Waters Xevo G2 QTof Operating manual

Waters Xevo G2 QTof
Operator’s Overview and Maintenance Guide
Revision B
Copyright © Waters Corporation 20102011
All rights reserved

ii
Copyright notice
© 2010–2011 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.
Trademarks
ACQUITY, ACQUITY UPLC, Connections INSIGHT, ESCi, UPLC, and
Waters are registered trademarks of Waters Corporation. IntelliStart,
LockSpray, MassLynx, NanoFlow, NanoLockSpray, T-Wave, THE SCIENCE
OF WHAT'S POSSIBLE., UNIFI, Xevo, and ZSpray are trademarks of Waters
Corporation.
GELoader is a registered trademark of Eppendorf-Netheler-Hinz GmbH.
PEEK is a trademark of Victrex plc.
POZIDRIV is a registered trademark of Phillips Screw Company, Inc.
Swagelok is a registered trademark of Swagelok Company.
Super Flangeless and SealTight are trademarks of Upchurch Scientific, Inc.
TaperTip is a trademark of New Objective, Inc.
Teflon and Viton are registered trademarks of E. I. du Pont de Nemours and
Company.
Valco is a trademark of Valco Instruments, Inc.
Xylan is a registered trademark of Whitford Corporation.
Other trademarks or registered trademarks are the sole property of their
respective owners.

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Customer comments
Waters’ Technical Communications department invites you to tell us of any
errors you encounter in this document or to suggest ideas for otherwise
improving it. Please 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 From the USA or Canada, phone 800
252-HPLC, or fax [phone].
For other locations worldwide, phone and fax
numbers appear on the Waters Web site.
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

iv
Safety considerations
Some reagents and samples used with Waters instruments and devices can
pose chemical, biological, and radiological hazards. 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 G2 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.
Flammable-solvents hazard
Never let the nitrogen supply pressure fall below 690 kPa (6.9 bar, 100 psi)
during analyses that require flammable solvents. Connect to the LC output
with a gas-fail connector to stop the LC solvent if the nitrogen supply 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 C-3), determine whether any
solvents you use that are not listed are chemically compatible
with the composition of the O-rings.
Warning: To prevent the ignition of accumulated solvent vapors inside
the source, maintain a continuous flow of nitrogen through the source
whenever significant amounts of flammable solvents are used during
the instrument’s operation.

v
Glass-breakage hazard
High-temperature hazard
Xevo G2 QTof high-temperature hazard:
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.
Warning: To avoid burn injuries, do not touch the source ion block
assembly when operating or servicing the instrument.
Source ion block assembly

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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. Management 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
carcinogenic, toxic, or biohazardous substances, you must wear
chemical-resistant gloves when handling or disposing of used oil.
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.
Warning: To avoid personal contamination with
biohazardous or toxic 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 care.

vii
Operating this instrument
When operating this instrument, follow standard quality control 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.
Intended use
Waters designed the orthogonal-acceleration, time-of-flight Xevo™ G2 QTof
for use as a research tool to deliver authenticated mass measurement. The
Xevo G2 QTof is for research use only and is not intended for use in diagnostic
applications.
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

viii
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.
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.
ISM classification
ISM Classification: ISM Group 1 Class A
This classification has been assigned in accordance with 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.

ix
EC authorized representative
Waters Corporation (Micromass UK Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

x

Table of Contents xi
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iv
Considerations specific to the Xevo G2 QTof..................................................... iv
Safety advisories................................................................................................. vi
Operating this instrument ................................................................................ vii
Applicable symbols ........................................................................................... vii
Audience and purpose....................................................................................... vii
Intended use...................................................................................................... vii
Calibrating ....................................................................................................... viii
Quality control ................................................................................................. viii
ISM classification .............................................................................................. viii
ISM Classification: ISM Group 1 Class A ...................................................... viii
EC authorized representative ........................................................................... ix
1 Waters Xevo G2 QTof Overview .......................................................... 1-1
Waters Xevo G2 QTof ........................................................................................ 1-2
IntelliStart technology..................................................................................... 1-2
ACQUITY and nanoACQUITY Xevo G2 QTof UPLC/MS systems............... 1-3
Software and data system ............................................................................... 1-6
Instrument Console ......................................................................................... 1-6
LockSpray source and ionization modes .................................................... 1-6
Electrospray ionization (ESI).......................................................................... 1-7
Atmospheric pressure chemical ionization (APCI) ........................................ 1-8
Combined electrospray and atmospheric pressure chemical
ionization (ESCi)........................................................................................ 1-9
Table of Contents

xii Table of Contents
NanoLockSpray source and ionization modes .......................................... 1-9
Combined APPI/APCI source ....................................................................... 1-11
IntelliStart Fluidics system .......................................................................... 1-11
IntelliStart Fluidics system physical layout ................................................ 1-12
System operation ........................................................................................... 1-13
Ion optics ........................................................................................................... 1-14
Leak sensors ..................................................................................................... 1-15
Vacuum system ................................................................................................ 1-15
2 Preparing the Mass Spectrometer for Operation ........................... 2-1
Starting the mass spectrometer .................................................................... 2-2
Verifying the instrument’s state of readiness ................................................ 2-3
Monitoring the mass spectrometer LEDs....................................................... 2-3
Calibration ....................................................................................................... 2-3
Flow rates for the Xevo G2 QTof system ........................................................ 2-4
Preparing the IntelliStart Fluidics system ................................................. 2-4
Installing the reservoir bottles........................................................................ 2-4
Adjusting the solvent delivery tube positions ................................................ 2-7
Purging the pump ............................................................................................ 2-8
Rebooting the mass spectrometer ................................................................. 2-8
Leaving the mass spectrometer ready for operation ............................... 2-8
Emergency shutdown of the mass spectrometer ....................................... 2-9
3 Configuring the LockSpray Source ................................................... 3-1
Configuring the LockSpray source ............................................................... 3-2
Configuring for ESI mode ............................................................................... 3-2
Installing the ESI probe .................................................................................. 3-2
Removing the ESI probe.................................................................................. 3-6
Installing the small-bore capillary option .................................................. 3-7

Table of Contents xiii
Configuring for APCI mode .......................................................................... 3-13
Installing the APCI probe ............................................................................. 3-13
Removing the APCI probe ............................................................................. 3-17
Configuring for ESCi mode .......................................................................... 3-18
Optimizing the ESI probe for ESCi operation.............................................. 3-18
4 Configuring the NanoLockSpray Source ......................................... 4-1
Overview of the NanoLockSpray source ..................................................... 4-2
Sample sprayer ................................................................................................ 4-3
Lock-spray sprayer .......................................................................................... 4-3
NanoFlow gas supply....................................................................................... 4-4
Purge gas.......................................................................................................... 4-4
Sprayer platform adjuster assembly............................................................... 4-4
Configuring the NanoLockSpray source ..................................................... 4-4
Source type selection ....................................................................................... 4-5
Advancing and retracting the sprayer platform ....................................... 4-6
Adjusting the sprayer tip position ................................................................ 4-7
Setting up the camera ...................................................................................... 4-8
Optional glass capillary sprayer ................................................................... 4-9
Plumbing the backpressure gas ...................................................................... 4-9
Installing the glass capillary sprayer ........................................................... 4-10
Fitting and loading the glass capillary......................................................... 4-11
5 Maintenance Procedures ..................................................................... 5-1
Maintenance schedule ..................................................................................... 5-3
Spare parts ......................................................................................................... 5-4
Troubleshooting with Connections INSIGHT ............................................ 5-5
Safety and handling ......................................................................................... 5-6
Preparing the instrument for working on the source ............................. 5-7

xiv Table of Contents
Removal and refitting of the source enclosure .......................................... 5-7
Removing the source enclosure from the instrument.................................... 5-7
Fitting the source enclosure to the instrument............................................ 5-10
Installing and removing the corona pin .................................................... 5-11
Installing the corona pin in the source......................................................... 5-11
Removing the corona pin from the source .................................................... 5-13
Operating the source isolation valve ......................................................... 5-14
Removing O-rings and seals ......................................................................... 5-17
Cleaning the instrument case ...................................................................... 5-17
Emptying the nitrogen exhaust trap bottle .............................................. 5-18
Inspecting the Varian roughing pump oil level ....................................... 5-20
Adding oil to the Varian roughing pump .................................................. 5-21
Replacing the Varian roughing pump’s oil and oil mist filter ............. 5-23
Emptying the roughing pump’s oil................................................................ 5-23
Replacing the oil mist filter........................................................................... 5-24
To fill the pump with oil ................................................................................ 5-26
Cleaning the source components ................................................................ 5-28
Cleaning the sampling cone assembly ....................................................... 5-29
Removing the sampling cone assembly from the source ............................. 5-29
Disassembling the sampling cone assembly................................................. 5-31
Cleaning the sample cone and cone gas nozzle ............................................ 5-34
Assembling the sampling cone assembly...................................................... 5-36
Fitting the sampling cone assembly to the source ....................................... 5-36
Cleaning the extraction cone ....................................................................... 5-38
Removing the ion block assembly from the source assembly...................... 5-38
Removing the extraction cone from the ion block ........................................ 5-41
Cleaning the extraction cone......................................................................... 5-42
Fitting the extraction cone to the ion block.................................................. 5-44
Fitting the ion block assembly to the source assembly................................ 5-45

Table of Contents xv
Cleaning the ion block assembly ................................................................. 5-46
Disassembling the source ion block assembly.............................................. 5-46
Cleaning the ion block components .............................................................. 5-53
Assembling the source ion block assembly................................................... 5-55
Cleaning the source hexapole assembly .................................................... 5-57
Removing the ion block assembly, ion block support, and hexapole
from the source assembly ........................................................................ 5-57
Cleaning the hexapole assembly................................................................... 5-59
Fitting the hexapole assembly, PEEK ion block support, and ion
block assembly to the source assembly................................................... 5-61
Replacing the ESI probe tip and gasket .................................................... 5-63
Removing the ESI probe tip and gasket ....................................................... 5-63
Fitting the ESI probe tip and gasket............................................................ 5-65
Replacing the ESI probe sample capillary ............................................... 5-66
Removing the existing capillary.................................................................... 5-66
Installing the new capillary .......................................................................... 5-71
Cleaning the APCI probe tip ........................................................................ 5-75
Replacing the APCI probe sample capillary ............................................ 5-75
Removing the existing capillary.................................................................... 5-75
Installing the new capillary .......................................................................... 5-78
Replacing the reference probe capillary (LockSpray source) ............. 5-82
Removing the existing capillary.................................................................... 5-82
Installing the new capillary .......................................................................... 5-84
Replacing the reference probe capillary (NanoLockSpray source) ... 5-85
Removing the reference probe from the NanoLockSpray source ................ 5-85
Installing the new TaperTip and capillary................................................... 5-88
Cleaning or replacing the corona pin ........................................................ 5-90
Replacing the APCI probe heater ............................................................... 5-91
Removing the APCI probe heater ................................................................. 5-91
Fitting the new APCI probe heater .............................................................. 5-93
Replacing the ion block source heater ...................................................... 5-94

xvi Table of Contents
Replacing the LockSpray source’s assembly seals ................................. 5-98
Removing the probe adjuster assembly probe and source
enclosure seals ......................................................................................... 5-98
Fitting the new source enclosure and probe adjuster assembly
probe seals.............................................................................................. 5-100
Replacing the mass spectrometer’s air filters ........................................ 5-102
Replacing the air filter inside the front door.............................................. 5-102
Replacing the air filters on the sides of the instrument............................ 5-104
Replacing the IntelliStart Fluidics tubing ............................................. 5-106
Removing the IntelliStart Fluidics tubing ................................................. 5-107
Plumbing the IntelliStart Fluidics lock-spray system............................... 5-108
Plumbing the IntelliStart Fluidics sample delivery system...................... 5-116
A Safety Advisories .................................................................................. A-1
Warning symbols ............................................................................................... A-2
Task-specific hazard warnings........................................................................ A-2
Specific warnings ............................................................................................. A-3
Caution symbol .................................................................................................. A-5
Warnings that apply to all Waters instruments ......................................... A-6
Electrical and handling symbols ................................................................. A-11
Electrical symbols .......................................................................................... A-11
Handling symbols .......................................................................................... A-12
B External Connections .......................................................................... B-1
Mass spectrometer external wiring and vacuum connections ............. B-2
Connecting the Varian oil-filled roughing pump ..................................... B-3
Making the electrical connections to the Varian oil-filled
roughing pump........................................................................................... B-6
Connecting the Edwards oil-free roughing pump ................................... B-7
Making the electrical connections to the Edwards oil-free
roughing pump......................................................................................... B-10
Connecting to the nitrogen gas supply ..................................................... B-10

Table of Contents xvii
Connecting to the collision cell gas supply ............................................. B-12
Connecting the nitrogen exhaust line ...................................................... B-12
Connecting the liquid waste line ............................................................... B-15
Connecting the EPC ...................................................................................... B-18
Connecting the workstation (systems with no ACQUITY LC) ............ B-19
Connecting Ethernet cables (systems with ACQUITY LC) .................. B-20
Input/output signal connectors .................................................................. B-20
Signal connections ......................................................................................... B-23
Connecting to the electricity source ......................................................... B-26
Connecting the NanoLockSpray source camera .................................... B-26
Installing the camera driver software .......................................................... B-27
C Materials of Construction and Compatible Solvents ................... C-1
Preventing contamination ............................................................................. C-2
Items exposed to solvent ................................................................................ C-2
Solvents used to prepare mobile phases .................................................... C-3
Index ..................................................................................................... Index-1

xviii Table of Contents

1-1
1Waters Xevo G2 QTof Overview
This chapter describes the instrument, including its controls, sources
and IntelliStart™ Fluidics system.
Contents:
Topic Page
Waters Xevo G2 QTof 1-2
LockSpray source and ionization modes 1-6
NanoLockSpray source and ionization modes 1-9
Combined APPI/APCI source 1-11
IntelliStart Fluidics system 1-11
Ion optics 1-14
Leak sensors 1-15
Vacuum system 1-15

1-2 Waters Xevo G2 QTof Overview
Waters Xevo G2 QTof
The Xevo™ G2 QTof Mass Spectrometry (MS) system is a hybrid, quadrupole,
orthogonal acceleration, time-of-flight (oaTOF) mass spectrometer operated by
Waters® informatics software.
Either of the following high-performance, ZSpray™, dual-orthogonal, API
sources is fitted as standard equipment:
• LockSpray™ electrospray ionization/atmospheric pressure chemical
ionization/combined electrospray ionization and atmospheric pressure
chemical ionization (ESI/APCI/ESCi®) source, see “LockSpray source
and ionization modes” on page 1-6.
• NanoLockSpray™ ESI source, see “NanoLockSpray source and
ionization modes” on page 1-9.
You can also use the optional combined APPI/APCI source with the
Xevo G2 QTof (see the Waters APPI Source Operator’s Guide Supplement).
For the instrument’s specifications, see the Waters Xevo G2 QTof Site
Preparation Guide.
IntelliStart technology
IntelliStart technology monitors instrument performance and reports when it
is ready for use.
The console software automatically mass calibrates the mass spectrometer
and displays performance readbacks to enable simplified setup of the system
for use in routine analytical and open access applications.
The IntelliStart Fluidics1system is built into the mass spectrometer. It
delivers sample directly to the MS probe from the LC column or from three
integral reservoirs. The reservoirs can also deliver sample through direct or
combined infusion so that you can optimize instrument performance at
analytical flow rates. An additional reservoir contains solvent for the
automated flushing of the solvent delivery system.
1. In this document, the term “fluidics” is used to describe plumbing components and fluid
pathways within and between instruments and devices.