Waters Xevo TQ MS Operating manual

Waters Xevo TQ MS
Operator’s Overview and Maintenance Guide
71500130002 / Revision D
Copyright © Waters Corporation 2013.
All rights reserved

ii February 11, 2013, 71500130002 Rev. D

February 11, 2013, 71500130002 Rev. D iii
General Information
Copyright notice
© 2013 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS
DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY
FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use. For the
most recent revision of this document, consult the Waters Web site
(waters.com).
Trademarks
ACQUITY, ACQUITY UPLC, Connections INSIGHT, ESCi, MassLynx,
nanoACQUITY UPLC, UltraPerformance LC, UNIFI, UPLC, Xevo, Waters,
and Waters Quality Parts are registered trademarks of Waters Corporation,
and IntelliStart, NanoFlow, OpenLynx, ScanWave, T-Wave, TargetLynx,
“THE SCIENCE OF WHAT'S POSSIBLE.”, and ZSpray are trademarks of
Waters Corporation.
GELoader is a registered trademark of New Brunswick Scientific, Co., Inc.
Phillips is a registered trademark of Phillips Screw Company, Inc.
PEEK is a trademark of Victrex Corporation.
snoop and Swagelok are registered trademarks of Swagelok Company.
Teflon and Viton are registered trademarks of DuPont.
Varian is a trademark of Varian, Inc.
Xylan is a registered trademark of Whitford Corporation.
Other registered trademarks or trademarks are the sole property of their
owners.

iv February 11, 2013, 71500130002 Rev. D
Customer comments
Waters’ Technical Communications organization invites you to report any
errors that you encounter in this document or to suggest ideas for otherwise
improving it. Help us better understand what you expect from our
documentation so that we can continuously improve its accuracy and
usability.
We seriously consider every customer comment we receive. You can reach us
at [email protected].
Contacting Waters
Contact Waters®with enhancement requests or technical questions regarding
the use, transportation, removal, or disposal of any Waters product. You can
reach us via the Internet, telephone, or conventional mail.
Waters contact information:
Contacting medium Information
Internet The Waters Web site includes contact
information for Waters locations worldwide.
Visit www.waters.com.
Telephone and fax From the USA or Canada, phone 800
252-HPLC, or fax [phone].
For other locations worldwide, phone and fax
numbers appear in the Waters Web site.
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

February 11, 2013, 71500130002 Rev. D v
Safety considerations
Some reagents and samples used with Waters instruments and devices can
pose chemical, biological, or radiological hazards (or any combination thereof).
You must know the potentially hazardous effects of all substances you work
with. Always follow Good Laboratory Practice, and consult your organization’s
safety representative for guidance.
Considerations specific to the Xevo TQ MS
Solvent leakage hazard
The source exhaust system is designed to be robust and leak-tight. Waters
recommends you perform a hazard analysis, assuming a maximum leak into
the laboratory atmosphere of 10% LC eluate.
Flammable solvents hazard
When using flammable solvents, ensure that a stream of nitrogen
continuously flushes the instrument’s source, and the nitrogen supply
pressure remains above 690 kPa (6.9 bar, 100 psi). You must also install a
gas-fail device that interrupts the solvent flowing from the LC system in the
event the supply of nitrogen fails.
Warning:
• To confirm the integrity of the source exhaust system, renew
the source O-rings at intervals not exceeding one year.
• To avoid chemical degradation of the source O-rings, which can
withstand exposure only to certain solvents (see “Solvents used
to prepare mobile phases” on page 213), determine whether any
solvents you use that are not listed are chemically compatible
with the composition of the O-rings.
Warning: To prevent ignition of flammable solvent vapors in the enclosed
space of a mass spectrometer’s ion source, ensure that nitrogen flows
continuously through the source. The nitrogen supply pressure must not
fall below 690 kPa (6.9 bar, 100 psi) during an analysis requiring the use
of flammable solvents. Also a gas-fail device must be installed, to
interrupt the flow of LC solvent should the nitrogen supply fail.

vi February 11, 2013, 71500130002 Rev. D
High temperature hazard
Xevo TQ MS high temperature hazard:
Warning: To avoid burn injuries, avoid touching the source ion block
assembly when operating or servicing the instrument.
TP03127
TQMS
TQ MS
Source ion block assembly

February 11, 2013, 71500130002 Rev. D vii
Hazards associated with removing an instrument from service
When you remove the instrument from use to repair or dispose of it, you must
decontaminate all of its vacuum areas. These are the areas in which you can
expect to encounter the highest levels of contamination:
• Source interior
• Waste tubing
• Exhaust system
• Rotary pump oil (where applicable)
The need to decontaminate other vacuum areas of the instrument depends on
the kinds of samples the instrument analyzed and their levels of
concentration. Do not dispose of the instrument or return it to Waters for
repair until the authority responsible for approving its removal from the
premises specifies the extent of decontamination required and the level of
residual contamination permissible. That authority must also prescribe the
method of decontamination to be used and the appropriate protection for
personnel undertaking the decontamination process.
You must handle items such as syringes, fused silica lines, and borosilicate
tips used to carry sample into the source area in accordance with laboratory
procedures for contaminated vessels and sharps. To avoid contamination by
carcinogens, toxic substances, or biohazards, you must wear
chemical-resistant gloves when handling or disposing of used oil.
Warning: To avoid personal contamination with biohazards,
toxic materials, and corrosive materials, wear
chemical-resistant gloves during all phases of instrument
decontamination.
Warning: To avoid puncture injuries, handle syringes, fused
silica lines, and borosilicate tips with extreme care.

viii February 11, 2013, 71500130002 Rev. D
FCC radiation emissions notice
Changes or modifications not expressly approved by the party responsible for
compliance, could void the users authority to operate the equipment. This
device complies with Part 15 of the FCC Rules. Operation is subject to the
following two conditions: (1) this device may not cause harmful interference,
and (2) this device must accept any interference received, including
interference that may cause undesired operation.
Canada spectrum management emissions notice
This class A digital product apparatus complies with Canadian ICES-003.
Cet appareil numérique de la classe A est conforme à la norme NMB-003.
Electrical power safety notice
Do not position the instrument so that it is difficult to operate the
disconnecting device.
Safety hazard symbol notice
Documentation needs to be consulted in all cases where the symbol is
used to find out the nature of the potential hazard and any actions which have
to be taken.
Equipment misuse notice
If the equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired.
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.

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Operating this instrument
When operating this instrument, follow standard quality-control (QC)
procedures and the guidelines presented in this section.
Applicable symbols
Audience and purpose
This guide is for operators of varying levels of experience. It gives an overview
of the instrument, and explains how to prepare it, change its modes of
operation, and maintain it.
Symbol Definition
Manufacturer
Authorized representative of the European
Community
Confirms that a manufactured product complies
with all applicable European Community
directives
Australia C-Tick EMC compliant
Confirms that a manufactured product complies
with all applicable United States and Canadian
safety requirements
Consult instructions for use
Contact Waters Corporation for the correct
disposal and recycling instructions

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Intended use of the Xevo TQ MS
Waters designed the tandem quadrupole Xevo®TQ MS for use as a research
tool to deliver authenticated mass measurement in both MS and MS/MS
modes.
Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards should include the entire range of QC samples, typical specimens,
and atypical specimens.
When calibrating mass spectrometers, consult the calibration section of the
operator’s guide for the instrument you are calibrating. In cases where an
overview and maintenance guide, not operator’s guide, accompanies the
instrument, consult the instrument’s online Help system for calibration
instructions.
Quality-control
Routinely run three QC samples that represent subnormal, normal, and
above-normal levels of a compound. Ensure that QC sample results fall within
an acceptable range, and evaluate precision from day to day and run to run.
Data collected when QC samples are out of range might not be valid. Do not
report these data until you are certain that the instrument performs
satisfactorily.
When analyzing samples from a complex matrix such as soil, tissue,
serum/plasma, whole blood, and other sources, note that the matrix
components can adversely affect LC/MS results, enhancing or suppressing
ionization. To minimize these matrix effects, Waters recommends you adopt
the following measures:
• Prior to the instrumental analysis, use appropriate sample
pretreatment such as protein precipitation, liquid/liquid extraction
(LLE), or solid phase extraction (SPE) to remove matrix interferences.
• Whenever possible, verify method accuracy and precision using
matrix-matched calibrators and QC samples.
• Use one or more internal standard compounds, preferably isotopically
labeled analytes.

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ISM classification
ISM Classification: ISM Group 1 Class A
This classification has been assigned in accordance with IEC CISPR 11
Industrial Scientific and Medical (ISM) instruments requirements. Group 1
products apply to intentionally generated and/or used conductively coupled
radio-frequency energy that is necessary for the internal functioning of the
equipment. Class A products are suitable for use in commercial (that is,
nonresidential) locations and can be directly connected to a low voltage,
power-supply network.
EC authorized representative
Waters Corporation (Micromass UK Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

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February 11, 2013, 71500130002 Rev. D xiii
General Information .................................................................................... iii
Copyright notice .................................................................................................. iii
Trademarks ........................................................................................................... iii
Customer comments ............................................................................................ iv
Contacting Waters ............................................................................................... iv
Safety considerations ........................................................................................... v
Considerations specific to the Xevo TQ MS........................................................ v
FCC radiation emissions notice ...................................................................... viii
Canada spectrum management emissions notice .......................................... viii
Electrical power safety notice ......................................................................... viii
Safety hazard symbol notice............................................................................ viii
Equipment misuse notice ................................................................................ viii
Safety advisories.............................................................................................. viii
Operating this instrument ................................................................................. ix
Applicable symbols ............................................................................................. ix
Audience and purpose......................................................................................... ix
Intended use of the Xevo TQ MS ........................................................................ x
Calibrating ........................................................................................................... x
Quality-control ..................................................................................................... x
ISM classification ................................................................................................. xi
ISM Classification: ISM Group 1 Class A ......................................................... xi
EC authorized representative ........................................................................... xi
1 Waters Xevo TQ MS Overview .............................................................. 21
Waters Xevo TQ MS ........................................................................................... 22
ACQUITY Xevo TQ MS UPLC/MS systems..................................................... 24
Non-ACQUITY devices for use with the Xevo TQ MS..................................... 25
Software and data system ................................................................................. 26
Table of Contents

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Ionization techniques and source probes .................................................... 27
Electrospray ionization (ESI)............................................................................ 27
Combined electrospray ionization and atmospheric pressure chemical
ionization (ESCi)................................................................................................ 27
Atmospheric pressure chemical ionization (APCI) .......................................... 27
Dual-mode APPI/APCI source........................................................................... 28
NanoFlow ESI source ........................................................................................ 28
IntelliStart Fluidics system ............................................................................. 29
Overview............................................................................................................. 29
System components ........................................................................................... 30
System operation ............................................................................................... 30
Ion optics .............................................................................................................. 31
MS operating modes .......................................................................................... 32
MS/MS operating modes ................................................................................... 33
Product (daughter) ion mode............................................................................. 34
Precursor (parent) ion mode.............................................................................. 34
Multiple reaction monitoring mode .................................................................. 35
Constant neutral loss mode............................................................................... 36
ScanWave daughter scan mode......................................................................... 37
Leak sensors ........................................................................................................ 38
Vacuum system ................................................................................................... 38
Rear panel ............................................................................................................ 39
2 Preparing the Mass Spectrometer for Operation ............................ 41
Starting the mass spectrometer ..................................................................... 42
Verifying the instrument’s state of readiness .................................................. 45
Monitoring the mass spectrometer LEDs......................................................... 45
Tuning and calibration information ................................................................. 45
Running the mass spectrometer at high flow rates ......................................... 46
Preparing the IntelliStart Fluidics system .................................................. 47
Installing the reservoir bottles.......................................................................... 47
Purging the infusion pump................................................................................ 48

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Rebooting the mass spectrometer .................................................................. 49
Leaving the mass spectrometer ready for operation ................................ 50
Emergency shutdown of the mass spectrometer ....................................... 50
3 Changing the Mode of Operation ........................................................ 51
ESI mode .............................................................................................................. 52
Installing the ESI probe .................................................................................... 52
Removing the ESI probe.................................................................................... 56
ESCi mode ............................................................................................................ 57
Optimizing the ESI probe for ESCi operation.................................................. 57
APCI mode ........................................................................................................... 57
Installing the APCI probe ................................................................................. 58
Removing the APCI probe ................................................................................. 60
Combined APPI/APCI source .......................................................................... 61
APPI operation................................................................................................... 61
APCI operation................................................................................................... 62
Dual-mode operation ......................................................................................... 63
The combined APPI/APCI source components................................................. 64
Installing the Combined APPI/APCI Source software..................................... 66
Removing the APCI probe and APPI source enclosure.................................... 68
NanoFlow ESI source ........................................................................................ 69
Installing the NanoFlow source ........................................................................ 70
Fitting a borosilicate glass capillary (nanovial)............................................... 73
Positioning the borosilicate glass capillary tip................................................. 77
Restarting a stalled borosilicate glass capillary electrospray ......................... 77

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4 Maintenance Procedures ...................................................................... 79
Maintenance schedule ...................................................................................... 81
Spare parts .......................................................................................................... 82
Troubleshooting with Connections INSIGHT ............................................. 83
Safety and handling .......................................................................................... 84
Preparing the instrument for working on the source .............................. 85
Removing and refitting the source enclosure ............................................. 87
Removing the source enclosure from the instrument...................................... 87
Fitting the source enclosure to the instrument................................................ 89
Installing and removing the corona pin ....................................................... 90
Installing the corona pin in the source............................................................. 90
Removing the corona pin from the source ........................................................ 93
Operating the source isolation valve ............................................................ 94
Removing O-rings and seals ............................................................................ 97
Cleaning the instrument case ......................................................................... 98
Emptying the nitrogen exhaust trap bottle ................................................. 98
Inspecting the Varian roughing pump oil level ........................................ 101
Adding oil to the Varian roughing pump ................................................... 102
Replacing the Varian roughing pump oil and oil mist filter ................. 104
Emptying the roughing pump oil.................................................................... 104
Replacing the oil mist filter............................................................................. 106
To refill the pump with oil............................................................................... 108
Cleaning the source components ................................................................. 110
Cleaning the sampling cone assembly ........................................................ 111
Removing the sampling cone assembly from the source ............................... 111
Disassembling the sampling cone assembly................................................... 113
Cleaning the sample cone and cone gas nozzle .............................................. 115
Assembling the sampling cone assembly........................................................ 117

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Fitting the sampling cone assembly to the source ......................................... 118
Cleaning the extraction cone ........................................................................ 120
Removing the ion block assembly from the source assembly........................ 120
Removing the extraction cone from the ion block .......................................... 122
Cleaning the extraction cone........................................................................... 124
Fitting the extraction cone to the ion block.................................................... 126
Fitting the ion block assembly to the source assembly.................................. 126
Cleaning the ion block assembly .................................................................. 128
Disassembling the source ion block assembly................................................ 128
Cleaning the ion block components ................................................................ 136
Assembling the source ion block assembly..................................................... 138
Cleaning the source hexapole assembly ..................................................... 140
Removing the ion block assembly, ion block support, and hexapole from
the source assembly......................................................................................... 140
Cleaning the hexapole assembly..................................................................... 142
Fitting the hexapole assembly, PEEK ion block support, and ion block
assembly to the source assembly .................................................................... 144
Replacing the ESI probe tip and gasket ..................................................... 146
Removing the ESI probe tip and gasket ......................................................... 146
Fitting the ESI probe tip and gasket.............................................................. 149
Replacing the ESI probe sample capillary ................................................ 150
Removing the existing capillary...................................................................... 150
Installing the new capillary ............................................................................ 155
Cleaning the APCI probe tip ......................................................................... 158
Replacing the APCI probe sample capillary ............................................. 159
Removing the existing capillary...................................................................... 159
Installing the new capillary ............................................................................ 162
Cleaning or replacing the corona pin ......................................................... 165
Replacing the APCI probe heater ................................................................ 166
Removing the APCI probe heater ................................................................... 166
Fitting the new APCI probe heater ................................................................ 169

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Replacing the ion block source heater ....................................................... 170
Replacing the source assembly seals .......................................................... 174
Removing the probe adjuster assembly probe and source enclosure seals... 174
Fitting the new source enclosure and probe adjuster assembly probe seals 177
Replacing the air filter ................................................................................... 179
APPI/APCI source—changing the UV lamp bulb ..................................... 181
APPI/APCI source—Cleaning the lamp window ...................................... 184
APPI/APCI source—Replacing the APPI lamp drive seals .................... 185
Removing the APPI lamp drive assembly seals............................................. 185
Fitting the new APPI lamp drive assembly O-rings...................................... 191
A Safety Advisories .................................................................................. 195
Warning symbols .............................................................................................. 196
Specific warnings ............................................................................................. 197
Caution advisory .............................................................................................. 200
Warnings that apply to all Waters instruments and devices ................. 201
Warnings that address the replacing of fuses ........................................... 206
Electrical and handling symbols .................................................................. 208
Electrical symbols ............................................................................................ 208
Handling symbols ............................................................................................ 209
B Materials of Construction and Compliant Solvents ..................... 211
Preventing contamination ............................................................................. 212
Items exposed to solvent ................................................................................ 212
Solvents used to prepare mobile phases .................................................... 213
C External Connections .......................................................................... 215
External wiring and vacuum connections ................................................. 216
Connecting the Varian oil-filled roughing pump ..................................... 217
Making the electrical connections to the Varian oil-filled roughing pump .. 222

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Connecting the Edwards oil-free roughing pump ................................... 223
Making the electrical connections for the Edwards oil-free roughing pump 228
Connecting to the nitrogen gas supply ....................................................... 229
Connecting to the collision cell gas supply ............................................... 230
Connecting the nitrogen exhaust line ........................................................ 231
Connecting the liquid waste line ................................................................. 234
Connecting the workstation .......................................................................... 236
Connecting Ethernet cables .......................................................................... 237
Input/output signal connectors .................................................................... 237
Making signal connections .............................................................................. 240
Connecting to the electricity source ........................................................... 243
D Plumbing the IntelliStart Fluidics System .................................... 245
Preventing contamination ............................................................................. 246
Plumbing schematic ........................................................................................ 246
Pipe specifications ........................................................................................... 247

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