) scans.
The Q Trap LC/MS/MS system allows all modes of MS/MS and MS/MS/MS operation
for full characterization of biopharmaceutical compounds and the specificity needed for
new drug development. For pharmaceutical and pharmacokinetic samples, MS/MS has the
sensitivity and specificity required to analyze hundreds of samples per day without
extensive sample preparation.
For peptides and proteins, molecular weights can be determined with accuracies better
than 0.01% at 200 kDa.
The major components of the Q Trap LC/MS/MS system are shown in the figure Q Trap
LC/MS/MS system components with pump on page 7.
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Q Trap LC/MS/MS Hardware Manual
Introduction to the Q Trap LC/MS/MS System
Q Trap LC/MS/MS system components with pump
Principles of MS
In Single Quadrupole mode, the Q Trap LC/MS/MS system separates ions representative
of the sample molecular components based on their m/z ratio. Ions of a unique m/z ratio
can be separated by the single mass filter quadrupole and counted to provide mass spectra
for the sample.
The mass filter quadrupole consists of four cylindrical rods mounted in a ceramic collar
surrounding the ion path. Fixing the ratio of RF to DC voltages applied to the quadrupole
rods determines the mass of the ions exiting the quadrupole.
Ions of a unique m/z ratio pass unobstructed through the quadrupole as a function of the
quadrupole power supply (QPS) voltages applied. Ions of different m/z ratios have
unstable oscillations that increase in amplitude until they collide with the quadrupole rods
and are removed from the ion stream.
As an example, a sample mixture containing three molecules, R, M, and N, is introduced
into the ion source. Soft ionization in the ion source generates R+, M+, and N+ ions
(quasi-molecular ions formed typically by attaching one or more protons in the Positive
mode, or by removing one or more protons or attaching an electron in the Negative mode).
Isolation of mixture R, M, and N
Additional structural information can sometimes be obtained by fragmenting the precursor
ion in a primary collision region between the orifice and the skimmer. This process is
often referred to as collision induced dissociation mass spectrometry (CID/MS).
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Introduction to the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
Isolation of product ions from a sample using the orifice-skimmer technique
The ions generated in the ion source are drawn through a curtain of dry inert gas into the
ion optics housed inside the vacuum chamber. The mass filter quadrupole in the vacuum
chamber selectively filters the ions based on their m/z ratio. The filtered ions are focused
to the detector. As ions collide with the detector, they produce a pulse of electrons. The
electron pulse is collected and converted to a digital signal to provide an ion count as a
function of ion mass. The acquired data is relayed to the computer where it can be
displayed as either full mass spectra, intensity of single or multiple ions versus time, or
total ion current versus time.
Principles of MS/MS
In Triple Quadrupole mode, the Q Trap LC/MS/MS system uses two identical mass filter
quadrupoles (Q1 and Q3) separated by a collision cell, which encloses an RF-only
quadrupole (Q2). The fundamental principle of MS/MS is illustrated in the figure
Isolation of product ions from a mixture of R, M and N on page 8.
As an example, a sample mixture containing three molecules, R, M and N, is introduced
into the ion source. Soft ionization in the ion source generates R+, M+, and N+ ions
(quasi-molecular ions formed typically by attaching one or more protons in the Positive
mode, or by removing one or more protons or attaching an electron in the Negative mode).
Isolation of product ions from a mixture of R, M and N
In a Product Ion scan, the first mass filter, Q1, separates or filters ions according to their
m/z ratio, and allows only one ion to enter the collision cell (M+). The M+ ion enters Q2
where it is fragmented by collision with neutral gas molecules in a process referred to as
collision activated dissociation (CAD). The fragment ions generated are then passed into
Q3 and filtered to provide a mass spectrum. The ions created by the source are referred to
as precursor ions, the collision products are referred to as product or fragment ions.
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Q Trap LC/MS/MS Hardware Manual
Introduction to the Q Trap LC/MS/MS System
In a Precursor Ion scan, the third quadrupole (Q3) is fixed to the fragment mass of interest
and the first quadrupole (Q1) is scanned over a range. The resulting mass spectrum
displays the masses of all the compounds that produced the specified fragment mass.
In a Neutral Loss scan, both quadrupoles (Q1 and Q3) are scanned with a constant mass
difference between them. The resulting mass spectrum displays the mass of the
compounds that have undergone the specified loss. This type of scan is useful in
identifying compounds from similar functional groups.
The fragment ions are filtered in Q3 before they are collected at the detector. As ions
collide with the detector, they produce a pulse of electrons. The pulse is converted to a
digital signal that is counted to provide an ion count. The acquired data is relayed to the
computer where it can be displayed as either full mass spectra, intensity of single or
multiple ions versus time, or total ion current versus time.
The technique of MS/MS is well suited to mixture analysis because the characteristic
fragment ion spectra can be obtained for each component in a mixture without interference
from the other components, assuming that the ions have a unique m/z ratio. This analysis
can also be used for targeted analysis by monitoring specific precursor/product ions with
Q1 and Q3 respectively while the sample is eluting. This type of analysis is more specific
than single MS, which only discriminates on the basis of molecular weight.
The MS/MS technique is well suited to structural elucidation studies. The same
fragmentation pattern that provides identification of a compound in a complex mixture can
also reveal pertinent information regarding the structure of all their precursors.
Additional structural information can sometimes be obtained by fragmenting the precursor
ion in a primary collision region between the sampling orifice skimmer. The fragment ions
(for example, a second generation fragment ion spectrum), provide structural information
on both the original precursor ions and the first generation fragment ions.
Isolation of second generation product ions from mixture M
The triple quadrupole instruments contain the same components as the single quadrupole
instruments with the addition of a second mass filter (Q3). The high-pressure region is the
same, but the high vacuum region contains the Q1 prefilter (stubbies) and the Q1 and Q3
mass filter quadrupoles that are separated by the collision cell. The collision cell is a
ceramic housing enclosing the Q2 RF-only quadrupole, which when pressurized with
CAD gas provides a local high-pressure region for ion fragmentation.
Ions pass through the same path as in the single quadrupole instrument until they reach the
Q2 RF-only quadrupole. The selected ions arrive at Q2, while those rejected eventually
collide with the rods and are lost.
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Introduction to the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
The Q2 RF-only quadrupole is separated from the Q1 and Q3 mass filters by the interquad
lenses IQ2 and IQ3 (or ST3, depending on the triple quadrupole series). The Q2 region has
no mass filtering capabilities; it operates in Total Ion mode. If no CAD gas is present to
fragment the sample ions, Q2 transports the ions directly into Q3. If CAD gas is present,
the ions that enter Q2 collide with the neutral CAD gas molecules. If pressurized, the
voltage drop between the entrance lenses and Q2 provides the ions with the energy to
induce fragmentation when the ions collide with CAD gas molecules. Through the
energetic collisions, the ion translational energy is converted into internal energy that
fractures bonds and causes ion fragmentation. After collision, the unfragmented precursor
ions and the fragmented ions are transported to Q3 where they are again filtered.
When operating in MS/MS mode, the Q3 mass filter is physically and functionally
identical to Q1. The ions, including a mixture of precursor and fragment ions, enter Q3
where they are filtered according to mass. In Single MS Operating mode (Q1 scan type),
Q3 acts as an ion transporter (like a Q0 or RF-only quadrupole) with no filtering action.
Terms used to describe this operation are Total Ion mode, RF-only mode, and AC-only
mode.
Q Trap LC/MS/MS Enhanced Modes of Operation
The Q Trap LC/MS/MS system has a number of enhanced modes of operation. A common
factor of the enhanced modes is that ions are trapped in the Q3 quadrupole region and then
scanned out to produce full spectrum data. Many spectra are rapidly collected in a short
period of time and are significantly more intense than spectra collected in a comparable
standard quadrupole mode of operation. The widths of the peaks in the spectra are usually
much narrower than peaks observed in the standard quadrupole mode.
During the collection phase, ions pass through the Q2 collision cell where CAD gas
focuses the ions into the Q3 region. The Q3 quadrupole is operated with only the main RF
voltage applied. Ions are prevented from passing through the Q3 quadrupole rod set and
are reflected back by an exit lens to which a DC barrier voltage is applied. After the fill
time elapses (a time defined by the user), a DC barrier voltage is applied to a Q3 entrance
lens (IQ3). This confines the collected ions in Q3 and stops further ions from entering. The
entrance and exit lens DC voltage barriers and the RF voltage applied to the quadrupole
rods confine the ions within Q3.
During the scan out phase, a potential of a few volts is applied to the exit lens to repel the
charged ions. An auxiliary AC frequency is applied to the Q3 quadrupole. The main RF
voltage amplitude is ramped from low to high values, which sequentially brings masses
into resonance with the auxiliary AC frequency. When ions are brought into resonance
with the AC frequency, they acquire enough axial velocity to overcome the exit lens
barrier and are axially ejected towards the mass spectrometer ion detector. Full spectra
data can be acquired from the ions collected in Q3 by rapidly scanning the main RF
voltage.
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Introduction to the Q Trap LC/MS/MS System
The enhanced modes of operation are:
•
Enhanced MS (EMS): Ions are transferred directly from the ion source and orifice
region to the Q3 quadrupole where they are collected. These ions are scanned out of
Q3 to produce enhanced single-MS type spectra. Use the EMS mode when you need a
rapid enhanced sensitivity survey type scan.
•
Enhanced Resolution (ER): This mode is similar to the Enhanced Product Ion mode
except that the Q1 precursor ions pass gently through the Q2 collision cell without
fragmenting. A small range about the precursor mass is scanned out of Q3 at the
slowest scan rate to produce a narrow window of the best-resolved spectra.
•
Enhanced Product Ion (EPI): Product ions are generated in the Q2 collision cell by
the precursor ions from Q1 colliding with the CAD gas in Q2. These characteristic
product ions are transmitted and collected in Q3. These ions are scanned out of Q3 to
produce enhanced product ion spectra. Use the EPI mode if you need enhanced
resolution and intensity.
•
Enhanced Multi-Charge (EMC): This mode operates similarly to the Enhanced MS
mode except, before scanning the ions out of Q3, there is a delay period in which low
charge state ions (primarily singly charged ions) are allowed to preferentially escape
from the Q3 quadrupole. When the retained Q3 ions are scanned out, the multiply
charged ion population dominates the resulting spectra.
•
Time Delayed Fragmentation (TDF): Product ions are generated and collected in
Q3. During the first part of the collection period, the lower mass ions are not collected
in Q3. During the second part of the collection period, all masses over the mass range
of interest are collected. The resultant enhanced product ion spectra are simplified
compared to EPI scan type spectra. The nature of the spectra aids in the interpretation
of the structure and fragmentation pathways of the molecule of interest.
•
MS/MS/MS (MS3): In MS/MS/MS mode, product ions are generated in the Q2
collision cell by the precursor ions from Q1 colliding with the CAD gas in Q2. These
characteristic product ions are transmitted and collected in Q3. Applying the normal
mode resolving DC voltages to the Q3 quadrupole isolates a specified mass (m/z) of
ion and removes all other ions from Q3. By properly applying a second auxiliary AC
frequency to Q3, the specified ion can be resonantly excited. These excited ions
collide with the residual nitrogen in Q3 and may fragment, producing a characteristic
spectrum of ions. These secondary product ions of the isolated product ion result in
MS/MS/MS product spectra.
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Introduction to the Q Trap LC/MS/MS System
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3
Hardware Overview
Introduction
The Q Trap LC/MS/MS system consists of a table-top mounted instrument, an
applications computer, and a printer. The user controls the Q Trap LC/MS/MS system
through the Analyst software installed on the applications computer (running a Windows
operating system).
Q Trap LC/MS/MS system—front view
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Q Trap LC/MS/MS system—rear view
Data System
The Analyst software requires a computer running the Windows operating system. For
information on hardware and operating system requirements, refer to the Analyst
Laboratory Director’s Guide to Security and Regulatory Compliance. The computer with
the associated system software works with the system controller and associated firmware
to control the instrument and data acquisition routines. The system controller controls the
operation of the main console equipment. When operating the mass spectrometer, the
acquired data is relayed to the application software where it can be displayed as either full
mass spectra, intensity of single or multiple ions versus time, or total ion current versus
time.
Sample Introduction System
The sample introduction system for the Q Trap LC/MS/MS system uses one of three
removable ion sources (mounted one at a time). This system requires only two or three
mechanical adjustments. It provides excellent performance through high sensitivity and
low chemical noise.
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LC Pump or Syringe
The liquid sample stream is pumped to the ion source probe by an optional external pump
or syringe drive. Flow rates are determined by the inlet requirements, the chromatography,
or the volume of sample available. If introduced by an LC pump, the sample may be
injected through a loop injector (flow injection analysis, or FIA) or by a separation column
(LC/MS). Samples must be sufficiently prefiltered so that the capillary tubing in the inlets
is not blocked by particles, precipitated samples, or salts.
The various optional pumps, autosamplers, and syringe configurations are not described in
this manual. For information about a particular pump, autosampler, or syringe
configuration, refer to the Peripheral Devices Setup Manual.
Ion Sources
The Q Trap LC/MS/MS system supports three ion sources:
•
TurboIonSpray
•
Heated Nebulizer
•
Flow Nanospray
The TurboIonSpray source is the standard ion source shipped with the Q Trap LC/MS/MS
system. You can, however, install the optional Heated Nebulizer or the Flow Nanospray
source.
TurboIonSpray Ion Source
TurboIonSpray is ideally suited for LC/MS/MS quantitative analyses. The sensitivity
increases that are achieved with this technique are both flow rate and analyte dependent.
In the conventional IonSpray source, sensitivity decreases with increased flow rate, while
the heated TurboIonSpray process increases ionization efficiency, especially at the higher
flow rates. This results in improved sensitivity. Sensitivity is compound dependent and
compounds of extremely high polarity and low surface activity usually show the greatest
sensitivity increases. The TurboIonSpray technique is mild enough to be used with labile
compounds such as peptides, proteins, and thermally labile pharmaceuticals.
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TurboIonSpray ion source
The TurboIonSpray ion source provides the following features:
•
Able to function as a conventional IonSpray source when the heater gas is turned off
•
Able to function with flow rates from 1 µL/min to 1000 µL/min
•
Able to vaporize 100% aqueous to 100% organic solvents
The TurboIonSpray ion source is an atmospheric pressure ion source in which
preformed ions in solution are emitted into the gas phase with or without the application of
heat. In this way, quasi-molecular ions can be generated from very labile and high
molecular weight compounds with no thermal degradation.
The use of an orthogonal heated gas extends the rugged and versatile technique of
TurboIonSpray to accept higher flow rates with improved sensitivity. TurboIonSpray will
accept flows from 5 to 1000 µL/min of solvent compositions from 100% aqueous to
100% organic, such as acetonitrile, without splitting. This allows the use of 1 mm, 2 mm,
and 4.6 mm analytical columns with or without splitting.
A heater probe directs a jet of heated dry gas (up to a maximum of 500 °C) at the mist
produced by the sprayer. The gas is sprayed across the orifice at an angle of approximately
45 °C with respect to the curtain plate. The liquid spray emerging from the TurboIonSpray
is directed at an angle of about 45° from the opposite direction (or 135°). The
TurboIonSpray effluent and the heated dry gas intersect at an angle of approximately 90°
near the orifice. This interaction helps focus the TurboIonSpray stream and increases the
rate of droplet evaporation resulting in an increased ion signal.
For information about installing the TurboIonSpray, refer to the Q Trap LC/MS/MS
TurboIonSpray Ion Source Manual.
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Hardware Overview
Heated Nebulizer
The Heated Nebulizer ion source produces ions by nebulizing the sample in a heated tube
and causing the finely dispersed sample drops to vaporize. This process leaves the
molecular constituents of the sample intact. The molecules are ionized through the process
of atmospheric pressure chemical ionization (APCI), induced by a corona discharge
needle, as the molecules pass through the ion source chamber and into the interface region.
The Heated Nebulizer offers an alternative method of introducing samples to the
Q Trap LC/MS/MS system. The Heated Nebulizer, much like the standard IonSpray
source, generates ions representative of the molecular composition of the sample.
Heated Nebulizer ion source
The Heated Nebulizer ion source provides the following features:
•
Able to function with flow rates up to 1.5 mL/min, and can handle the entire flow
from a wide bore column without splitting.
•
Able to vaporize a 100% aqueous mobile phase.
•
Able to handle volatile mobile phase buffers.
•
Able to vaporize volatile and labile compounds with minimal thermal decomposition.
•
The simple APCI spectra is ideal for MS/MS analysis.
•
Capable of being used for rapid sample introduction by flow injection with or without
a liquid chromatography (LC) column.
For information about installing the Heated Nebulizer ion source, refer to the Q Trap
APCI Heated Nebulizer Ion Source Manual.
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Flow Nanospray Ion Source
The Flow Nanospray ion source extends the versatility of Q Trap’s ion source techniques
to offer lower flow rates with high sensitivity. The Flow Nanospray accommodates low
flows up to 500 nL/min of different solvent compositions. Unlike static or discrete flow
nanosprays, the Flow Nanospray ion source is intended for continuous flow using an
external pump with LC column for pre-separation, providing stable spray at very low flow
rates. The Flow Nanospray ion source can be connected to a variety of autosamplers and
pumps to provide automated capillary LC/MS/MS applications.
In nanospray applications, potential is placed on the sample as it passes through a steel
union into a fine-tipped needle. The sample is ionized by ion evaporation and the resulting
ions enter the mass spectrometer for filtering and detection. As a “soft” ionization
technique, nanospray is particularly useful for analyzing biological samples such as
proteins while using very small sample amounts, and for taking full advantage of capillary
chromatography.
Flow Nanospray ion source
The Flow Nanospray ion source provides the following features:
18
•
Low flow rates up to 500 nL/min
•
Near 100% sample utilization
•
Minimal sample amount requirement
•
Good sensitivity, as the ionization technique results in fine droplets for ionization
Q Trap LC/MS/MS Hardware Manual
Hardware Overview
•
Ease of installation and exchange for other ion sources with the Q Trap LC/MS/MS
system
•
CCTV monitors for positioning the emitter accurately and for observing spray
For information about installing the Flow Nanospray ion source, refer to the Q Trap Flow
Nanospray Ion Source Manual.
Source Exhaust System
All of the ion sources produce both sample and solvent vapors. These vapors are a
potential hazard to the laboratory environment. The source exhaust system is designed to
safely remove and allow for the appropriate handling of the ion source exhaust products.
The source exhaust system is a venturi system that uses a flow of gas through a venturi
tube to draw the exhaust away from the ion source. The exhaust, along with the air used to
drive the venturi, is delivered to the gas connections panel at the rear of the instrument
where an external connection is available to remove the exhaust from the laboratory. The
exhaust gas can be connected to a fume hood (or to some other means) to remove the gas
safely from the laboratory.
WARNING! Ensure the source exhaust system and laboratory exhaust systems are
operating correctly to ensure the safe disposal of the source exhaust gases.
The TurboIonSpray, Heated Nebulizer, and Flow Nanospray ion sources produce large
volumes of exhaust products because all three ion sources use additional volumes of gas
and heat to produce ions. As a result, the source exhaust system is an essential component
of these ion sources. In fact, when the TurboIonSpray, Heated Nebulizer, or the Flow
Nanospray source is installed, the firmware will not enable the instrument’s electronics
unless the source exhaust system is operating.
WARNING! If you are analyzing gases containing toxic or highly volatile chemicals
or solvents, ensure the source exhaust system and laboratory exhaust systems are
operating correctly.
Note: The source exhaust system slightly reduces the pressure in the ion source. The
reduction in pressure has proven to be beneficial for the ionization performance of the
TurboIonSpray, Heated Nebulizer, and Flow Nanospray ion sources.
Source Exhaust Venturi Gas Supply
The source exhaust pump is a venturi system that uses a flow of gas through a venturi tube
to draw the vapors and liquid from the drain chamber. Clean compressed air from an
external source is needed to drive the source exhaust gas flow. The flow of source exhaust
(venturi) gas and effluent creates a negative pressure on the input side of the pump,
drawing air into the drain chamber to dilute the gases.
The effluent output of the source exhaust pump connects through a fitting on the gas and
vacuum panel with a drain line to a 10-liter (3-gallon) drain vessel. The drain vessel can be
placed under a fume hood, or the gas output hose from the lid of the vessel can be loosely
coupled to an exhaust vent system, to remove the exhaust gases from the laboratory.
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Q Trap LC/MS/MS source exhaust system
The figure Q Trap LC/MS/MS source exhaust system on page 20 shows the gas flows
through the venturi system. A solenoid valve is operated by 24 VDC controlled by the
system controller that switches power to the solenoid valve whenever a valid ion source is
installed. When the power is switched to the solenoid valve, it opens, enabling the gas
flow through the venturi tube.
A pressure switch attached to the source exhaust line is monitored by the system
controller. The switch status indicates the operational status of the source exhaust system.
Should the pressure in the line rise above the trip point (0.1 in. water), the system
controller assumes that the source exhaust system is off. If this occurs when the Heated
Nebulizer source is installed, the system controller interrupts the Power Supply Enable
signal and shuts down the instrument’s electronics.
WARNING! With the TurboIonSpray source attached, the instrument will operate if
the pressure in the source exhaust line exceeds the trip point. The pressure switch
will be tripped, however, the Power Supply Enable signal will not be disrupted. It is
important that the source exhaust system be left on at all times.
Note: When the pressure in the exhaust line falls below the set point of the instrument’s
electronics, the system controller automatically restores the Power Supply Enable signal,
and the instrument’s electronics are activated.
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Hardware Overview
Whenever an instrument is switched on and an ion source is installed, power to the source
exhaust solenoid is switched on, initiating the venturi gas flow. The solenoid valve has no
manual or software control.
Note: Closing the valve causes pressure to rise and can trip the pressure switch.
Depending on the ion source attached, this can disable the instrument’s electronics and
interrupt any ongoing data acquisitions. Ensure that you open the valve when the pump is
operating normally.
Note: The Analyst software must be running before the source exhaust pump will turn on.
The pump will remain on after the Analyst software stops running. To shut down the
pump, click Standby from the Acquire menu.
Gas Connection Panel
The gas connection panel is located at the rear right-hand corner of the chassis. The
vacuum lines to the roughing pump are connected through the gas connection panel. The
panel also houses, on the left-hand side, the Gas 1/Gas 2 and curtain gas supply
connections, the CAD gas adjustment valve, and the external connections for the source
exhaust system.
Gas connection panel
Vacuum System
The vacuum system consists of the vacuum interface, vacuum control system, and vacuum
chamber. The vacuum interface includes the gas curtain plate, orifice plate, and skimmer
cone. The vacuum control system includes the turbo pump, vacuum gauge solenoid gas
controller, and analog gas controllers. The vacuum chamber or ion path chamber includes
ion optics, quadrupoles, collision cell, and the detector.
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Vacuum Interface
The vacuum interface separates the low-pressure vacuum chamber from the atmospheric
pressure in the ion source. The purpose of the vacuum interface is to allow the transfer of
ions from the ion source to the mass spectrometer while restricting sample, solvent, and
ambient air from entering the vacuum chamber. This is accomplished using a “gas curtain”
of dry nitrogen.
The vacuum interface, as shown in the figure Vacuum interface—side view on page 22
comprises two distinct pressure chambers: the gas curtain interface and the differentially
pumped interface. The two interface regions are separated by an orifice plate containing a
0.010'' orifice through which the ions and a small volume of curtain gas must pass before
entering the vacuum chamber.
Vacuum interface—side view
Ions are transferred from the ion source through the vacuum interface into the vacuum
chamber by the potential gradient across the vacuum interface. The operator can adjust the
ion flow by varying the voltages applied to the orifice plate. The curtain plate voltage is
fixed and varies only in the polarity of ions to be analyzed.
The vacuum interface is bolted to the main body of the vacuum chamber. For easy access
to the interface, the operator can remove the ion source housing without using tools.
Gas Curtain Interface
The gas curtain interface is a small volume chamber between the curtain plate and the
orifice plate. It operates at atmospheric pressure and is flushed with a pure, inert curtain
gas (99.999% nitrogen). The figure Vacuum interface—front view on page 23 shows the
curtain plate with the ion source removed.
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Hardware Overview
Vacuum interface—front view
Approximately 600 mL/min of curtain gas flows through the orifice into the differentially
pumped interface. The remaining gas flows back into the ion source through the aperture
in the curtain plate.
The gas curtain interface provides a region for ion declustering. In the interface, sample
ions collide with the gas molecules. The collision energy assists in breaking apart ion
clusters and separating the sample ions from solvent molecules. The controlled inert
atmosphere in the interface helps to retain the stable ion-molecule products from the ion
source.
The curtain gas flow rate is set from the acquisition computer and is physically controlled
by a variable orifice valve controller. The gas line is connected to the gas curtain interface
through a connection on the bottom of the vacuum interface.
To protect the sensitive components of the instrument, the curtain gas flow is interlocked
to the pumping system and ion optics. If the curtain gas pressure is more than 5 psig from
the required pressure, the system controller disables the high-voltage supplies, sets the ion
optics voltage to zero, and turns off the turbo pump. When the gas flow is restored, the
system controller automatically restarts the turbo pump and attempts to recover the
operating conditions.
Differentially Pumped Interface
The differentially pumped interface is the first low-pressure stage in the transition from
the atmospheric pressure ion source to the low-pressure vacuum chamber. The pressure in
the interface is maintained below 1.4 torr by the roughing pump located outside the main
console.
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Curtain gas and ions are drawn from the curtain gas interface into the differentially
pumped interface by the pressure differential across the orifice plate. The ions are further
drawn through the differentially pumped interface by the voltage difference (for example,
declustering voltage) between the orifice plate and the skimmer. The ions enter the
vacuum chamber through the aperture in the skimmer.
Vacuum lines connect the interface pump to the port underneath the differentially pumped
interface. The pump is interlocked to the ion optics and the pumping system by a pressure
switch connected to the vacuum port. If the pressure in the interface rises sharply, the
switch trips, notifying the system controller of an Interface Pump fault.
In the event of a pump fault, the system controller disables the high-voltage power
supplies, sets the ion optics voltages to zero, and turns off the turbo pump until the
pressure in the differentially pumped interface is restored.
Entrance Optics
The entrance optics consist of the curtain plate and the orifice plate. The voltages applied
to these elements control the ion flow through the vacuum interface. The curtain plate
voltage is set automatically depending on the polarity of the ions (determined by the user
from the application computer).
The Entrance Optics Functions table lists the curtain and orifice plate functions.
Entrance Optics Functions
Optic Element
Curtain Plate
Orifice Plate
Function
•
Separates the sample flow from the curtain gas flow.
•
Is electrically isolated from the vacuum housing so
that the ions are not constrained to pass through
ground potential at this point.
•
Ensures the voltage is controlled by the computer.
•
Provides a division between atmosphere and the
approximately 1.4 torr pressure of the differentially
pumped interface.
•
Contains the 0.010" orifice.
•
Is electrically isolated.
The power supplies used to generate the voltages applied to the curtain plate and the
orifice plate are located on the lens power supply board inside the system electronics box.
Vacuum Control System
The vacuum system is controlled transparently by the system controller. When the mass
spectrometer is switched on, the system controller automatically attempts to pump down
the vacuum chamber. Only after reaching a stable operating pressure does the system
controller enable the instrument’s analytical components.
The pressure inside the vacuum chamber is monitored using a hot cathode vacuum gauge.
The system controller continually monitors the vacuum gauge output and several physical
interlocks to determine the vacuum status. If the vacuum integrity is breached, the system
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Hardware Overview
controller shuts down the instrument’s high voltages until the vacuum operating
conditions are restored.
Vacuum Off Sequence
When the Vacuum Off sequence is initiated, the turbo pump, ion optics, and vacuum gauge
are disabled, and the gas flows are set to the values in the Pump-Down state. The sequence
then recycles to the beginning of the Pump-Down sequence. If the sequence fails in three
attempts to restore a stable operating pressure, a hard fault results and the system exits the
Pump-Down sequence.
Pumping System
The pumping system uses a staged combination of the turbo and roughing pump to
maintain the high vacuum pressure in the vacuum chamber. The turbo pump maintains the
Q0 region of the vacuum chamber at 8 × 10–3 torr, and the high vacuum Q1 region is
maintained at about 1 × 10–5 torr. A roughing pump maintains the differentially pumped
interface at a pressure below 1.4 torr.
Turbo Pump
The turbo pump is clamped horizontally to the side flanges at the back of the vacuum
chamber. The turbo pump is not connected directly to the system electronics, but is
controlled by a separate controller. The turbo pump and its controller are maintenancefree.
Turbo Pump Controller
The turbo pump controller (as well as the gas flow controller assembly for the gas control)
is mounted on the chassis on the bracket at the inlet end of the main console (see the figure
Turbo pump controller on page 26).
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Turbo pump controller
The controller is a frequency converter that converts the single-phase AC power into the
three-phase, variable frequency power required by the turbo pump’s induction motors. The
converter is controlled remotely by the system controller as part of the vacuum control
system.
The turbo pump controller has four LEDs labelled power, acceleration, normal and
failure. These indicate the pump’s operational status.
Upon receiving a signal from the system controller, the turbo pump controller initiates a
startup procedure for the turbo pump. This includes a self-diagnostic routine during which
the controller outputs are turned off and the four indicator lights on the controller’s front
panel are illuminated. If the diagnostics routine completes successfully, the indicator
lights, with the exception of the power indicator, are shut off. The turbo pump is then
started and the acceleration light illuminates as the turbomolecular fans accelerate. The
pump is in normal operating mode when it reaches its rated rotational speeds. In normal
operating mode, the power and normal indicators are illuminated.
During normal operation, the controller monitors the turbo pump for significant changes
in turbo speed, operating parameter temperature, and load faults. Should a fault occur, the
controller shuts off the pump, and the controller’s failure indicator is illuminated.
The instrument’s firmware detects the change in the turbo pump’s status and attempts to
reestablish operating vacuum conditions. If the turbo pump fails to stabilize after three
attempts within a set time-out period, a hard fault is registered and the operator must
restart the instrument.
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Hardware Overview
Roughing Pump
The second stage of the pumping system utilizes a roughing pump. The roughing pump is
connected to the exhaust ports of the turbo pump, and acts in support of the turbo pump.
The roughing pump eases the initial start up load on the turbo pump by reducing the
pressure in the vacuum chamber to about 0.3 torr. It also creates a pressure differential
across the turbo pump’s exhaust ports, ensuring that a back pressure does not overload the
pumps.
The intake port of the roughing pump is linked to a vacuum line connecting the turbo
pump exhaust ports through the vacuum pump bulkhead.
The roughing pump is housed outside the instrument’s main console and is not controlled
by the system firmware or the applications computer. It requires its own external
230 VAC, 50/60 Hz power supply, and is operated manually using switches mounted on
the pump.
The operational status of the pumps is monitored using pressure switch interlocks. The
pump must maintain a pressure low enough to satisfy the interlocks before the system
controller will initiate the turbo pump. If the pressure in the pump’s intake line rises
sufficiently to trip the interlocks, the system controller disables the turbo pump and the ion
optics power supplies.
The roughing pump features an anti-suckback valve and a gas ballast valve (see “AntiSuckback Valve” on page 28 and “Gas Ballast Valve” on page 29). An optional mist
eliminator is strongly recommended if the pump is operated in a closed environment. The
pumps require periodic maintenance that includes changing the pump oil and, if the mist
eliminator is installed, replacing the mist eliminator’s coalescing element.
WARNING! If hazardous, biohazardous, or radioactive material is injected into the
instrument, all appropriate safety precautions should be taken when handling the
pump’s oil and coalescing filter. The oil will be contaminated and should be handled
according to hazardous material safety regulations in the country of use. (For
example, WHMIS, in Canada.)
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Roughing Pump
Roughing pump example
Anti-Suckback Valve
The roughing pump has a built-in anti-suckback valve that prevents any pump oil vapors
from migrating into the vacuum chamber. The valve is triggered automatically when the
pump is shut off or there is a power failure. As the main shaft rotation slows, a valve
opens. This causes the pumping chamber to vent and the anti-suckback valve to close.
When closed, the valve seals the pump intake, isolating the pump chamber from the
instrument.
Interface Vacuum
Vacuum for the interface is developed by the external roughing pump. An outlet on the gas
and vacuum panel is internally connected to the vacuum flange on the bottom of the
vacuum interface. From the interface, the roughing pump withdraws curtain gas, which is
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Hardware Overview
drawn through the orifice by the pressure difference between the gas curtain interface and
the differentially pumped interface.
Gas Ballast Valve
The roughing pump includes a manually controlled gas ballast valve to eliminate water
vapor and other condensable gases. Condensation degrades the pump oil, limiting the
pump's performance and life expectancy.
When opened, the gas ballast valve permits a controlled volume of air to enter the pump
chamber. This lowers the partial pressure of condensable vapors in the pump and causes
the pump temperature to rise. Both these factors hinder condensation. However, operating
a roughing pump with the gas ballast valve open raises the pump’s ultimate pressure,
increases pump oil consumption, and increases the amount of pump oil in the exhaust.
Given the controlled, dry atmosphere in the vacuum interface and the vacuum chamber,
condensation is seldom a problem.
The gas ballast valve is controlled by the black knob on the top of the oil casing. It is
closed when set to zero.
CAUTION! Under normal instrument operating conditions, the roughing pump
should be operated with the gas ballast valve closed.
Mist Eliminator
Unless there is an oil exhaust system available, and the instrument is operated in a closed
environment, it is highly recommended that a mist eliminator be installed on the exhaust
port of the roughing pump. This will prevent the emission of oil vapors into the
environment.
Vacuum Gauge
A hot cathode vacuum gauge is used to monitor the pressure inside the vacuum chamber.
The gauge is connected directly to a port on the rear of the vacuum chamber near the turbo
pump. The gauge is controlled by the vacuum gauge controller.
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Vacuum gauge
The vacuum gauge produces and measures an ion current proportional to the pressure
inside the vacuum chamber. Electrons produced by a controlled current flowing through
the filament inside the vacuum gauge accelerate toward the grid electrode, which is held at
a potential of +150 V. The electrons collide with gas molecules inside the vacuum gauge
tube creating positive ions. These ions are attracted to the collector electrode, which is
held at -13 V.
The ion current measured at the collector is directly proportional to the vacuum pressure.
The electron emission current flowing between the filament and the grid is the gauge
sensitivity factor. By regulating the electron emission current, the pressure inside the
vacuum chamber can be directly determined from the ion current measured at the
collector.
Vacuum Gauge Controller
The vacuum gauge controller is located inside the system electronics box. It performs the
following functions:
30
•
Enables power to the vacuum gauge filament in response to the Gauge Enable signal
from the system controller. This occurs after the turbo pump reaches normal operating
condition (usually below 10-3 torr).
•
Regulates the voltage applied to the vacuum gauge filament to ensure a consistent
electron emission current of 0.1 mA.
•
Provides the Vacuum Ready signal to the system controller to enable the ion path
voltages once the pressure reaches 10-4 torr.
Q Trap LC/MS/MS Hardware Manual
•
Hardware Overview
Monitors the ion current signal at the vacuum gauge collector to ensure the pressure
inside the vacuum chamber remains below 5.0 X 10-5 torr.
If the pressure inside the vacuum chamber rises above 10–4 torr, the vacuum gauge
controller sends a digital signal to the system controller. The system controller then
initiates the Vacuum Off sequence, disables power to the high-voltage power supplies and
the turbo pump. The system controller then sets the ion path voltages to zero and instructs
the vacuum gauge controller to turn off the vacuum gauge (to protect the filament). After
the Vacuum Off sequence completes, the system controller restarts the Vacuum Pump On
sequence. The system controller attempts to recover the vacuum integrity automatically
without operator intervention.
Gas Control System
Four gas flows are required for the instrument:
•
CAD gas
•
Curtain gas
•
Nebulizer gas (Gas 1)
•
Heater gas (Gas 2)
Gas Flow Controller
The controller circuit works by sensing the pressure in the volume of gas between a
variable inlet and a fixed orifice outlet. It continually adjusts the pressure by varying the
inlet to match the sensed pressure with the set point pressure. If the pressure is too high,
the inlet closes, allowing the pressure to drop. If the pressure is too low, the inlet opens to
raise the pressure. As the measured pressure reaches the required set point, the analog
valve closes to the point where it keeps the flow through the controller the same as the
flow through the orifice, thereby keeping the pressure constant at the outlet.
CAD Gas Flow
The CAD gas is the target gas in the collision cell. Collisions between the ions speeding
along the ion path and the CAD gas molecules in the collision cell provide the energy for
ion dissociation.
The CAD gas is tapped from the curtain gas input, and pressure is relieved through a
metering valve into the roughing pump exhaust manifold. The gas is then directed through
the solenoid gas flow controller to the face plate at the right end of the vacuum chamber.
The CAD gas is routed along the mass filter rail and fed to the collision cell through the
hollow locating pin that locates the Q2 rod set.
Curtain Gas Flow
The curtain gas is used to isolate the ion source from the vacuum chamber. The gas acts as
its name suggests, like a curtain restricting the flow of air, sample, and solvent into the
vacuum chamber.
The curtain gas is connected through the gas connection panel on the chassis to the gas
flow controller assembly. For the gas flow controller, the curtain gas is connected to the
gas curtain interface through the vacuum interface housing. The flow is interlocked to the
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Hardware Overview
Q Trap LC/MS/MS Hardware Manual
vacuum control system and the ion optics by a pressure switch connected to the gas flow
controller’s intake manifold.
Nebulizer Gas (Gas 1) Flow
Nebulizer gas is used to optimize the signal’s stability and sensitivity. Typically, a value of
10 to 90 psig is used as applied by the applications computer.
Heater Gas (Gas 2) Flow
Heater gas aids in the evaporation of the solvent that aids in increasing the ionization of
the sample. The higher the liquid flow, or the higher the aqueous composition of the
solvent, the higher the heater gas temperature and gas flow required. However, a
temperature that is too high can cause premature vaporization of the solvent, and result in
a high chemical background noise. A heater gas flow that is too high can produce a noisy
or unstable signal.
Gas 1/Gas 2 control connection
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Hardware Overview
Gas Control Sequence
When the vacuum chamber pressure is stable below the Vacuum Ready set point of
1 X 10-4 torr, the three gas flows are controlled by the operator at the applications
computer. However, when the instrument is either pumping down or venting, the curtain
gas flow rates are set by the system controller independent of the software setting at the
applications computer. By overriding the software gas flow controller settings, the system
controller ensures the consistent, predictable behavior of the instrument when pumping
down or venting.
During the pumping down or venting process, the curtain gas is set to its maximum flow.
In the Pump-Down sequence (see “Pumping Down” on page 46), the vacuum gauge
controller informs the system controller that the vacuum is ready when the vacuum
pressure surpasses the setpoint (1 X 10-4 torr). Upon receiving the Vacuum Ready signal,
the system controller releases the gas control to the software.
After the curtain gas flow is returned to software control, the vacuum pressure typically
drops rapidly from the Vacuum Ready set point at 1 x 10-4 torr to the operating pressure
specification at 1 X 10-5 torr. This rapid decrease in vacuum pressure occurs because the
curtain gas software setting is generally considerably lower than the maximum flow set by
the system controller.
Safety Interlocks
The vacuum control system has safety interlocks to protect the instrument’s sensitive
electronic components. These interlocks prevent the normal operation of the instrument if
certain operating parameters outside the direct control of the system circuitry are not
maintained.
The two interlocks that directly affect the pumping sequence are:
•
Curtain gas flow
•
Roughing pump pressure
When an interlock is triggered, the Vacuum Off sequence is initiated The turbo pump is
disabled and the ion optics voltages are set to zero. When the interlocks are recovered, the
system automatically attempts the Pump-Down sequence.
A set of interlocks prevents the instrument from switching to Analysis mode if a valid ion
source is not properly installed. These interlocks do not, however, affect the pumping
system.
Curtain Gas Interlocks
Curtain gas flow is essential to the consistent and safe operation of the instrument.
Without a significant flow of curtain gas, the vacuum chamber draws ambient air from the
ion source, the moisture and composition of which can negatively affect the operation of
the instrument. Even though small amounts of curtain gas enter the vacuum chamber with
the sample, the operation of the instrument is not detrimentally affected because the
quantity and the composition is controlled.
A pressure switch connected to the curtain gas flow between the gas cylinder and the gas
flow controller is triggered if the pressure drops below a set point that corresponds to a
flow rate of 0.7 L/min. If the interlock is tripped, the Vacuum Off sequence is initiated and
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Hardware Overview
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the turbo pump and the ion optics voltages are disabled. The instrument automatically
attempts to pump down when the curtain gas flow interlock is satisfied.
Roughing Pump Interlock
A pressure switch attached to the vacuum line connects the exhaust port of the turbo pump
to the roughing pump and acts as the indicator of the roughing pump’s operational status.
If the pressure in the vacuum line rises significantly and triggers the interlock switch, the
Vacuum Off sequence is initiated. The turbo pump shuts down and the ion optics are
disabled.
The instrument automatically attempts to pump down when the vacuum pressure in the
roughing pump line is regained and the pressure switch interlock closes.
Vacuum Control Sequence
On power-up, the instrument goes directly into Pump-Down mode. The Pump-Down
sequence is controlled by the firmware independent of the applications computer. This
means that the Pump-Down sequence, once initiated, is transparent to the user.
When a stable operating vacuum pressure is established and the required safety interlocks
are satisfied, the instrument switches directly to Analysis mode. In Analysis mode, the
instrument is ready for spectrographic analysis; the ion path voltages, gas flows, and the
other operating parameters are controlled by the operator at the applications computer.
Operating modes
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Q Trap LC/MS/MS Hardware Manual
Hardware Overview
Ion Path Chamber
The vacuum chamber is a single aluminum extrusion housing the ion optics, collision cell,
and the detector. The quadrupoles, collision cell, and the associated ion optics are
assembled on the mass filter rail and inserted into the vacuum chamber as a single unit.
The ion detector, housed in the ion detector module, is installed inside the vacuum
chamber after the mass filter rail is in position.
A seal formed by the front bulkhead on the mass filter rail divides the vacuum chamber
into two distinct regions. The Q0 region contains the Q0 rod set. It is located between the
vacuum interface and the front bulkhead on the mass filter rail. This region is maintained
at 8 X 10-3 torr by the turbo pump.
The high vacuum region contains the three remaining rod sets and the associated ion
optics. It is maintained at about 1 X 10-5 torr by the turbo pump. The Q2 quadrupole rod
set is contained in the collision cell that forms part of the high vacuum region. The Q1 and
Q3 quadrupoles are located on either side of the collision cell and are open for free
pumping by the turbo pump.
Note: The vacuum chamber is safety interlocked such that if the pressure inside the high
vacuum region reaches 1 X 10 -4 torr or greater, all ion path voltages are set to zero.
Mass Filter Rail
The quadrupole rod sets and ion optics are installed, aligned, and wired on the mass filter
rail before the rail is inserted into the vacuum chamber. The front end of the mass fIlter rail
is supported by the front bulkhead. The other end of the mass filter rail is bolted to the rear
flange that seals the detector end of the vacuum chamber. The front bulkhead can be
accessed through the vacuum interface to easily remove the mass filter rail.
All gas lines and internal wires are routed along the mass filter rail. The external ion optics
and the gas connections are made through vacuum connectors on the rear flange.
Vacuum feedthroughs are used to connect the RF and DC voltages for the Q1 and Q3 mass
filter quadrupoles through the bottom of the vacuum chamber. The leads are connected
after the mass filter rail has been installed.
Quadrupoles
The four quadrupoles are mounted on the mass filter rail inside the vacuum chamber. The
Q1 and Q3 rod sets are mass filters that selectively filter ions based on their mass-tocharge ratio (m/z). The Q0 and Q2 rod sets are RF-only quadrupoles that have no filtering
effect.
Mass Filters (Q1 and Q3)
In the Q Trap LC/MS/MS system, the Q1 and Q3 quadrupoles consist of four cylindrical
electrodes (rods) to which precise DC and RF voltages are applied. The Q1 and Q3 rods
are enclosed by ceramic collars and positioned accurately on the mass filter rail using the
locating pins.
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Hardware Overview
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The Q1 and Q3 rod sets have very high mechanical precision necessary for achieving high
transmission and high resolution. The normal trade-off between high ion transmission and
narrow peak width must be optimized for each particular application. The Q1 and Q3 rod
sets normally operate at a constant mass width ( ∆M ) that is independent of the ion mass
(M). Hence, the resolution ( M ⁄ ∆M ) in this mode of operation is directly proportional to
the mass being observed.
The Q3 rod set is also capable of being operated in Total Ion mode in which only RF
voltage is applied to the quadrupole rods (other terms are RF-only mode and AC-only
mode). This essentially allows ions of all masses present in Q3 to be transmitted to the ion
detector.
Linear Ion Trap (LIT)
The Q Trap LC/MS/MS system has enhanced modes of operation. In any of the linear ion
trap modes, a pulse of ions is introduced into the linear ion trap (Q3). The main RF fields
trap the ions in the radial direction and DC voltages applied to the lenses at both ends of
the linear ion trap are used to trap the ions axially. The trapped ions are allowed to cool for
several milliseconds, and then the RF voltage is scanned in the presence of a low-voltage
auxiliary AC applied to the rods. The ions that are ejected axially toward the detector are
counted.
During the collection phase, ions pass through the Q2 collision cell where CAD gas
focuses the ions into the Q3 region. The Q3 quadrupole is operated with only the main RF
voltage applied. Ions are prevented from passing through the Q3 quadrupole rod set and
are reflected back by an exit lens to which a DC barrier voltage is applied. After the fill
time (a time defined by the user), a DC barrier voltage is applied to a Q3 entrance lens.
This confines the collected ions in Q3 and stops more ions from entering. The entrance
and exit lens DC voltage barriers and the RF voltage applied to the quadrupole rods
confine the ions within Q3.
During the scan out phase, a potential of a few volts is applied to the exit lens to repel the
charged ions. An auxiliary AC frequency is applied to the Q3 quadrupole. The main RF
voltage amplitude is ramped from low to high values, which sequentially brings masses
into resonance with the auxiliary AC frequency. When ions are brought into resonance
with the AC frequency, they acquire enough axial velocity to overcome the exit lens
barrier and are axially ejected towards the mass spectrometer ion detector.
RF-Only Quadrupoles (Q0 and Q2) and Stubbies
An RF-only quadrupole is similar in construction to a quadrupole mass filter, but is only
capable of being operated in Total Ion mode (only RF voltage is applied to the rods). In the
Q Trap LC/MS/MS system, both Q0 and Q2 are RF-only quadrupoles.
The Q0 rod set is mounted in the front bulkhead of the mass filter rail. The Q0 rod set
focuses and transfers ions from the vacuum interface through the interquad lens Q1 into
the stubbies and in the high vacuum region. The stubbies prefilter and transfer the ions
into the Q1 mass filter. To optimize ion transfer, both Q0 and the stubbies are electrically
connected to the Q1 RF voltage. The RF voltage applied to Q0 and the stubbies is a
consistent fraction of the RF voltage applied to Q1.
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Q Trap LC/MS/MS Hardware Manual
Hardware Overview
The Q2 rod set is housed inside the collision cell that is mounted between Q1 and Q3 on
the mass filter rail. It transmits ions through the collision cell into Q3. Similar to Q0, the
Q2 RF voltage is capacitively coupled to the Q3 RF voltage. The Q3 RF voltage is
capacitively coupled to the Q2 voltage so that the Q2 RF voltage is ramped in a constant
ratio with respect to that of Q3.
Vacuum Feedthroughs
The amplified RF and DC voltages for Q1 and Q3 are connected through the bottom of the
vacuum chamber through the vacuum feedthroughs. There are four feedthroughs: two for
Q1 and two for Q3. Each feedthrough carries the combined RF and DC voltages for one
pair of opposing quadrupole rods.
The feedthroughs are installed through punch-outs in the tops of the Q1 and Q3 coil boxes
into designated holes in the bottom of the vacuum chamber. One end of each feedthrough
lead is connected to the respective interconnect circuit board inside the vacuum chamber;
the other end is connected to a sleeve in the respective coil box.
Collision Cell
The collision cell is a ceramic housing pressurized with CAD gas. The housing contains
Q2 and is closed at both ends by interquad lenses IQ2 and IQ3.
Ions enter Q2 through IQ2 and collide with the CAD gas molecules in the cell. The
collisions provide the energy needed to dissociate precursor ions into fragment ions. All
ions in the collision cell are transferred to Q3 where the precursor or fragment ions can be
selectively filtered and transferred to the ion detector for counting.
CAD gas is fed through a vacuum fitting on the end of the flange of the vacuum chamber.
The CAD gas line is then routed along the mass filter rail and fed through a hollow
locating pin in the top of the collision cell. The user controls the gas flow from the
applications computer.
Since the degree of fragmentation is a function of collision gas thickness (CGT), the CGT
must be controlled. This is accomplished by controlling the flow of gas that has been
redirected from the differentially pumped interface and fed through a gas flow controller
to the collision cell. The gas flow is set by the operator from the applications computer.
Ion Optics
The ion optics are designed to help guide and focus the sample ions through the mass
filters and deliver these selected ions to the ion detector. Voltage potentials are applied to
the ion optics by the operator at the applications computer and can be varied for different
sample and application requirements. The figure Q Trap LC/MS/MS ion optics path on
page 38 shows the ion optics path.
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Q Trap LC/MS/MS ion optics path
The ion optics consist of the following:
•
Curtain plate
•
Orifice plate (OR)
•
Stubbies (ST)
•
Interquad lenses (IQ1, IQ2, IQ3)
•
Exit lens (EX)
•
Deflector (DF)
The curtain plate and the orifice plate are part of the vacuum interface.
The stubbies, high vacuum region, and the exit lens are mounted on the mass filter rail.
The stubbies help transfer the ions from the Q0 region to the Q1 mass filter in the high
vacuum region. This lens is actually a shortened version of an RF-only quadrupole. The
interquad lenses help the transmission of ions into the respective quadrupoles, while the
deflector helps to improve the collection efficiency of the ion detector.
The deflector, ion detector, and support electronics are contained in a separate module that
attaches to the front of the vacuum chamber at the detector end of the instrument.
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Q Trap LC/MS/MS Hardware Manual
Hardware Overview
Ion Detector and Signal Handling
Ion detector
Deflector Voltage
The deflector voltage is supplied by the lens power supply board. It varies from –400 to
+400 volts and can be set by the operator at the acquisitions computer. The gas resistor
(DS1) acts as a surge voltage protector for this circuit.
Power Distribution Module
The power distribution module is the interface between the external 230 VAC power
supply and the instrument’s electronics. The module supplies all required power for
operating the mass spectrometer.
The instrument requires two separate 230 VAC power sources operated at 50 or 60 Hz.
One single phase 230 VAC power source is required for the instrument’s main console.
The second power source is required for the roughing pump. The applications computer,
printer, and other accessories (including LC equipment) are powered separately from
standard wall outlets. An optional line adjustment transformer (LAT) can be purchased to
provide accurate, consistent power for the instrument and the roughing pump.
The instrument operates within design specification with line voltage variations of
230 VAC +5%. The OEM equipment including the roughing pump specify that line
variations also be minimized to +5%.
A DC power supply converts the AC input power into DC voltages.
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AC Power Distribution
The 230 VAC power enters the main console by a detachable cable and is fed through a
filter to the main power switch on the power distribution panel. The switch doubles as a
circuit breaker that trips and disables power to the instrument (if there is a power surge).
When the power switch is on, power is directed straight to the power distribution panel
where it is divided and connected by detachable cables to the following equipment on the
main console:
•
Main DC power supply
•
Card cage blower
•
Heated Nebulizer inlet (optional)
DC Power Distribution
The DC power supply converts the 230 VAC input power into four DC voltages:
+5.0 V, -18 V, +24 V A and +24 V B. The DC voltages are supplied to the motherboard
where they are available to the system electronics box and the main module equipment.
The DC power supply has a feedback sensing circuit that ensures the consistency of the
DC voltages across the motherboard.
ARF Module
The ARF power supply module supplies Q3 with an RF voltage allowing the mass
spectrometer to operate as a linear ion trap. The ARF module is located adjacent to the
vacuum chamber.
The System Electronics Box
The system electronics box houses the following seven printed circuit boards:
•
System controller
•
Ion path DACs and vacuum gauge controller
•
Lens power supply
•
HV power supply
•
QPS exciter
•
Q1 amplifier board
•
Q3 amplifier board
These boards are contained in individual modules. Each module plugs into the common
motherboard that forms the back of the system electronics box. Together, the modules
control the instrument and convert the input power into the precise RF and DC voltages
that drive the mass filters and supporting ion optics.
The QPS exciter board and the Q1 and Q3 amplifiers form part of the quadrupole power
supply, providing the precise AC and DC voltages to the Q1 and Q3 mass filters.
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4
Operating the Q Trap LC/MS/MS
System
Work Process Flow
Performing qualitative and quantitative analysis, from start to finish, involves various
modes and steps which you set in the Analyst software. The following figure Work process
flow illustrates the process flow from beginning to end at a very basic level.
Work process flow
The top half of the figure indicates the instrument parameters. These parameters can be
divided into three types:
•
Instrument-specific (set up on initial installation and on mass calibration)
•
Compound-specific (set up for each analysis)
•
Source-specific (set up for each analysis)
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Q Trap LC/MS/MS Hardware Manual
Once you assign values to instrument parameters for a particular analysis, they become the
“working parameters,” describing the control parameters for the instrument.
The bottom half of the figure describes the processing of the sample data according to the
instrument parameters; you introduce samples and quantitate them.
To process another batch, no further parameter setup is required; you simply submit
another batch. To process another compound, you should redefine the compound- and
source-specific parameters.
Setting Up Instrument-Specific Parameters
You need to set up instrument parameters on a periodic basis, either on initial installation
or if you need to recalibrate the instrument. This process is not required for each analysis.
For more information, refer to the Analyst 1.3 Operator’s Guide or the Analyst online
Help.
To set up instrument-specific parameters
1. Create a hardware profile in the Analyst Hardware Configuration Editor.
2. Introduce a sample containing the compound of interest (usually a reference
compound, such as PPG).
3. Tune the mass spectrometer:
a) Define the acquisition method (scan type and masses).
b) Examine the shape for sensitivity, peak width, resolution, and mass assignment.
(The last two verify the mass spectrometer’s performance.)
c) Adjust your method as necessary to obtain the maximum sensitivity for your
analyte(s) or mass(es) of interest.
Setting Up Compound-Specific Parameters
Each time you want to quantitate a new compound, you need to define the analysis
conditions for the compound. Depending upon your level of expertise, you set compoundspecific parameters in two ways:
•
Automatically (for novice users)
•
Manually (for experienced users)
To set up compound-specific parameters automatically
1. Introduce the compound into the mass spectrometer.
2. Start the Quantitation Optimization wizard. Analyst produces an acquisition method
for the mass spectrometer. Refer to the online Help for detailed instructions about
using the Quantitation Optimization wizard.
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Operating the Q Trap LC/MS/MS System
To set up compound-specific parameters manually
1. Introduce the compound into the mass spectrometer.
2. Start Manual Tune. Refer to the Analyst online Help for detailed instructions about
using Manual Tune.
3. Optimize individual instrument parameters as needed. The application software
produces an acquisition method for the mass spectrometer.
Setting Up Source-Specific Parameters
Source parameters can be optimized for the LC conditions used during analysis. These
parameters are accessed either by clicking the Source/Gas tab in the Tune Method Editor,
or by clicking Edit Parameters in the Acquisition Method Editor while in Acquire mode.
Once you have created an acquisition method for the mass spectrometer, you need to
define or modify the acquisition methods for the peripheral devices (such as LC pumps
and autosamplers) so that they synchronize with the instrument.
For more information, refer to the Analyst 1.3 Operator’s Guide or the Analyst online
Help.
Shutting Down and Powering Up the
Q Trap LC/MS/MS System
The power to the Q Trap LC/MS/MS system should be left on to maintain the high
vacuum conditions required for operation. The instrument remains in a warmed-up state
so that operation can begin immediately. If the instrument is already on and warmed up,
the green status light on the front panel will be on and will not be flashing. If the
instrument is not on, you should follow the procedure “Powering Up the Q Trap LC/MS/
MS System” on page 44.
The instrument power is only turned off when service on the vacuum or electrical
components is required. When first powered up, the instrument, under control of the
system firmware, goes into Pump-Down mode and attempts to start the turbo pump and
bring the vacuum chamber to operating pressure. The process is transparent and does not
require operator intervention. While the system is pumping down, the ion optics, detector,
and ion source voltages are disabled. When the necessary vacuum conditions are reached
and the safety interlocks are satisfied, the instrument switches to Analysis mode and the
operating voltages are enabled.
Certain conditions outside the direct control of the instrument firmware must be satisfied
before the turbo pump will be initiated. The curtain gas must be turned on at the source,
and the roughing pump must be turned on manually. Interlocks monitored by the firmware
detect if the curtain gas and the roughing pump are switched on. If the interlocks are not
satisfied, the turbo pump is not initiated.
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Powering Up the Q Trap LC/MS/MS System
If the instrument was vented during the shut-down procedure, the covers must be replaced
before the mass spectrometer can be powered up. For more information, see “Removing
the Instrument Covers” on page 48.
To power up the Q Trap LC/MS/MS system
1. Replace the venting screw on the front of the vacuum chamber, if the instrument was
vented during the shut-down procedure.
2. Replace the instrument covers.
3. Turn on the roughing pump, if it was turned off.
4. Ensure that the curtain gas supply is flowing to the instrument. The pressure should be
regulated to 60 psig.
5. Ensure that the 207 V to 242 V main power supply is plugged into the electrical
connections panel.
6. Turn on the main power switch.
7. Ensure that the General Purpose Interface Bus (GPIB) cable is connected to both the
Q Trap LC/MS/MS system and the applications computer.
8. Turn on the applications computer.
Note: Should the ion source be removed, the system electronics will be disabled
interrupting any data acquisition tasks. The turbo pump and the vacuum system will not be
affected.
Instrument Warmup
The mass filters must be adequately warmed up before proper performance can be
achieved.
If the power has been off for more than five minutes, the instrument should warm up for
approximately one hour after the operating vacuum conditions are established. If the
instrument has been off for an extended period of time (for example, overnight), a warm
up period of four hours is recommended.
Shutting Down the Q Trap LC/MS/MS System
The power to the Q Trap LC/MS/MS system is typically always left on, thereby
maintaining the high vacuum conditions required for operation. The instrument also
remains in a warmed up state so that operation can begin immediately. The instrument
power is usually only turned off when service to the vacuum or electrical components is
required.
When shutting down the instrument, care must be taken to prevent the roughing pump’s
exhaust from being drawn into the vacuum chamber through the turbo pump’s exhaust
ports. The likelihood of this occurring is reduced because the roughing pump has a valve
that isolates the pump exhaust from the pump intake when the pump is shut off or fails.
Shutting down the instrument properly will greatly reduce the possibility of pump exhaust
being drawn into the vacuum chamber.
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Operating the Q Trap LC/MS/MS System
To shut down the Q Trap LC/MS/MS system
1. Complete any ongoing scans, or select the Abort Sample from the Acquire menu.
2. Shut off the sample flow to the instrument.
CAUTION! The sample flow must be shut off before shutting down the instrument.
3. Close the application software.
4. Shut off the main power switch to the instrument. The switch is located on the
bulkhead at the back right corner of the chassis.
Note: When the main power switch is turned off, the turbo pump continues to rotate
without power for a few minutes and continues to provide vacuum to the vacuum
chamber. If, during this time, the roughing pump is powered down, the pressure in the
vacuum line between the roughing pump and the turbo pump increases. The increase in
back pressure can create an incorrect load on the turbo pump bearings and cause a
catastrophic failure of the turbo pump.
CAUTION! To prevent damage to the turbo pump, leave the roughing pump running
for a minimum of five minutes after shutting off the instrument’s main power switch.
This prevents the buildup of pressure in the vacuum lines from the turbo pump to
the roughing pump.
CAUTION! If the instrument is to be shut down for any length of time, we
recommend that the vacuum chamber be vented to prevent the roughing pump
exhaust from being sucked back into the vacuum chamber. (To vent the vacuum
chamber, follow steps 5 to 7.)
CAUTION! If the vacuum chamber is not going to be vented while the instrument is
shut down, we recommend the roughing pump remain turned on to prevent the
pump exhaust from being sucked back into the vacuum chamber. (If you do not
want to vent the vacuum chamber, skip steps 5 to 7.)
5. Shut off the roughing pump. The power switch is located beside the power supply
input attachment on the roughing pump.
6. Unplug the main power source to the instrument from the rear panel at the back right
corner of the chassis.
7. Vent the vacuum chamber for twenty minutes. To do so, remove the venting screw
(with a 5 mm socket wrench) from the front of the chamber.
Note: To vent the vacuum chamber, you must first remove the instrument covers. For
more information, see “Removing the Instrument Covers” on page 48.
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Pumping Down
The following chart shows the Pump-Down sequence.
Vacuum Pump-Down sequence
Pump-Down Sequence
The Pump-Down sequence is initiated when the instrument’s power is switched on. Before
attempting to initiate the turbo pump, the status of the system interlocks and fault
conditions, including the vacuum gauge and the turbo pump status, are evaluated. The
proper setting of the curtain gas is verified and, when the initial conditions are correct, the
control sequence initiates the turbo pump.
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The status of the turbo pump is monitored by the firmware control circuitry. If the turbo
pump does not reach the normal operating mode within a specified time-out period, the
sequence triggers a Turbo Transition fault. The system attempts to start the pump three
times. If the pump fails to stabilize after the three attempts, the firmware controller
registers a hard fault and aborts the Pump-Down sequence.
The turbo pump switches to normal operating mode when its turbo blades reach their rated
rotational speeds. Power to the vacuum gauge filament is enabled 55 seconds after the
turbo pump has reached its normal status. The vacuum gauge output is not monitored until
ten seconds after the gauge has been enabled. This delay allows the gauge output to
stabilize before it is used as a variable in the Pump-Down sequence.
There is a two-stage Pump-Down sequence. When the vacuum chamber pressure reaches
10-4 torr, the gases are put under the control of the Analyst software. Before the
electronics are enabled, the vacuum must reach 2 X 10-5 torr.
To initiate the Pump-Down sequence
1. Replace the venting screw on the front of the vacuum chamber, if the instrument was
vented.
2. Replace the instrument covers. See “Removing the Instrument Covers” on page 48.
3. Turn on the roughing pump, if it was turned off.
4. Ensure that the curtain gas supply is flowing to the instrument. The pressure should be
regulated to 60 psig.
5. Ensure that the 207 V to 242 V main power supply is plugged into the electrical
connections panel.
6. Turn on the main power switch.
7. Ensure that the General Purpose Interface Bus (GPIB) cable is connected to both the
Q Trap LC/MS/MS system and the applications computer.
8. Turn on the applications computer.
47
Operating the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
Removing the Instrument Covers
There are four covers that enclose the operating modules of the Q Trap LC/MS/MS
system. The covers can be opened to allow access to the instrument's component modules,
the system electronics box, and the operational parameter checkpoints. The covers are
designed to prevent access to the instrument when high operating voltages are engaged.
Removing the Front Cover
You must remove the front cover before you can open the remaining covers.
Q Trap LC/MS/MS system—front cover
Opening the front cover exposes the main components of the Q Trap LC/MS/MS system,
including many of the system test points. The cover is secured at the top by three quarterturn screws that are mounted on top of the card cage and coil box. The cover is not hinged
to the chassis but is anchored at the bottom by the three tabs. You must lift the cover off
the tabs and away from the chassis to access the front of the Q Trap LC/MS/MS system.
To remove the front cover
1. Shut down the instrument. See “To shut down the Q Trap LC/MS/MS system” on page
45.
2. Remove the ion source. See “Removing the TurboIonSpray Ion Source” on page 51.
WARNING! Do not remove the Q Trap LC/MS/MS system covers unless the
instrument has been shut down properly and the main power disconnected (see
“Shutting Down the Q Trap LC/MS/MS System” on page 44). Failure to follow this
sequence will expose the operator to hazardous voltages.
3. Unscrew the three captured bolts that secure the front cover to the instrument.
4. Grasp the top corners of the front cover and gently pull and lift the cover to remove it.
48
Q Trap LC/MS/MS Hardware Manual
Operating the Q Trap LC/MS/MS System
Removing the Top Cover
Q Trap LC/MS/MS system—top cover
WARNING! Do not remove the Q Trap LC/MS/MS system covers unless the
instrument has been shut down properly and the main power disconnected (see
“Shutting Down the Q Trap LC/MS/MS System” on page 44). Failure to follow this
sequence will expose the operator to hazardous voltages.
1. Remove the front cover.
2. Unscrew the two captured bolts that secure the top cover to the back of the instrument.
3. Tilt the front end of the cover up and gently pull towards the rear. Lift the cover to
remove it.
49
Operating the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
Removing the Back Cover
The back cover encloses most of the systems cabling. It is not hinged and must be
removed to access the back of the Q Trap LC/MS/MS system.
Q Trap LC/MS/MS system—back cover
WARNING! Do not remove the Q Trap LC/MS/MS system covers unless the
instrument has been shut down properly and the main power disconnected (see
“Shutting Down the Q Trap LC/MS/MS System” on page 44). Failure to follow this
sequence will expose the operator to hazardous voltages.
1. Remove the front cover.
2. Remove the top cover.
3. Unscrew the two captured bolts that secure the back cover to the back of the
instrument.
4. Gently lift the cover to remove it.
50
Q Trap LC/MS/MS Hardware Manual
Operating the Q Trap LC/MS/MS System
Power Distribution Cover
Q Trap LC/MS/MS system—power distribution cover
WARNING! There are no operator serviceable items located behind the power
distribution cover.
Removing the TurboIonSpray Ion Source
If you intend to vent the vacuum chamber during the shut-down procedure, the ion source
must be removed.
Note: This procedure instructs you on how to remove the TurboIonSpray source. For
instructions on removing the Heated Nebulizer or the Flow Nanospray ion sources, refer
to either the Q Trap APCI Heated Nebulizer Ion Source Manual or the Q Trap Flow
Nanospray Ion Source Manual.
To remove the TurboIonSpray ion source
1. Finish or abort any ongoing scans.
2. Shut down the sample flow to the ion source.
3. Turn the latches on the front plate of the source. Loosen the latches completely, but be
aware that they cannot be removed. Remove the TurboIonSpray source from the front
of the Q Trap LC/MS/MS system. Pull the ion source away from the vacuum chamber
so that the latches clear the connections in the vacuum interface housing. For more
information, refer to the Q Trap LC/MS/MS TurboIonSpray Ion Source Manual.
51
Operating the Q Trap LC/MS/MS System
Q Trap LC/MS/MS Hardware Manual
Replacing the TurboIonSpray Ion Source
1. Install the ion source against the vacuum chamber so that the latches slide over the
connections in the vacuum interface housing.
2. Turn the latches on the front plate of the ion source until the ion source is locked in
position against the vacuum chamber.
52
Q Trap LC/MS/MS Hardware Manual
Appendix A: Maintenance Checklist
Appendix A:
Maintenance Checklist
Q Trap LC/MS/MS System Periodic
Maintenance
The Q Trap LC/MS/MS system requires regular maintenance to ensure optimum
performance. You should ensure that the proper maintenance procedures are performed at
regular intervals. These procedures can only be performed by a Qualified Maintenance
Person or a Service Engineer. You should consult the appropriate person before
performing any of the maintenance procedures listed below.
A Qualified Maintenance Person can perform the following procedures:
•
Cleaning the curtain plate
•
Cleaning the orifice and skimmer
•
Cleaning Q0
•
Replacing the card cage blower filter
A Service Engineer can perform all of the above procedures as well as the additional
procedures below:
•
Replacing the roughing pump oil
•
Replacing the roughing pump filter trap
•
Replacing the roughing pump mist eliminator filter
Serial No._________ Year_________
Procedure
Performed by
Interval
Clean the
curtain plate
Qualified
Maintenance Person
When it appears dirty
or performance
suffers
Clean the orifice and
skimmer
Qualified
Maintenance Person
When it appears dirty
or performance
suffers
Clean Q0
Qualified
Maintenance Person
When it appears dirty
or performance
suffers
Replace the card cage
blower filter
Qualified
Maintenance Person
Maximum every three
months, when it
appears dirty, or
performance suffers
Date
Date
Date
Date
Date
53
Appendix A: Maintenance Checklist
Q Trap LC/MS/MS Hardware Manual
Serial No._________ Year_________
Procedure
Performed by
Interval
Replace the roughing
pump oil
Service Engineer
Maximum every six
months, when it
appears dirty, or if the
instrument has been
stored for an extended
period.
Replace the roughing
pump filter trap
Service Engineer
When it becomes
clogged or performance suffers
Replace the roughing
pump mist eliminator
filter
Service Engineer
When it appears dirty
or performance
suffers
54
Date
Date
Date
Date
Date
Q Trap LC/MS/MS Hardware Manual
Appendix B: PPG Exact Mass Table
Appendix B:
PPG Exact Mass Table
The following table contains the exact monoisotopic masses and charged species (positive
and negative) observed with the polypropylene glycol (PPG) calibration solutions. The
masses and ions were calculated using the formula M = H[OC3H6]nOH, while the
positive ion MS/MS fragments used the formula [OC3H6]n(H+). In all calculations,
H = 1.007825, O = 15.99491, C = 12.00000, and N = 14.00307.
Note: When performing calibration with the PPG solutions, ensure that the correct
isotope peak is used.
n
Exact Mass
(M)
(M = NH4)+
MS/MS
Fragments
(M = 2NH4)2+
(M = COOH)-
1
76.052
94.087
59.0
56.061
121.050
2
134.094
152.129
117.1
85.082
179.092
3
192.136
210.171
175.1
114.102
237.134
4
250.178
268.212
233.2
143.123
295.176
5
308.220
326.254
291.2
172.144
353.218
6
366.262
384.296
349.2
201.165
411.259
7
424.304
442.338
407.3
230.186
469.301
8
482.346
500.380
465.3
259.207
527.343
9
540.388
558.422
523.4
288.228
585.385
10
598.430
616.464
581.4
317.249
643.427
11
656.471
674.506
639.4
346.270
701.469
12
714.513
732.548
697.5
375.291
759.511
13
772.555
790.590
755.5
404.312
817.552
14
830.597
848.631
813.6
433.333
875.594
15
888.639
906.673
871.6
462.354
933.636
16
946.681
964.715
929.7
491.373
991.678
17
1004.723
1022.757
987.7
520.396
1049.720
18
1062.765
1080.799
1045.7
549.417
1107.762
19
1120.807
1138.841
1103.8
578.438
1165.804
20
1178.849
1196.883
1161.8
607.459
1223.845
21
1236.890
1254.925
1219.9
636.480
1281.887
22
1294.932
1312.967
1277.9
665.501
1339.929
23
1352.974
1371.009
1335.9
694.521
1397.971
24
1411.016
1429.050
1394.0
723.542
1456.013
25
1469.058
1487.092
1452.0
752.563
1514.055
26
1527.100
1545.134
1510.1
781.584
1572.097
55
Appendix B: PPG Exact Mass Table
56
Q Trap LC/MS/MS Hardware Manual
n
Exact Mass
(M)
(M = NH4)+
MS/MS
Fragments
(M = 2NH4)2+
(M = COOH)-
27
1585.142
1603.176
1568.1
810.605
1630.138
28
1643.184
1661.218
1626.2
839.626
1688.180
29
1701.226
1719.260
1684.2
868.647
1746.222
30
1759.268
1777.302
1742.2
897.668
1804.264
31
1817.309
1835.344
1800.3
926.689
1862.306
32
1875.351
1893.386
1858.3
955.710
1920.348
33
1933.393
1951.428
1916.4
984.731
1978.390
34
1991.435
2009.469
1974.4
1013.752
2036.431
35
2049.477
2067.511
2032.5
1042.773
2094.473
36
2107.519
2125.553
2090.5
1071.794
2152.515
37
2165.561
2183.595
2148.5
1100.815
2210.557
38
2223.603
2241.637
2206.6
1129.836
2268.599
39
2281.645
2299.679
2264.6
1158.857
2326.641
40
2339.687
2357.721
2322.7
1187.878
2384.683
41
2397.728
2415.783
2380.7
1216.899
2442.724
42
2455.770
2473.805
2438.7
1245.920
2500.766
43
2513.812
2531.847
2496.8
1274.940
2558.808
44
2571.854
2589.888
2554.8
1303.961
2616.850
45
2629.896
2647.930
2612.9
1332.982
2674.892
46
2687.938
2705.972
2670.9
1362.003
2732.934
47
2745.980
2764.014
2729.0
1391.024
2790.976
48
2804.022
2822.056
2787.0
1420.045
2849.017
49
2862.064
2880.098
2845.0
1449.066
2907.059
50
2920.106
2938.140
2903.1
1478.087
2965.101
51
2978.147
2996.182
2961.1
1507.108
3023.143
52
3036.189
3054.224
3019.2
1536.129
3081.185
53
3094.231
3112.266
3077.2
1565.150
3139.227
54
3152.273
3170.307
3135.2
1594.171
3197.269
55
3210.315
3228.349
3193.3
1623.192
3255.311
56
3268.357
3286.391
3251.3
1652.213
3313.352
57
3326.399
3344.433
3309.4
1681.234
3371.394
58
3384.441
3402.475
3367.4
1710.255
3429.436
59
3442.483
3460.517
3425.5
1739.276
3487.478
60
3500.525
3518.559
3483.5
1768.297
3545.5202
61
3558.566
3576.601
3541.5
1797.318
3603.562
62
3616.608
3634.643
3599.6
1826.339
3661.604
63
3674.650
3692.685
3657.6
1855.359
3719.645
64
3732.692
3750.726
3715.7
1884.380
3777.687
Q Trap LC/MS/MS Hardware Manual
Appendix B: PPG Exact Mass Table
n
Exact Mass
(M)
(M = NH4)+
MS/MS
Fragments
(M = 2NH4)2+
(M = COOH)-
65
3790.734
3808.768
3773.7
1913.401
3835.729
66
3848.776
3866.810
3831.7
1942.422
3893.771
67
3906.818
3924.852
3889.8
1971.443
3951.813
68
3964.860
3982.894
3947.8
2000464
4009.855
69
4022.902
4040.936
4005.9
2029.485
4067.897
70
4080.944
4098.978
4063.9
2058.506
4125.938
71
4138.985
4157.020
4122.0
2087.527
4183.980
72
4197.027
4215.062
4180.0
2116.548
4242.022
73
4255.069
4273.104
4238.0
2145.569
4300.064
74
4313.111
4331.145
4296.1
2174.590
4358.106
75
4371.153
4389.187
4354.1
2203.611
4416.148
76
4429.195
4447.229
4412.2
2232.632
4474.190
77
4487.237
4505.271
4470.2
2261.653
4532.231
78
4545.279
4563.313
4528.3
2290.674
4590.273
79
4603.321
4621.355
4586.3
2319.695
4648.315
80
4661.363
4679.397
4644.3
2348.716
4706.357
81
4719.404
4737.439
4702.4
2377.737
4764.399
82
4777.446
4795.481
4760.4
2406.758
4822.441
57
Appendix B: PPG Exact Mass Table
58
Q Trap LC/MS/MS Hardware Manual
Q Trap LC/MS/MS Hardware Manual
Appendix C: Scan Parameter Settings
Appendix C: Scan Parameter
Settings
Q1 Scan Parameter Settings
Parameter
ID
Parameter
Name
Parameter
Group
Ion
Sources
Access
Rule
Access
ID
Access Name
IS
IonSpray
Voltage
Source / Gas
FNS
Operator
IS
IS
IonSpray
Voltage
Source / Gas
IS, TIS
Operator
NC
Nebulizer
Current
Source / Gas
HN
TEM
Temperature
Source / Gas
GS1
Gas 1
GS2
Equation
Default
(Offset)
Access
Min.
Access
Max
IonSpray
Voltage
700
0
3000
IS
IonSpray
Voltage
5000
(- 4200)
0
5000
Operator
NC
Nebulizer
Current
2
0
6
TIS,
HN
Operator
TEM
Temperature
0
0
550
Source / Gas
ALL
Operator
GS1
Gas 1
20
0
90
Gas 2
Source / Gas
ALL
Operator
GS2
Gas 2
0
0
90
CUR
Curtain Gas
Source / Gas
ALL
Operator
CUR
Curtain Gas
20
10
55
CAD
Collision Gas
Source / Gas
ALL
Fixed
CAD
Collision Gas
0
OR
Orifice Plate
Compound
ALL
Potential
Diff.
DP
Declustering
Potential
DP = OR
20
0
200
Q0
Focusing
Rod
Offset
Compound
ALL
Potential
Diff.
EP
Entrance
Potential
EP = -Q0 *
10
1
12
IQ1
Focusing
Lens 1
Compound
ALL
Param.
Dep.
IQ1 = Q0 +
offset
–1
ST
Prefilter
Compound
ALL
Param.
Dep.
ST = Q0 +
offset
–5
RO1
Q1 Rod
Offset
Resolution
ALL
Potential
Diff.
IE1 = Q0 –
RO1
1
FI2
Focusing
Interface 2
Compound
ALL
Hidden
RO2
Collision
Cell Rod
Offset
Compound
ALL
Fixed
AF2
Excitation
RF
Amplitude
Compound
ALL
Hidden
IQ3
Focusing
Lens 3
Compound
ALL
RO3
Q3 Rod
Offset
Compound
AF3
QTrap RF
Amplitude
EX
IE1
Ion Energy 1
RO2
Collision
Cell Rod
Offset
–30
Fixed
IQ3
Focusing
Lens 3
–150
ALL
Fixed
RO3
Q3 Rod
Offset
–150
Compound
ALL
Hidden
Exit Lens
Detector
ALL
Fixed
EX
Exit Lens
–100
EXB
Exit Barrier
Compound
ALL
Hidden
DF
Deflector
Detector
ALL
Fixed
DF
Deflector
–200
0.5
59
Appendix C: Scan Parameter Settings
Q Trap LC/MS/MS Hardware Manual
Q1 Scan Parameter Settings (Continued)
Parameter
ID
Parameter
Name
Parameter
Group
Ion
Sources
Access
Rule
Access
ID
Access Name
CEM
CEM
Detector
ALL
Operator
CEM
ihe
Interface
Heater
Source / Gas
ALL
Operator
C2
Collar 2
Compound
ALL
Fixed
C2B
Collar 2
Barrier
Compound
ALL
Hidden
XA3
Trap RF
Amplitude
(original)
Compound
ALL
XA2
Excitation
Energy
(original)
Compound
ALL
60
Equation
Default
(Offset)
Access
Min.
Access
Max
CEM
1800
500
3000
ihe
Interface
Heater
1
0
1
C2
Collar 2
0
Fixed
XA3
Trap RF
Amplitude
(original)
0
Fixed
XA2
Excitation
Energy
(original)
0
Q Trap LC/MS/MS Hardware Manual
Appendix C: Scan Parameter Settings
.
Q3 Scan Parameter Settings
Parameter
ID
Parameter
Name
Parameter.
Group
Ion
Source
Access
Rule
Access ID
Access Name
IS
IonSpray
Default
(Offset)
Access
Min.
Access
Max
Source / Gas
FNS
Operator
IS
IonSpray
Voltage
700
0
3000
Source / Gas
FNS
Operator
IS
IonSpray
Voltage
5000
(-4200)
0
5500
Source / Gas
IS, TIS
Operator
NC
Nebulizer
Current
2
0
6
Voltage
IS
IonSpray
Voltage
NC
Nebulizer
Current
Equation
TEM
Temperature
Source / Gas
HN
Operator
TEM
Temperature
0
0
550
GS1
Gas 1
Source / Gas
TIS,
HN
Operator
GS1
Gas 1
20
0
90
GS2
Gas 2
Source / Gas
ALL
Operator
GS2
Gas 2
0
0
90
CUR
Curtain Gas
Source / Gas
ALL
Operator
CUR
Curtain Gas
20
10
55
CAD
Collision
Gas
Source / Gas
ALL
Fixed
CAD
Collision Gas
1
OR
Orifice Plate
Compound
ALL
Potential
Diff.
DP
Declustering
Potential
DP = OR
20
0
200
Q0
Focusing
Rod Offset
Compound
ALL
Potential
Diff.
EP
Entrance
Potential
EP = –Q0
10
1
12
IQ1
Focusing
Lens 1
Compound
ALL
Param.
Dep.
IQ1 = Q0
+ offset
–1
ST
Prefilter
Compound
ALL
Param.
Dep.
ST = Q0
+ offset
–5
RO1
Q1 Rod
Offset
Compound
ALL
Param.
Dep.
RO1 = Q0
–1
IQ2
Focusing
Lens 2
Compound
ALL
Param.
Dep.
IQ2 = RO2
+2
FI2
Focusing
Compound
ALL
Hidden
–20
–142
–1
Interface 2
RO2
Collision
Cell Rod
Offset
Compound
ALL
Operator
RO2
Collision
Cell Rod
Offset
AF2
Excitation
RF
Amplitude
Compound
ALL
Hidden
IQ3
Focusing
Lens 3
Compound
ALL
Potential
Diff.
CXP
Collision
Cell Exit
Potential
CXP = RO2
– IQ3
Q3mass
0
58
RO3
Q3 Rod
Offset
Resolution
ALL
Potential
Diff.
IE3
Ion Energy 3
IE3 = RO2
– RO3
4
0.5
8
AF3
QTrap RF
Amplitude
Compound
ALL
Hidden
EX
Exit Lens
Detector
ALL
Fixed
EX
Exit Lens
–100
EXB
Exit Barrier
Compound
ALL
Hidden
DF
Deflector
Detector
ALL
Fixed
DF
Deflector
–200
61
Appendix C: Scan Parameter Settings
Q Trap LC/MS/MS Hardware Manual
Q3 Scan Parameter Settings (Continued)
Parameter
ID
Parameter
Name
Parameter.
Group
Ion
Source
Access
Rule
Access ID
Access Name
CEM
CEM
Detector
ALL
Operator
CEM
ihe
Interface
Heater
Source / Gas
ALL
Operator
C2
Collar 2
Compound
ALL
Fixed
C2B
Collar 2
Barrier
Compound
ALL
Hidden
XA3
Trap RF
Amplitude
(original)
Compound
ALL
XA2
Excitation
Energy
(original)
Compound
ALL
62
Equation
Default
(Offset)
Access
Min.
Access
Max
CEM
1800
500
3000
ihe
Interface
Heater
1
0
1
C2
Collar 2
0
Fixed
XA3
Trap RF
Amplitude
(original)
0
Fixed
XA2
Excitation
Energy
(original)
0
Q Trap LC/MS/MS Hardware Manual
Appendix C: Scan Parameter Settings
.
MS/MS Scan Parameter Settings
Parameter
ID
Parameter
Name
Parameter
Group
Ion
Source
Access
Rule
Access
ID
Access Name
IS
IonSpray
Voltage
Source / Gas
FNS
Operator
IS
IS
IonSpray
Voltage
Source / Gas
FNS
Operator
NC
Nebulizer
Current
Source / Gas
FNS
TEM
Temperature
Source / Gas
GS1
Gas 1
GS2
Default
(Offset)
Access
Min.
Access
Max
IonSpray
Voltage
700
0
3000
IS
IonSpray
Voltage
5000
(-4200)
0
5500
Operator
NC
Nebulizer
Current
2
0
6
IS, TIS
Operator
TEM
Temperature
0
0
550
Source / Gas
HN
Operator
GS1
Gas 1
20
0
90
Gas 2
Source / Gas
TIS,
HN
Operator
GS2
Gas 2
0
0
90
CUR
Curtain Gas
Source / Gas
ALL
Operator
CUR
Curtain Gas
20
10
55
CAD
Collision Gas
Source / Gas
ALL
Simplified
CAD
Collision Gas
medium
low
high
OR
Orifice Plate
Compound
ALL
Potential
Diff.
DP
Declustering
Potential
DP = OR
20
0
200
Q0
Focusing
Rod Offset
Compound
ALL
Potential
Diff.
EP
Entrance
Potential
EP = – Q0
10
1
12
IQ1
Focusing
Lens 1
Compound
ALL
Param.
Dep.
IQ1 = Q0
+ offset
–1
ST
Prefilter
Compound
ALL
Param.
Dep.
ST = Q0
+ offset
–5
RO1
Q1 Rod
Offset
Resolution
ALL
Potential
Diff.
IE1
Ion Energy 1
IE1 = Q0
– RO1
1
0.5
2
IQ2
Focusing
Lens 2
Compound
ALL
Potential
Diff.
CEP
Collision
Cell Ent.
Potential
CEP = Q0
– IQ2
Q1 mass
0
188
FI2
Focusing
Interface 2
Compound
ALL
Hidden
RO2
Collision
Cell Rod
Offset
Compound
ALL
Potential
Diff.
CE
Collision
Energy
CE = Q0
– RO2
30
5
130
AF2
Excitation
RF
Amplitude
Compound
ALL
Hidden
IQ3
Focusing
Lens 3
Compound
ALL
Potential
Diff.
CXP
Collision
Cell Exit
Potential
CXP = RO2
– IQ3
15
0
58
RO3
Q3 Rod
Offset
Resolution
ALL
Potential
Diff.
IE3
Ion Energy 3
IE3 = RO2
– RO3
4
0.5
8
AF3
QTrap RF
Amplitude
Compound
ALL
Hidden
EX
Exit Lens
Detector
ALL
Fixed
EXB
Exit Barrier
Compound
ALL
Hidden
DF
Deflector
Detector
ALL
Fixed
DF
Deflector
–200
CEM
CEM
Detector
ALL
Operator
CEM
CEM
1800
500
3000
EX
Equation
–100
63
Appendix C: Scan Parameter Settings
Q Trap LC/MS/MS Hardware Manual
MS/MS Scan Parameter Settings (Continued)
Parameter
ID
Parameter
Name
Parameter
Group
Ion
Source
Access
Rule
Access
ID
Access Name
ihe
Interface
Heater
Source / Gas
ALL
Operator
ihe
C2
Collar 2
Compound
ALL
Fixed
C2B
Collar 2
Barrier
Compound
ALL
Hidden
XA3
Trap RF
Amplitude
(original)
Compound
ALL
XA2
Excitation
Energy
(original)
Compound
ALL
64
Equation
Default
(Offset)
Access
Min.
Access
Max
Interface
Heater
1
0
1
C2
Collar 2
0
Fixed
XA3
Trap RF
Amplitude
(original)
0
Fixed
XA2
Excitation
Energy
(original)
0
Q Trap LC/MS/MS Hardware Manual
.
.
LIT Scan Parameter Settings
Parameter
ID
Parameter
Name
Parameter
Group
IS
IonSpray
Voltage
NC
Ion
Source
Access
Rule
Access
ID
Access Name
Source / Gas
Operator
IS
Nebulizer
Current
Source / Gas
Operator
TEM
Temperature
Source / Gas
GS1
Gas 1
GS2
Equation
Default
(Offset)
Access
Min.
Access
Max
IonSpray
Voltage
5000
(-4200)
0
5500
NC
Nebulizer
Current
2
0
6
Operator
TEM
Temperature
0
0
550
Source / Gas
Operator
GS1
Gas 1
20
0
90
Gas 2
Source / Gas
Operator
GS2
Gas 2
0
0
90
CUR
Curtain Gas
Source / Gas
Operator
CUR
Curtain Gas
20
10
55
CAD
Collision Gas
Source / Gas
Simplified
CAD
Collision Gas
mediu
m
low
high
OR
Orifice Plate
Compound
Potential
Diff.
DP
Declustering
Potential
DP = OR
20
0
200
Q0
Focusing
Rod Offset
Compound
Potential
Diff.
Q0
Entrance
Potential
EP = -Q0*
10
1
12
IQ1
Focusing
Lens 1
Compound
Hidden
ST
Prefilter
Compound
Parameter
Dep.
ST = Q0
+ offset
–5
RO1
Q1 Rod
Offset
Resolution
Potential
Diff.
IQ2
Focusing
Lens 2
Compound
Hidden
FI2
Focusing
Interface 2
Compound
RO2
Collision
Cell Rod
Offset
AF2
IE1
Ion Energy 1
IE1 = Q0
– RO1
1
0.5
2
Potential
Diff.
CEP
Collision
Cell Ent.
Potential
CEP = Q0
– FI2
Q1
mass
0
188
Compound
Potential
Diff.
CE
Collision
Energy
CE = Q0
– RO2
30
5
130
Excitation
RF
Amplitude
Compound
Operator
AF2
Q2 Auxiliary
RF
Amplitude
0
0
20
IQ3
Focusing
Lens 3
Compound
Hidden
RO3
Q3 Rod
Offset
Compound
Hidden
AF3
QTrap RF
Amplitude
Compound
Operator
AF3
Q3 Auxiliary
RF
Amplitude
Q3
mass
and
scan
speed
0
5
EX
Exit Lens
Compound
Hidden
Q3
mass
and
scan
speed
0
5
EXB
Exit Barrier
Compound
Operator
4
2
15
EXB
Exit Barrier
65
.
Q Trap LC/MS/MS Hardware Manual
LIT Scan Parameter Settings (Continued)
Parameter
ID
Parameter
Name
Parameter
Group
DF
Deflector
CEM
Access
Rule
Access
ID
Access Name
Detector
Fixed
DF
Deflector
–400
CEM
Detector
Operator
CEM
CEM
ihe
Interface
Heater
Source / Gas
Operator
ihe
Interface
Heater
C2
Collar 2
Compound
ALL
Hidden
C2B
Collar 2
Barrier
Compound
ALL
Operator
XA3
Trap RF
Amplitude
(original)
Compound
ALL
Hidden
Q3
mass
and
scan
XA2
Excitation
Energy
(original)
Compound
ALL
Hidden
0
66
Ion
Source
Equation
Default
(Offset)
Access
Min.
Access
Max
1800
500
3000
1
0
1
-500
500
0
C2B
Collar 2
Barrier
Q Trap LC/MS/MS Hardware Manual
Appendix D: Consumables
Appendix D:
Consumables
The following is a list of consumables for the Q Trap LC/MS/MS system:
Item
Part No.
Description
1
011556
Tube, Teflon 1/32"ID × 1/16"OD
2
011555
Tube, Teflon 1/16" × .007"ID
3
016316
Tube 1/16 OD × .005 BORE
4
015968
Fitting, Union 1/16, .010 ORIF
5
012627
Fitting, Rheflex 1/16
6
012637
Ferrule, Rheflex 1/16
7
014629
Tool, Swab, Anti-Static Foam
8
020783
Fuse, 2.5A 250V 5 × 2 OMM SB
9
017363
Filter, Intake Air
10
010615
Syringe, Gas Tight, 1.0 mL
11
024676
Syringe, Gas Tight, 10 uL
12
010613
Needle, Syringe, Removable
13
010616
Needle, Syringe, Luer Hub, 2"
14
001935
Tube, TFL 1/8 OD × 0.15 WALL
15
019670
Tool, Swab Anti-Static Foam
16
016492
Cap, Tubing Fused SIL 0.16 OD
17
010352
Fuse, 4A 250V 5x20 SLO-BLO
18
019667
Tube, Loop Diverter Valve 10UL
19
019668
Fitting, Adapter Syringe 1/16"
20
011281
Tool, Tube Cutter, Peek
67
Appendix D: Consumables
68
Q Trap LC/MS/MS Hardware Manual
Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
Appendix E:
Sample Experiments
The examples below are sample experiments you can set up to familiarize yourself with
the function of the Q Trap LC/MS/MS system. The examples indicate the procedures you
should follow for creating small and large molecule experiments.
Small Molecules: EPI
Use the example experiment below as a guide when creating EPI experiments.
To create an EPI scan
1. On the Analyst Navigation bar, click Acquire, and then double-click Build
Acquisition Method.
The Acquisition Method Editor appears.
2. In the Acquisition method pane, highlight Period, right-click, and then select Add
Experiment
3. Click the MS tab.
4. In the Scan Type list, select Enhanced Product Ion (EPI).
5. Specify parameters as shown in the example below.
6. Click Edit Parameters.
The Period/Experiment/Parameter Table dialog box appears.
7. Click the Source/Gas tab.
The dialog box below shows typical values for the parameters. You may have to alter
these parameters for optimal performance based on the LC flow rate. For example, if
69
Appendix E: Sample Experiments
Q Trap LC/MS/MS Hardware Manual
you are not in Simplified mode, you will need to set the CAD gas high enough to
achieve a base pressure of 4e-5 torr.
8. Click the Compound tab.
The dialog box below shows typical values for the parameters.
9. Click OK.
10. Click the Advanced MS tab.
Specify parameters as shown in the following figure. You may have to alter these
parameters for optimal performance. For example, a resolution of 1000 amu/s will
give you high sensitivity, however, if you want to see more points across a
chromatographic peak, set the resolution to 4000 amu/s.
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Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
To increase sensitivity you can select Q0 Trapping or increase the Trap fill time. Be
aware that too much ion current can saturate the ion trap, cause space charge, and
result in poor resolution of peaks.
Small Molecules: MS3
Use the MS/MS/MS (MS3) scan to gather further information about a fragment ion. This
is useful in determining the structure of metabolites, for example, where the modification
occurred in the molecule. You can use the example experiment below as a guide when
creating MS3 experiments.
To create an MS3 scan
1. On the Navigation bar, click Acquire, and then double-click Build Acquisition
Method.
The Acquisition Method Editor appears.
2. In the Acquisition method pane, highlight Period, right-click, and then select Add
Experiment
3. Click the MS tab.
4. In the Scan Type list, select MS/MS/MS (MS3).
5. Specify parameters as shown in the example below. You may want to alter these
parameters for optimal performance. For example, if you select No Fragmentation,
the second precursor ion is isolated but not fragmented. Therefore the spectrum will
display only the second precursor ion.
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Appendix E: Sample Experiments
Q Trap LC/MS/MS Hardware Manual
6. Click Edit Parameters.
The Period/Experiment/Parameter Table dialog box appears.
7. Click the Source/Gas tab.
The dialog box below shows typical values for the parameters.
8. Click the Compound tab.
The following dialog box shows typical values for the parameters. You may want to
alter these parameters for optimal performance. For example, you should set CE to
give the best results for the second precursor ion. You can also optimize AF2. A good
starting point for AF2 is 60.
72
Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
9. Click OK.
10. Click the Advanced MS tab.
Specify parameters as shown in the example below. You may have to alter these
parameters for optimal performance. For example, you can increase the Excitation
Time to increase the energy applied to the second precursor ion.
To increase the sensitivity of the scan, set the Q1 Resolution to Low or Open. The
Q3 Resolution determines the isolation window of the second precursor ion. Set Q3
Resolution to Open to see the entire isotope pattern in the spectrum.
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Appendix E: Sample Experiments
Q Trap LC/MS/MS Hardware Manual
Large Molecules:
Protein Identification—Tryptic Digest
The QTrap LC/MS/MS system provides better sensitivity, higher resolution and faster
scan speeds than a conventional triple quadrupole mass spectrometer when analyzing
proteolytic digests. This new technology, integrated with information dependent data
acquisition (IDA), provides a powerful tool to design specific experiments based on each
protein applications. You can use the example experiment below as a guide when creating
your own experiments.
This example requires you to create multiple scans. You must perform the following steps
in order:
1. Create an Enhanced MS scan.
2. Create an Enhanced Resolution scan.
3. Create an IDA experiment.
4. Create an Enhanced Product Ion scan.
5. Submit the samples.
6. View the results in Explore mode.
Step 1: Create an EMS scan
1. On the Analyst Navigation bar, click Acquire, and then double-click Build
Acquisition Method.
The Acquisition Method Editor appears.
2. In the Acquisition method pane, highlight Period, right-click, and then select Add
Experiment
3. Click the MS tab.
4. In the Scan Type list, select Enhanced MS (EMS).
5. Specify parameters as shown in the following example.
6. Click Edit Parameters.
74
Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
The Period/Experiment/Parameter Table dialog box appears.
7. Click the Source/Gas tab.
The dialog box below shows typical values for the parameters.
8. Click the Compound tab.
The dialog box below shows typical values for the parameters.
9. Click OK.
10. Click the Advanced MS tab.
Specify parameters as shown in the dialog box below.
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Appendix E: Sample Experiments
Q Trap LC/MS/MS Hardware Manual
Step 2: Create an ER scan
1. In the Acquisition method pane, highlight Period, right-click, and then select Add
Experiment
2. Click the MS tab.
3. In the Scan Type list, select Enhanced Resolution (ER).
4. Specify parameters as shown in the example below.
5. Click the Advanced MS tab.
Specify parameters as shown in the figure below.
76
Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
Step 3: Create an IDA experiment
1. In the Acquisition method pane, highlight Period, right-click, and then select Add
IDA Criteria Level.
2. Click the IDA First Criteria Level tab.
3. Set a range for the most intense peaks.
4. Specify parameters as shown in the example below.
Step 4: Create an EPI scan
1. In the Acquisition method pane, highlight Period, right-click, and then select Add
Experiment
2. Click the MS tab.
77
Appendix E: Sample Experiments
Q Trap LC/MS/MS Hardware Manual
3. In the Scan Type list, select Enhanced Product Ion (EPI).
4. Specify parameters as shown in the example below.
5. Click the Advanced MS tab.
Specify parameters as shown in the figure below.
6. On the toolbar, click the Save button to save the acquisition method.
Step 5: Submit the samples
1. On the Navigation bar, click Acquire, and then double-click Build Acquisition
Batch.
2. Click the Sample tab.
3. Click Add Set.
The Add Samples dialog box appears.
78
Q Trap LC/MS/MS Hardware Manual
Appendix E: Sample Experiments
4. Select an Acquisition method from the list.
5. Click the Submit tab.
6. Click Submit.
7. From the Acquire menu, click Start Sample.
Step 6: View the results in Explore mode
1. On the Navigation bar, click Explore, and then double click Open Data File.
The Select Sample dialog box appears.
2. Click the data file and sample you just created, and then click OK.
The data is displayed in four spectra: TIC, EMS, ER, EPI.
79
Appendix E: Sample Experiments
80
Q Trap LC/MS/MS Hardware Manual
Q Trap LC/MS/MS Hardware Manual
Index
Index
A
anti-suckback valve 28
C
CAD process 8
collision cell 9, 36, 37
collisionally activated dissociation 8
components of the system electronics
box 40
compound-specific parameters,
setting instrument parameters 42
Curtain gas 23–24, 37
turning on the Curtain gas 43
Curtain gas interlocks 33
D
DC distribution board 39
deflector voltage 39
differentially pumped interface 23–24
E
elucidation, structural 9
enhanced modes 11
enhanced product ions scans 6
entrance optics 24
F
fragmenting
precursor ions 7, 37
product ions 8
G
gas ballast valve 29
gas control assembly 25–26
gas control sequence 33
gas control system 31
gas curtain interface 22
gas flow controllers 31
H
Heated Nebulizer inlet 40
Heated Nebulizer ion source 6, 17
Heater gas flow 32
I
instrument
warming up 44
instrument parameters 41
instrument-specific parameters,
setting 42
interface vacuum 28
interquad lenses 10
ion count 9
ion optics path 37
ion path chamber 35
ion source
Heated Nebulizer 17
ions
fragmentation 9
precursor 8, 9, 10
product 8, 9
L
lenses, interquad 10
Linear Ion Trap 36
linear ion trap mode 5
M
maintenance checklist 53
mass filter rail 35
mass filters 35
mass spectrometry
principles 7
principles of MS 7–8
principles of MS/MS 8–10
principles of MS/MS/MS 10–11
single quadrupole 7
triple quadrupole 8, 9
modes
enhanced 11
N
Nebulizer gas flow 32
P
parameters
compound-specific 41
instrument-specific 41
source-specific 41
power distribution module, AC, DC
distribution boards 39
powering up the mass spectrometer
43
PPG Exact Mass Table 55
precursor 6
precursor ions 8, 10
precursor ions, fragmenting 7
principles, mass spectrometry 7
product ions 8
product ions, fragmenting 8
pump-down sequence 46
pumping down 46
pumping system 25
Q
Q Trap
enhanced scans 6
quadrupole 36
quadrupole, single 7
quadrupoles, RF-only 9, 35–36
R
removing
instrument covers 48
ion source 51
RF-only
quadrupoles 9, 35–36
roughing pump 28
roughing pump interlock 34
S
safe disposal, source exhaust gases 19
safety interlocks, vacuum control
system 33
sample introduction system 14
setting parameters
compound-specific 42
instrument-specific 42
81
Index
Q Trap LC/MS/MS Hardware Manual
source-specific 43
shutting down the mass spectrometer
44
source exhaust gases
safe disposal 19
toxic gases 19
source exhaust system, overview 19
structural elucidation 9
support, technical 3
system electronics 48
systems electronic box, components
of 40
T
tables, PPG Exact Mass 55
technical support 3
toxic gases
source exhuast gases 19
turbo pump 24–27, 33, 43, 46
turbo pump controllers 25–26
TurboIonSpray ion source 15
V
vacuum control system 24
vacuum control system, safety
interlocks 33
vacuum feedthroughs 37
vacuum gauge 24, 29–30, 46, 47
vacuum gauge controller 30–31
vacuum interface 22, 24, 28
vacuum off sequence 25, 31–33
vacuum system 21, 44
W
warming up instrument 44
work flow process 41
82