Waters Xevo TQ-S Operating manual

Waters Xevo TQ-S
Mass Spectrometry
System
Operator’s Overview and Maintenance Guide
Revision A
Copyright © Waters Corporation 2010
All rights reserved

ii
Copyright notice
© 2010 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, Xevo, and
Waters are registered trademarks of Waters Corporation. IonSABRE,
IntelliStart, MassLynx, NanoFlow, OpenLynx, RADAR, ScanWave,
StepWave, T-Wave, TargetLynx, “THE SCIENCE OF WHAT'S POSSIBLE.”,
TRIZAIC, 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.
Phillips and Pozidriv are registered trademarks of the Phillips Screw
Company.
Swagelok is a registered trademark of Swagelok Company.
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
respective owners.

iii
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 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

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 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.
Flammable solvents hazard
Never let the nitrogen supply pressure fall below 400 kPa (4 bar, 58 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
instrument operation.

v
Glass breakage hazard
High temperature hazard
Mass spectrometer 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, avoid touching the source ion block
assembly when operating or servicing the instrument.
TQ-S
TP03127
Source ion block assembly

vi
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
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 (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 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.
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
When fitted with Waters APCI, APGC, APPI, ASAP, ESCi®, NanoFlow™ ESI,
or TRIZAIC™ UPLC® options, 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 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.

ix
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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Table of Contents xi
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iv
Considerations specific to the Xevo TQ-S system ............................................. iv
Safety advisories................................................................................................. vi
Operating this instrument ................................................................................ vii
Applicable symbols ........................................................................................... vii
Audience and purpose....................................................................................... vii
Intended use of the Xevo TQ-S......................................................................... vii
Calibrating ....................................................................................................... viii
Quality control ................................................................................................. viii
ISM classification ................................................................................................. ix
ISM Classification: ISM Group 1 Class A ......................................................... ix
EC authorized representative ........................................................................... ix
1 Waters Xevo TQ-S Overview ................................................................ 1-1
Waters Xevo TQ-S .............................................................................................. 1-2
ACQUITY UPLC/MS Xevo TQ-S systems ...................................................... 1-4
Non-ACQUITY devices for use with the Xevo TQ-S ...................................... 1-6
Software and data system ............................................................................... 1-6
Instrument Console software .......................................................................... 1-7
Ionization techniques and source probes ................................................... 1-7
Electrospray ionization (ESI).......................................................................... 1-7
Combined electrospray ionization and atmospheric pressure
chemical ionization (ESCi) ........................................................................ 1-7
Atmospheric pressure chemical ionization (APCI) ........................................ 1-8
Dual-mode APPI/APCI source......................................................................... 1-8
Table of Contents

xii Table of Contents
NanoFlow ESI source ...................................................................................... 1-8
Atmospheric solids analysis probe (ASAP)..................................................... 1-9
Atmospheric pressure gas chromatography (APGC) ..................................... 1-9
TRIZAIC UPLC source .................................................................................. 1-10
IntelliStart Fluidics system .......................................................................... 1-10
Overview......................................................................................................... 1-10
System components ....................................................................................... 1-11
System operation ........................................................................................... 1-11
Ion optics ........................................................................................................... 1-12
MS operating modes ....................................................................................... 1-13
MS/MS operating modes ................................................................................ 1-14
Product (daughter) ion mode......................................................................... 1-15
Precursor (parent) ion mode.......................................................................... 1-16
Multiple reaction monitoring mode .............................................................. 1-16
Constant neutral loss mode........................................................................... 1-17
ScanWave daughter scan mode..................................................................... 1-18
Leak sensors ..................................................................................................... 1-18
Vacuum system ................................................................................................ 1-18
Rear panel ......................................................................................................... 1-19
2 Preparing the Mass Spectrometer for Operation ........................... 2-1
Starting the mass spectrometer .................................................................... 2-2
Verifying the instrument’s state of readiness ................................................ 2-4
Monitoring the mass spectrometer LEDs....................................................... 2-4
Tuning and calibration information ............................................................... 2-4
Running the mass spectrometer at high flow rates ....................................... 2-5
Preparing the IntelliStart Fluidics system ................................................. 2-6
Installing the reservoir bottles........................................................................ 2-6
Adjusting the solvent delivery tube positions ................................................ 2-7
Purging the infusion pump.............................................................................. 2-8
Rebooting the mass spectrometer ................................................................. 2-9

Table of Contents xiii
Leaving the mass spectrometer ready for operation ............................. 2-10
Emergency shutdown of the mass spectrometer ..................................... 2-10
3 Changing the Mode of Operation ....................................................... 3-1
ESI mode ............................................................................................................. 3-2
Installing the ESI probe .................................................................................. 3-2
Removing the ESI probe.................................................................................. 3-6
ESCi mode ........................................................................................................... 3-6
Optimizing the ESI probe for ESCi operation................................................ 3-6
APCI mode .......................................................................................................... 3-7
Installing the IonSABRE II probe .................................................................. 3-7
Removing the IonSABRE II probe ................................................................ 3-10
Combined APPI/APCI source ....................................................................... 3-11
APPI operation............................................................................................... 3-11
APCI operation............................................................................................... 3-12
Dual-mode operation ..................................................................................... 3-13
The combined APPI/APCI source components............................................. 3-14
Installing the combined APPI/APCI source ................................................. 3-16
Removing the IonSABRE II probe and combined APPI/APCI
source enclosure....................................................................................... 3-17
NanoFlow ESI source ..................................................................................... 3-18
Installing the NanoFlow source .................................................................... 3-19
Fitting a borosilicate glass capillary (nanovial)........................................... 3-21
Positioning the borosilicate glass capillary tip............................................. 3-25
Restarting a stalled borosilicate glass capillary electrospray ..................... 3-25
4 Maintenance Procedures ..................................................................... 4-1
Maintenance schedule ..................................................................................... 4-3
Spare parts ......................................................................................................... 4-5
Troubleshooting with Connections INSIGHT ............................................ 4-5
Safety and handling ......................................................................................... 4-7

xiv Table of Contents
Preparing the instrument for working on the source ............................. 4-8
Removal and refitting of the source enclosure .......................................... 4-9
Removing the source enclosure from the instrument.................................... 4-9
Fitting the source enclosure to the instrument............................................ 4-11
Installing and removing the corona pin .................................................... 4-12
Installing the corona pin in the source......................................................... 4-12
Removing the corona pin from the source .................................................... 4-15
Operating the source isolation valve ......................................................... 4-16
Removing O-rings and seals ......................................................................... 4-19
Cleaning the instrument case ...................................................................... 4-20
Emptying the nitrogen exhaust trap bottle .............................................. 4-20
Maintaining the Oerlikon Leybold oil-filled roughing pumps ............. 4-22
Gas ballasting the Oerlikon Leybold roughing pumps ................................ 4-23
Inspecting the roughing pump oil levels....................................................... 4-24
Adding oil to a roughing pump...................................................................... 4-24
Replacing the roughing pumps’ oil and oil demister elements.................... 4-27
Gas ballasting the Edwards XDS46i oil-free roughing pump ............... 4-36
Cleaning the source components ................................................................ 4-37
Cleaning the sampling cone assembly ....................................................... 4-38
Removing the sampling cone assembly from the source ............................. 4-38
Disassembling the sampling cone assembly................................................. 4-40
Cleaning the sample cone and cone gas nozzle ............................................ 4-42
Assembling the sampling cone assembly...................................................... 4-44
Fitting the sampling cone assembly to the source ....................................... 4-45
Cleaning the ion block assembly ................................................................. 4-47
Removing the ion block assembly from the source assembly...................... 4-47
Disassembling the source ion block assembly.............................................. 4-49
Cleaning the ion block components .............................................................. 4-55
Assembling the source ion block assembly................................................... 4-56
Fitting the ion block assembly to the source assembly................................ 4-58

Table of Contents xv
Cleaning the StepWave ion guide assembly ............................................. 4-59
Handling the StepWave ion guide assembly................................................ 4-59
Removing the ion block support from the source assembly......................... 4-59
Removing the StepWave assembly from the source assembly.................... 4-61
Disassembling the StepWave ion guide assembly ....................................... 4-64
Cleaning the StepWave ion guide assembly................................................. 4-69
Assembling the StepWave ion guide assembly ............................................ 4-73
Fitting the StepWave assembly to the source assembly.............................. 4-75
Fitting the ion block support to the source................................................... 4-77
Replacing the ESI probe tip and gasket .................................................... 4-78
Removing the ESI probe tip and gasket ....................................................... 4-78
Fitting the ESI probe tip and gasket............................................................ 4-81
Replacing the ESI probe sample capillary ............................................... 4-82
Removing the existing capillary.................................................................... 4-82
Installing the new capillary .......................................................................... 4-86
Cleaning the IonSABRE II probe tip .......................................................... 4-90
Replacing the IonSABRE II probe sample capillary .............................. 4-91
Removing the existing capillary.................................................................... 4-91
Installing the new capillary .......................................................................... 4-93
Cleaning or replacing the corona pin ........................................................ 4-97
Replacing the IonSABRE II probe heater ................................................. 4-98
Removing the IonSABRE II probe heater .................................................... 4-98
Fitting the new IonSABRE II probe heater................................................ 4-100
Replacing the ion block source heater .................................................... 4-101
Replacing the source assembly seals ....................................................... 4-105
Removing the probe adjuster assembly probe and source
enclosure seals ....................................................................................... 4-105
Fitting the new source enclosure and probe adjuster assembly
probe seals.............................................................................................. 4-107
Replacing the air filter ................................................................................ 4-108
APPI/APCI source—changing the UV lamp bulb .................................. 4-110

xvi Table of Contents
APPI/APCI source—cleaning the lamp window .................................... 4-113
APPI/APCI source—replacing the APPI lamp drive seals .................. 4-114
Removing the APPI lamp drive assembly seals......................................... 4-114
Fitting the new APPI lamp drive assembly O-rings.................................. 4-120
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 Oerlikon Leybold oil-filled roughing pumps ............... B-3
Making tubing connections ............................................................................. B-4
Connecting the Edwards oil-free roughing pumps ................................ B-10
Making the roughing pump connections to the Xevo TQ-S ................. B-16
Connecting to the nitrogen supply ............................................................ B-17
Connecting to the collision cell gas supply ............................................. B-18
Connecting the nitrogen exhaust line ...................................................... B-19
Connecting the liquid waste line ............................................................... B-22
Connecting the workstation ........................................................................ B-24
Connecting Ethernet cables ........................................................................ B-25
Input/output signal connectors .................................................................. B-25
Making signal connections ............................................................................ B-28

Table of Contents xvii
Connecting to the electricity source ......................................................... B-31
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
D Plumbing the IntelliStart Fluidics system ..................................... D-1
Preventing contamination ............................................................................. D-2
Plumbing schematic ........................................................................................ D-2
Tubing specifications ...................................................................................... D-3
Index ..................................................................................................... Index-1

xviii Table of Contents

1-1
1Waters Xevo TQ-S Overview
This chapter describes the instrument, including its controls and
connections for gas and plumbing.
Contents
Topic Page
Waters Xevo TQ-S 1-2
Ionization techniques and source probes 1-7
IntelliStart Fluidics system 1-10
Ion optics 1-12
MS operating modes 1-13
MS/MS operating modes 1-14
Leak sensors 1-18
Vacuum system 1-18
Rear panel 1-19

1-2 Waters Xevo TQ-S Overview
Waters Xevo TQ-S
The Waters®Xevo®TQ-S is a tandem quadrupole, atmospheric pressure
ionization (API) mass spectrometer. Designed for routine HPLC/MS/MS and
UPLC®/MS/MS analyses in quantitative and qualitative applications, it can
operate at fast acquisition speeds compatible with UltraPerformance LC®.
You can use the Xevo TQ-S with the following high-performance Waters
ZSpray™ dual-orthogonal API sources:
• Standard multi-mode electrospray ionization/atmospheric pressure
chemical ionization/combined electrospray ionization and atmospheric
pressure chemical ionization (ESI/APCI/ESCi®) source.
Requirement: Dedicated APCI operation requires an additional probe
(IonSABRE™ II).
• Optional dual-mode APPI/APCI source.
• Optional NanoFlow™ ESI source.
• Optional TRIZAIC™ UPLC source.
• Optional APGC source.
You can also use the Xevo TQ-S with the following optional third-party
sources:
•DART
®
•DESI
• LDTD™
For further details, refer to the appropriate manufacturer’s documentation.
For mass spectrometer specifications, see the Waters Xevo TQ-S Site
Preparation Guide.