Waters Xevo G2-XS QTof Operating manual

Waters Xevo G2-XS QTof
Overview and Maintenance Guide
715004496/Revision B
Copyright © Waters Corporation 2015
All rights reserved

ii April 2, 2015, 715004496 Rev. B

April 2, 2015, 715004496 Rev. B iii
General Inform ation
Copyright notice
© 2014 – 2015 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
Waters, “THE SCIENCE OF WHAT’S POSSIBLE.”, ACQUITY,
ACQUITY UPC2, ACQUITY UPLC, Connections INSIGHT, ESCi, MassLynx,
UNIFI, UPLC, Waters Quality Parts, and Xevo are registered trademarks of
Waters Corporation, and iKey, IntelliStart, ionKey, ionKey/MS, IonSABRE,
LockSpray, NanoFlow, NanoLockSpray, OpenLynx, pDRE, StepWave,
TargetLynx, and ZSpray are trademarks of Waters Corporation.
LEYBONOL is a registered trademark of Oerlikon Leybold Vacuum GmbH.
POZIDRIV is a registered trademark of Phillips Screw Company, Inc.
Swagelok is a registered trademark of Swagelok Company.
Tygon is a registered trademark of Saint-Gobain Performance Plastics Corp.
Viton is a registered trademark of E. I. du Pont de Nemours and Company.
Windows is a registered trademark of Microsoft Corporation in the United
States and/or other countries.
Xylan is a registered trademark of Whitford Corporation.
PEEK is a trademark of Victrex plc.
Super Flangeless and SealTight are trademarks of Upchurch Scientific, Inc.

iv April 2, 2015, 715004496 Rev. B
TaperTip is a trademark of New Objective, Inc.
Valco is a trademark of Valco Instruments, Inc.
Other registered trademarks or trademarks are the sole property of their
owners.
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
800 252-4752, 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

April 2, 2015, 715004496 Rev. B 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
standard operating procedures.
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.
Considerations specific to the Xevo G2-XS QTof
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 page 305),
determine whether any solvents you use that are not listed are
chemically compatible with the composition of the O-rings.

vi April 2, 2015, 715004496 Rev. B
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 (4.0 bar, 60 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.
Prohibited: 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 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 400 kPa (4.0 bar, 60 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.

April 2, 2015, 715004496 Rev. B vii
High temperature hazard
Mass spectrometer high temperature hazard:
Warning: The source ion block, located behind the source enclosure
assembly, can become hot. To avoid burn injuries, ensure the source
heater is turned off and the ion block is cool before performing
maintenance on these components.
Source ion block assembly

viii April 2, 2015, 715004496 Rev. B
High voltage hazard
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
Warning:
• To avoid electric shock, do not remove the mass spectrometer’s
protective panels. The components they cover are not
user-serviceable.
• To avoid nonlethal electric shock when the instrument is in Operate
mode, avoid touching the areas marked with the high voltage
warning symbol. To touch those areas, first put the instrument in
Standby mode.
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.

April 2, 2015, 715004496 Rev. B ix
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.
Bottle placement prohibition
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.
Electrical power safety notice
Position the instrument and ancillary equipment in positions where it is easy
to reach and disconnect the power cable from the instrument’s rear panel.
Safety advisories
Consult Appendix A for a comprehensive list of warning advisories and
notices.
Prohibited: To avoid injury from electric shock or fire, and to prevent
damage to the workstation and ancillary equipment, do not place objects
filled with liquid—such as solvent bottles—on these items, or expose
them to dripping or splashing liquids.
Notice: To prevent spillages, do not lift the bottle tray while it is full of
bottles.

x April 2, 2015, 715004496 Rev. B
Operating the Xevo G2-XS QTof
When operating the Xevo®G2-XS QTof, follow standard quality-control (QC)
procedures and the guidelines presented in this section.
Applicable symbols
Symbol Definition
Manufacturer
Date of manufacture
Authorized representative of the European
Community
Confirms that a manufactured product complies
with all applicable European Community
directives
or
Australia EMC compliant
Confirms that a manufactured product complies
with all applicable United States and Canadian
safety requirements
Consult instructions for use
Alternating current

April 2, 2015, 715004496 Rev. B xi
Audience and purpose
This guide is intended for operators of varying levels of experience. It provides
an overview of the instrument, and explains how to prepare it, change its
modes of operation, and maintain it.
Intended use of the Xevo G2-XS QTof
Waters designed the orthogonal acceleration, time-of-flight Xevo G2-XS QTof
for use as a research tool to deliver authenticated mass measurement. The
Xevo G2-XS QTof is for research use only and is not intended for use in
diagnostic applications.
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 cover the entire range of QC samples, typical specimens,
and atypical specimens.
To calibrate the Xevo G2-XS QTof, consult the instrument’s online Help
system.
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.
Serial number
Part number catalog number
Symbol Definition
5()

xii April 2, 2015, 715004496 Rev. B
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. 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, 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.
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.

April 2, 2015, 715004496 Rev. B xiii
EMC considerations
Canada spectrum management emissions notice
This class A digital product apparatus complies with Canadian ICES-001.
Cet appareil numérique de la classe A est conforme à la norme NMB-001.
ISM Classification: ISM Group 1 Class A
This classification has been assigned in accordance with CISPR 11 Industrial
Scientific and Medical, (ISM) instrument 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 all establishments other
than residential locations and those directly connected to a low voltage power
supply network supplying a building for domestic purposes.
There may be potential difficulties in ensuring electromagnetic compatibility
in other environments due to conducted as well as radiated disturbances.
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.

xiv April 2, 2015, 715004496 Rev. B
EC authorized representative
Waters Corporation
Stamford Avenue
Altrincham Road
Wilmslow SK9 4AX UK
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

April 2, 2015, 715004496 Rev. B xv
General Information .................................................................................... iii
Copyright notice .................................................................................................. iii
Trademarks ........................................................................................................... iii
Customer comments ............................................................................................ iv
Contacting Waters ............................................................................................... iv
Safety considerations ........................................................................................... v
Safety hazard symbol notice................................................................................ v
Considerations specific to the Xevo G2-XS QTof................................................ v
FCC radiation emissions notice ......................................................................... ix
Electrical power safety notice ............................................................................ ix
Safety advisories................................................................................................. ix
Operating the Xevo G2-XS QTof ........................................................................ x
Applicable symbols .............................................................................................. x
Audience and purpose......................................................................................... xi
Intended use of the Xevo G2-XS QTof ............................................................... xi
Calibrating .......................................................................................................... xi
Quality control .................................................................................................. xii
Equipment misuse notice ................................................................................. xii
EMC considerations ......................................................................................... xiii
Canada spectrum management emissions notice .......................................... xiii
ISM Classification: ISM Group 1 Class A ...................................................... xiii
EC authorized representative ......................................................................... xiv
1 Waters Xevo G2-XS QTof Overview ..................................................... 23
Waters Xevo G2-XS QTof .................................................................................. 24
IntelliStart technology....................................................................................... 25
ACQUITY Xevo G2-XS QTof UPLC/MS systems............................................. 26
Software and data system ................................................................................. 29
Table of Contents

xvi April 2, 2015, 715004496 Rev. B
LockSpray source and ionization modes ..................................................... 31
Electrospray ionization (ESI)............................................................................ 32
Atmospheric pressure chemical ionization (APCI) .......................................... 32
Combined electrospray/atmospheric pressure chemical ionization (ESCi) .... 33
Atmospheric solids analysis probe (ASAP)....................................................... 33
NanoLockSpray source and ionization modes ........................................... 34
Combined APPI/APCI source .......................................................................... 36
Atmospheric pressure gas chromotography (APGC) source ................... 36
ionKey source ..................................................................................................... 37
IntelliStart Fluidics system ............................................................................. 38
IntelliStart Fluidics system physical layout .................................................... 39
System operation ............................................................................................... 40
Ion optics .............................................................................................................. 41
Leak sensors ........................................................................................................ 43
Vacuum system ................................................................................................... 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
Calibration ......................................................................................................... 48
Flow rates for the Xevo G2-XS QTof system .................................................... 49
Preparing the IntelliStart Fluidics system .................................................. 49
Installing the reservoir bottles.......................................................................... 49
Adjusting the solvent delivery tube positions .................................................. 52
Purging the pump .............................................................................................. 53

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Rebooting the mass spectrometer .................................................................. 53
Leaving the mass spectrometer ready for operation ................................ 54
Emergency shutdown of the mass spectrometer ........................................ 54
3 Configuring the LockSpray Source .................................................... 55
Configuring the LockSpray source ................................................................ 56
Configuring for ESI mode ................................................................................ 57
Installing the ESI probe .................................................................................... 57
Removing the ESI probe.................................................................................... 61
Configuring for APCI mode ............................................................................. 62
Installing the IonSABRE II probe .................................................................... 62
Removing the IonSABRE II probe .................................................................... 65
Configuring for ESCi mode ............................................................................. 66
Optimizing the ESI probe for ESCi operation.................................................. 66
4 Configuring the NanoLockSpray Source .......................................... 67
Overview of the NanoLockSpray source ...................................................... 68
Sample sprayer .................................................................................................. 69
LockSpray sprayer............................................................................................. 69
NanoFlow gas supply......................................................................................... 70
Purge gas............................................................................................................ 70
Sprayer platform adjuster assembly................................................................. 70

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Selecting and configuring the NanoLockSpray source ............................ 71
Deploying the sprayer platform adjuster assembly .................................. 72
Adjusting the sprayer tip position ................................................................. 73
Setting up the camera ....................................................................................... 74
Optional glass-capillary sprayer .................................................................... 75
5 Installing and removing the ionKey source ..................................... 77
Installing the ionKey source ........................................................................... 78
Installing ionKey source software ................................................................. 87
Installing the camera in the ionKey source ................................................ 87
Removing the ionKey source .......................................................................... 88
6 Maintenance Procedures ...................................................................... 91
Maintenance schedule ...................................................................................... 93
Spare parts .......................................................................................................... 95
Troubleshooting with Connections INSIGHT ............................................. 96
Safety and handling .......................................................................................... 97
Preparing the instrument for working on the source .............................. 99
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 ..................................................... 103
Installing the corona pin in the source........................................................... 103
Removing the corona pin from the source ...................................................... 106

April 2, 2015, 715004496 Rev. B xix
Operating the source isolation valve .......................................................... 107
Removing O-rings and seals .......................................................................... 110
Cleaning the instrument case ....................................................................... 111
Emptying the nitrogen exhaust-trap bottle ............................................... 112
Maintaining the roughing pump .................................................................. 115
Maintaining the Oerlikon Leybold oil-filled roughing pump ................ 115
Gas ballasting the Oerlikon Leybold roughing pump.................................... 116
Inspecting the roughing pump oil level .......................................................... 117
Adding oil to the roughing pump .................................................................... 117
Replacing the roughing pump’s oil and oil demister elements...................... 120
Cleaning the source components ................................................................. 127
Cleaning the sampling cone assembly ........................................................ 128
Removing the sampling cone assembly from the source ............................... 128
Disassembling the sampling cone assembly................................................... 130
Cleaning the sample cone and cone gas nozzle .............................................. 133
Assembling the sampling cone assembly........................................................ 135
Fitting the sampling cone assembly to the source ......................................... 136
Cleaning the ion block assembly .................................................................. 138
Removing the ion block assembly from the source assembly........................ 138
Disassembling the source ion block assembly................................................ 141
Cleaning the ion block components ................................................................ 147
Assembling the source ion block assembly..................................................... 149
Fitting the ion block assembly to the source assembly.................................. 151
Cleaning the StepWave ion guide assembly .............................................. 152
Handling the StepWave ion guide assembly.................................................. 152
Removing the ion block support from the source assembly........................... 152
Removing the StepWave assembly from the source assembly...................... 154
Disassembling the StepWave ion guide assembly ......................................... 158
Cleaning the StepWave ion guide assembly................................................... 161
Assembling the StepWave ion guide assembly .............................................. 165
Fitting the StepWave assembly to the source assembly................................ 167
Fitting the ion block support to the source..................................................... 170

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Replacing the ESI probe tip and gasket ..................................................... 171
Removing the ESI probe tip and gasket ......................................................... 171
Fitting the ESI probe tip and gasket.............................................................. 174
Replacing the ESI probe sample capillary ................................................ 175
Removing the existing capillary...................................................................... 175
Installing the new capillary ............................................................................ 180
Cleaning the IonSABRE II probe tip ........................................................... 184
Replacing the IonSABRE II probe sample capillary ............................... 184
Removing the existing capillary...................................................................... 184
Installing the new capillary ............................................................................ 187
Replacing the LockSpray reference probe capillary .............................. 191
Removing the existing capillary...................................................................... 191
Installing the new capillary ............................................................................ 194
Replacing the NanoLockSpray reference-probe TaperTip emitter or
capillary ...................................................................................................... 197
Removing the NanoLockSpray reference probe ............................................. 197
Installing the new TaperTip emitter and capillary ....................................... 199
Replacing the ionKey reference-probe capillary ..................................... 202
Removing the ionKey reference probe ............................................................ 202
Installing the new TaperTip emitter and capillary ....................................... 204
Cleaning or replacing the corona pin ......................................................... 207
Replacing the IonSABRE II probe heater .................................................. 208
Removing the IonSABRE II probe heater ...................................................... 208
Fitting the new IonSABRE II probe heater.................................................... 210
Replacing the ion block source heater ....................................................... 211
Replacing the LockSpray source’s assembly seals .................................. 215
Removing the probe adjuster assembly probe and source
enclosure seals ........................................................................................... 215
Fitting the new source enclosure and probe adjuster assembly
probe seals.................................................................................................. 217