Waters Xevo TQ-S Operating manual

Waters Xevo TQ-S
Mass Spectrometry
System
Operator’s Overview and Maintenance Guide
715002212 / Revision C
Copyright © Waters Corporation 2014
All rights reserved

ii February 28, 2014, 715002212 Rev. C

February 28, 2014, 715002212 Rev. C iii
General Information
Copyright notice
© 2014 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
“THE SCIENCE OF WHAT'S POSSIBLE.”, ACQUITY, ACQUITY UPLC,
Alliance, Connections INSIGHT, ESCi, MassLynx, nanoACQUITY, TRIZAIC,
UltraPerformance LC, UNIFI, UPLC, Xevo, and Waters are registered
trademarks of Waters Corporation. iKey, ionKey, IonSABRE, IntelliStart,
LockSpray, Nano LC, NanoFlow, nanoTile, OpenLynx, RADAR, ScanWave,
StepWave, T-Wave, TargetLynx, and ZSpray are trademarks of Waters
Corporation.
GELoader is a registered trademark of Cell Technology.
DART is a registered trademark of ionSense™ Inc.
Edwards is a trademark of Edwards Limited.
LDTD is a trademark of Phytronix Inc.
Leybold is a trademark of Oerlikon Leybold Vacuum GmbH.
Oerlikon is a registered trademark of Oerlikon-Schweisstechnik AG.
PEEK is a trademark of Victrex plc.
Swagelok is a registered trademark of Swagelok Company.

iv February 28, 2014, 715002212 Rev. C
Symbiosis is a registered trademark of Spark Holland Inc.
Viton is a registered trademark of DuPont Performance Elastomers.
Other registered trademarks or trademarks are the sole property of their
owners.

February 28, 2014, 715002212 Rev. C v
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
800 252-4752, 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

vi February 28, 2014, 715002212 Rev. C
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-S system
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.
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 273), determine whether any
solvents you use that are not listed are chemically compatible
with the composition of the O-rings.

February 28, 2014, 715002212 Rev. C vii
Spilled solvents hazard
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 400 kPa (4 bar, 58 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.
Glass-breakage hazard
Warning: To avoid injury or equipment damage caused by spilled
solvent, do not place reservoir bottles on top of the instrument or on its
front ledge, unless in the bottle tray provided.
Warning: To prevent the ignition of flammable solvent vapors in the
enclosed space of a mass spectrometer’s ion source, ensure that these
conditions are met:
• Nitrogen flows continuously through the source.
• A gas-fail device is installed, to interrupt the flow of LC solvent
should the nitrogen supply fail.
• The nitrogen supply pressure does not fall below 400 kPa (4 bar,
58 psi) during an analysis requiring the use of flammable solvents.
Warning: To avoid injuries from broken glass, falling objects, or
exposure to toxic substances, never place containers on top of the
instrument or on its front covers.

viii February 28, 2014, 715002212 Rev. C
High-temperature hazard
Mass spectrometer high temperature hazard:
Warning: To avoid burn injuries, avoid touching the source ion block
assembly when operating or servicing the instrument.
TQ-S
TP03127
Source ion block assembly

February 28, 2014, 715002212 Rev. C ix
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.

x February 28, 2014, 715002212 Rev. C
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.

February 28, 2014, 715002212 Rev. C xi
Operating this instrument
When operating this instrument, follow standard quality-control (QC)
procedures and the guidelines presented in this section.
Applicable symbols
Symbol Definition
Manufacturer
Date of manufacture
Part number
Serial number
Supply ratings
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

xii February 28, 2014, 715002212 Rev. C
Electrical and electronic equipment with this
symbol may contain hazardous substances and
should not be disposed of as general waste.
For compliance with the Waste Electrical and
Electronic Equipment Directive (WEEE)
2012/19/EU, contact Waters Corporation for the
correct disposal and recycling instructions.
Symbol Definition

February 28, 2014, 715002212 Rev. C xiii
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 for operation, change its
modes of operation, and maintain it.
Intended use of the Xevo TQ-S
Waters designed the Xevo® TQ-S for use as a research tool to accurately,
reproducibly, and robustly quantify target compounds present at the lowest
possible levels in highly complex sample matrices. It is not for use in
diagnostic procedures.
When fitted with Waters options (APCI, APGC, APPI, ASAP, ESCi®,
NanoFlow™ ESI, TRIZAIC®, UPLC® , ionKey™/MS), or optional third-party
sources (DART®, DESI, or LDTD™), the Xevo TQ-S does not comply with the
European Union In Vitro Diagnostic Device Directive 98/79/EC.
Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards must 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.

xiv February 28, 2014, 715002212 Rev. C
Quality control
Routinely run three QC samples that represent subnormal, normal, and
above-normal levels of a compound. If sample trays are the same or very
similar, vary the location of the QC samples in the trays. Ensure that QC
sample results fall within an acceptable range, and evaluate precision from
day to day and run to run. It is possible for data collected when QC samples
are out of range to be invalid. 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 minimize 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.
• To ensure data integrity, Waters recommends you run QC samples
before and after test samples within a single analysis. Additionally, you
can periodically run known samples as unknowns to verify assay results
for a single analysis.
Instrument maintenance frequency also depends on the complexity of the
matrix and the number of samples being analyzed. To maintain performance
levels, routine cleaning of user-serviceable components must be conducted.
Waters Performance Maintenance Services are available and can be
scheduled as required, based on the combined sample throughput and sample
complexity.
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

February 28, 2014, 715002212 Rev. C xv
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.
In a domestic environment, the equipment may cause radio interference. You
may need to take measures to mitigate the interference.
Do not use the equipment in close proximity to sources of strong
electromagnetic radiation (for example, unshielded intentional RF sources), as
these may interfere with the equipment’s proper operation.
This equipment complies with the emission and immunity requirements
described in the relevant parts of IEC/EN 61326: Electrical equipment for
measurement, control and laboratory use — EMC requirements.
EC authorized representative
Waters Corporation
Stamford Avenue
Altrincham Road
Wilmslow
SK9 4AX
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

xvi February 28, 2014, 715002212 Rev. C

February 28, 2014, 715002212 Rev. C xvii
General Information .................................................................................... iii
Copyright notice .................................................................................................. iii
Trademarks ........................................................................................................... iii
Contacting Waters ................................................................................................ v
Safety considerations .......................................................................................... vi
Considerations specific to the Xevo TQ-S system ............................................. vi
FCC radiation emissions notice .......................................................................... x
Canada spectrum management emissions notice .............................................. x
Electrical power safety notice ............................................................................. x
Safety hazard symbol notice................................................................................ x
Equipment misuse notice .................................................................................... x
Safety advisories.................................................................................................. x
Operating this instrument ................................................................................. xi
Applicable symbols ............................................................................................. xi
Audience and purpose...................................................................................... xiii
Intended use of the Xevo TQ-S........................................................................ xiii
Calibrating ....................................................................................................... xiii
Quality control .................................................................................................. xiv
ISM classification ............................................................................................... xiv
ISM Classification: ISM Group 1 Class A ....................................................... xiv
EC authorized representative .......................................................................... xv
1 Waters Xevo TQ-S Overview ................................................................. 25
Waters Xevo TQ-S ............................................................................................... 26
ACQUITY UPLC/MS Xevo TQ-S systems ........................................................ 28
Non-ACQUITY devices for use with the Xevo TQ-S ........................................ 30
Software and data system ................................................................................. 31
Table of Contents

xviii February 28, 2014, 715002212 Rev. C
Ionization techniques and source probes .................................................... 32
ESI ...................................................................................................................... 32
ESCi.................................................................................................................... 32
APCI ................................................................................................................... 32
Dual-mode APPI/APCI source........................................................................... 33
Low-flow ESI probe............................................................................................ 33
NanoFlow ESI source ........................................................................................ 33
Atmospheric solids analysis probe.................................................................... 34
APGC.................................................................................................................. 34
TRIZAIC UPLC source ...................................................................................... 34
ionKey source ..................................................................................................... 34
IntelliStart fluidics system .............................................................................. 35
Overview............................................................................................................. 35
System components ........................................................................................... 36
System operation ............................................................................................... 36
Ion optics .............................................................................................................. 36
MS operating modes .......................................................................................... 37
MS/MS operating modes ................................................................................... 38
Product (daughter) ion mode............................................................................. 39
Precursor (parent) ion mode.............................................................................. 40
MRM mode ......................................................................................................... 40
Constant neutral loss mode............................................................................... 41
ScanWave daughter scan mode......................................................................... 42
Leak sensors ........................................................................................................ 42
Vacuum system ................................................................................................... 43
Rear panel ............................................................................................................ 43
2 Preparing the Mass Spectrometer for Operation ............................ 45
Starting the mass spectrometer ..................................................................... 46
Verifying the instrument’s state of readiness .................................................. 48
Monitoring the mass spectrometer LEDs......................................................... 48
Tuning and calibration information ................................................................. 49
Running the mass spectrometer at high flow rates ......................................... 50

February 28, 2014, 715002212 Rev. C xix
Preparing the IntelliStart Fluidics system .................................................. 51
Installing the reservoir bottles.......................................................................... 51
Adjusting the solvent delivery tube positions .................................................. 53
Purging the infusion pump................................................................................ 54
Rebooting the mass spectrometer .................................................................. 55
Leaving the mass spectrometer ready for operation ................................ 56
Emergency shutdown of the mass spectrometer ........................................ 56
3 Changing the Mode of Operation ........................................................ 57
ESI mode .............................................................................................................. 57
Installing the ESI probe .................................................................................... 58
Removing the ESI probe.................................................................................... 62
ESCi mode ............................................................................................................ 62
Optimizing the ESI probe for ESCi operation.................................................. 63
APCI mode ........................................................................................................... 63
Installing the IonSABRE II probe .................................................................... 64
Removing the IonSABRE II probe .................................................................... 67
Combined APPI/APCI source .......................................................................... 67
APPI operation................................................................................................... 67
APCI operation................................................................................................... 68
Dual-mode operation ......................................................................................... 69
The combined APPI/APCI source components................................................. 70
Installing the combined APPI/APCI source ..................................................... 72
Removing the IonSABRE II probe and combined APPI/APCI source enclosure..
73
NanoFlow ESI source ........................................................................................ 74
Installing the NanoFlow source ........................................................................ 76
Fitting a borosilicate glass capillary (nanovial)............................................... 78
Positioning the borosilicate glass capillary tip................................................. 81
Restarting a stalled borosilicate glass capillary electrospray ......................... 82
ionKey source ..................................................................................................... 82
Installing the ionKey source ............................................................................. 83

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Installing ionKey source software..................................................................... 88
Installing the camera in the ionKey source...................................................... 89
Removing an ionKey source .............................................................................. 89
4 Maintenance Procedures ...................................................................... 91
Maintenance schedule ...................................................................................... 92
Spare parts .......................................................................................................... 95
Troubleshooting with Connections INSIGHT ............................................. 96
Safety and handling .......................................................................................... 97
Preparing the instrument for working on the source .............................. 98
Removing and refitting the source enclosure ........................................... 100
Removing the source enclosure from the instrument.................................... 100
Fitting the source enclosure to the instrument.............................................. 102
Installing and removing the corona pin ..................................................... 102
Installing the corona pin in the source........................................................... 103
Removing the corona pin from the source ...................................................... 105
Operating the source isolation valve .......................................................... 107
Removing O-rings and seals .......................................................................... 110
Cleaning the instrument case ....................................................................... 111
Emptying the nitrogen exhaust trap bottle ............................................... 111
Maintaining the Oerlikon Leybold oil-filled roughing pumps .............. 113
Gas ballasting the Oerlikon Leybold roughing pumps .................................. 115
Inspecting the roughing pump oil levels......................................................... 116
Adding oil to a roughing pump........................................................................ 116
Replacing the roughing pumps’ oil and oil demister elements...................... 119
Gas ballasting the Edwards XDS35i oil-free roughing pump ................ 127
Cleaning the source components ................................................................. 128
Cleaning the sampling cone assembly ........................................................ 129
Removing the sampling cone assembly from the source ............................... 129