Waters Xevo TQD Operating manual

Waters Xevo TQD
Operator’s Overview and Maintenance Guide
Revision A
Copyright © Waters Corporation 2011
All rights reserved

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Copyright notice
© 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, UPLC, ACQUITY UPLC, Connections INSIGHT, ESCi, Waters,
and Xevo are registered trademarks of Waters Corporation. IntelliStart,
IonSABRE, MassLynx, T-Wave, “THE SCIENCE OF WHAT’S POSSIBLE,”
and ZSpray are trademarks of Waters Corporation.
PEEK is a trademark of Victrex Corporation.
Snoop and Swagelok are registered trademarks of Swagelok Company.
Other trademarks or registered trademarks are the sole property of their
respective owners.
Customer comments
Waters’ Technical Communications department invites you to tell us of any
errors you encounter in this document or to suggest ideas for improvement.
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].

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Contacting Waters
Contact Waters®with questions regarding 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

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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 TQD
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 avoid biohazardous and toxic solvent leaks, follow
these guidelines:
• 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 C-2),
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 using significant amounts of flammable solvents during the
instrument’s operation.

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Overload hazard
Glass-breakage hazard
Warning: To prevent personal injury, ensure equipment placed on top of
the Xevo TQD does not exceed 15kg.
Warning: To avoid injuries from broken glass, falling objects,
or exposure to toxic or biohazardous substances, never place
containers on top of the instrument or on its front covers.

vi
High-temperature hazard
Xevo TQD high temperature hazard:
Hazards associated with removing an instrument from service
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.
Warning: To avoid personal contamination with
biohazardous, toxic, or corrosive materials, wear
chemical-resistant gloves during all phases of instrument
decontamination.
TP03406
Source enclosure assembly

vii
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.
To avoid puncture injuries, handle syringes, fused silica lines, and
borosilicate tips with care.

viii
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

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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, switch between
modes of operation, and maintain it.
Intended use of the Xevo TQD
Waters designed the Xevo® TQD 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 APCI, APGC, APPI, ASAP, ESCi®, NanoFlow™ ESI,
or TRIZAIC™ UPLC® options, or optional third-party sources (DART®, DESI,
or LDTD™), the Xevo TQD 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 cover the entire range of quality-control samples, typical
specimens, and atypical specimens.
To calibrate the Xevo TQD, consult the instrument’s online Help system.
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 are sometimes 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, adopt the following measures:

x
• 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.

xi
ISM classification
ISM Classification: ISM Group 1 Class A
This classification is assigned in accordance with IEC 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 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

xii

Table of Contents xiii
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................. ii
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iv
Considerations specific to the Xevo TQD........................................................... iv
Safety advisories............................................................................................... vii
Operating this instrument .............................................................................. viii
Applicable symbols .......................................................................................... viii
Audience and purpose......................................................................................... ix
Intended use of the Xevo TQD ........................................................................... ix
Calibrating .......................................................................................................... ix
Quality control .................................................................................................... ix
ISM classification ................................................................................................. xi
ISM Classification: ISM Group 1 Class A ..................................................... 1-xi
EC authorized representative ........................................................................... xi
1 Specifications and Operating Modes ................................................ 1-1
Uses and compatibility .................................................................................... 1-2
ACQUITY H-Class and nanoACQUITY Xevo TQD UPLC/MS systems....... 1-5
Non-ACQUITY devices for use with the Xevo TQD....................................... 1-7
Software and data system ............................................................................... 1-7
Instrument Console software .......................................................................... 1-8
Ionization techniques and source probes ................................................... 1-9
Electrospray ionization (ESI).......................................................................... 1-9
Combined ESI and APCI (ESCi)..................................................................... 1-9
Atmospheric pressure chemical ionization (APCI) ........................................ 1-9
Dual-mode APPI/APCI source......................................................................... 1-9
Table of Contents

xiv Table of Contents
NanoFlow source............................................................................................ 1-10
Atmospheric solids analysis probe (ASAP)................................................... 1-10
Atmospheric pressure gas chromatography (APGC) ................................... 1-11
TRIZAIC UPLC source .................................................................................. 1-11
IntelliStart Fluidics system .......................................................................... 1-11
Functionality.................................................................................................. 1-11
System operation ........................................................................................... 1-12
Ion optics ........................................................................................................... 1-13
MS operating modes ....................................................................................... 1-14
MS/MS operating modes ................................................................................ 1-15
Product (daughter) ion mode......................................................................... 1-16
Precursor (parent) ion mode.......................................................................... 1-17
Multiple reaction monitoring mode .............................................................. 1-17
Constant neutral loss mode........................................................................... 1-19
Sample inlet ...................................................................................................... 1-19
Leak sensors ..................................................................................................... 1-20
Vacuum system ................................................................................................ 1-20
Rear panel connections ................................................................................. 1-21
2 Preparing for Operation ...................................................................... 2-1
Starting the mass spectrometer .................................................................... 2-2
Verifying the instrument’s state of readiness ................................................ 2-4
Monitoring the instrument LEDs ................................................................... 2-4
Tuning and calibration information ............................................................... 2-4
Running the instrument at different flow rates............................................. 2-5
Preparing the IntelliStart Fluidics system ................................................. 2-6
Installing the reservoir bottles........................................................................ 2-6
Purging the infusion pump.............................................................................. 2-8
Rebooting the instrument ............................................................................... 2-8
Leaving the mass spectrometer ready for operation ............................... 2-9
Emergency shutdown of the mass spectrometer............................................ 2-9

Table of Contents xv
3 Changing the Mode of Operation ....................................................... 3-1
ESI mode ............................................................................................................. 3-2
Installing the ESI probe .................................................................................. 3-2
Removing the ESI probe.................................................................................. 3-4
ESCi mode ........................................................................................................... 3-5
Optimizing the ESI probe for ESCi operation................................................ 3-5
APCI mode .......................................................................................................... 3-5
Installing the IonSABRE II probe .................................................................. 3-6
Removing the IonSABRE II probe .................................................................. 3-8
Combined APPI/APCI source ......................................................................... 3-9
APPI operation................................................................................................. 3-9
APCI operation............................................................................................... 3-10
Dual-mode operation ..................................................................................... 3-11
The combined APPI/APCI source components............................................. 3-12
Installing the combined APPI/APCI source ................................................. 3-13
Removing the IonSABRE II probe and APPI/APCI source enclosure ........ 3-15
NanoFlow source ............................................................................................. 3-16
Installing the NanoFlow source .................................................................... 3-17
Fitting a borosilicate glass capillary (nanovial)........................................... 3-19
Positioning the borosilicate glass capillary tip............................................. 3-22
Restarting a stalled borosilicate glass capillary electrospray ..................... 3-23
4 Maintenance Procedures ..................................................................... 4-1
Maintenance schedule ..................................................................................... 4-3
Spare parts ......................................................................................................... 4-5
Troubleshooting with Connections INSIGHT ............................................ 4-6
Safety and handling ......................................................................................... 4-7
Preparing the instrument for working on the source ............................. 4-7
Removing and refitting the source enclosure ............................................ 4-8
Removing the source enclosure from the instrument.................................... 4-8
Fitting the source enclosure to the instrument............................................ 4-11

xvi Table of Contents
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 exhaust trap bottle ............................................................... 4-20
Gas ballasting the roughing pump ............................................................. 4-22
Gas ballasting a pump with a screwdriver-operated gas ballast valve ...... 4-23
Gas ballasting a pump with a handle-operated gas ballast valve .............. 4-24
Checking the roughing pump oil level ....................................................... 4-25
Adding oil to the roughing pump ................................................................ 4-25
Cleaning the source components ................................................................ 4-27
Cleaning the sampling cone assembly ....................................................... 4-28
Removing the sampling cone assembly from the source ............................. 4-28
Disassembling the sampling cone assembly................................................. 4-30
Cleaning the sample cone and cone gas nozzle ............................................ 4-32
Assembling the sampling cone assembly...................................................... 4-34
Fitting the sampling cone assembly to the source ....................................... 4-35
Cleaning the extraction cone ....................................................................... 4-37
Removing the ion block assembly from the source assembly...................... 4-37
Removing the extraction cone from the ion block ........................................ 4-39
Cleaning the extraction cone......................................................................... 4-40
Fitting the extraction cone to the ion block.................................................. 4-42
Fitting the ion block assembly to the source assembly................................ 4-43
Cleaning the ion block assembly ................................................................. 4-44
Disassembling the source ion block assembly.............................................. 4-44
Cleaning the ion block components .............................................................. 4-51
Assembling the source ion block assembly................................................... 4-53

Table of Contents xvii
Cleaning the ion guide assembly ................................................................. 4-55
Removing the ion block assembly and ion guide from the source assembly 4-55
Cleaning the ion guide assembly .................................................................. 4-57
Removing the differential aperture from the ion guide............................... 4-60
Fitting the differential aperture to the ion guide assembly ........................ 4-62
Fitting the ion guide assembly to the source assembly ............................... 4-63
Fitting the ion block support to the source................................................... 4-63
Replacing the ESI probe tip and gasket .................................................... 4-65
Removing the ESI probe tip and gasket ....................................................... 4-65
Fitting the ESI probe tip and gasket............................................................ 4-67
Replacing the ESI probe sample capillary ............................................... 4-69
Removing the existing capillary.................................................................... 4-69
Installing the new capillary .......................................................................... 4-73
Cleaning the IonSABRE II probe tip .......................................................... 4-77
Replacing the IonSABRE II probe sample capillary .............................. 4-78
Removing the existing capillary.................................................................... 4-78
Installing the new capillary .......................................................................... 4-80
Cleaning or replacing the corona pin ........................................................ 4-84
Replacing the IonSABRE II probe heater ................................................. 4-85
Removing the IonSABRE II probe heater .................................................... 4-85
Fitting the new IonSABRE II probe heater.................................................. 4-86
Replacing the ion block source heater ...................................................... 4-87
Replacing the source assembly seals ......................................................... 4-92
Removing the probe adjuster assembly probe and source enclosure seals. 4-92
Fitting the new source enclosure and probe adjuster assembly seals ........ 4-94

xviii Table of Contents
Replacing the air filter .................................................................................. 4-95
Replacing the roughing pump oil ............................................................... 4-97
Replacing the roughing pump’s oil demister element ......................... 4-100
APPI/APCI source—changing the UV lamp bulb .................................. 4-106
APPI/APCI source—cleaning the lamp window .................................... 4-107
APPI/APCI source—replacing the APPI lamp drive seals .................. 4-108
Removing the APPI lamp drive assembly seals......................................... 4-108
Fitting the new APPI lamp drive assembly O-rings.................................. 4-115
Replacing the instrument’s fuses .............................................................. 4-117
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-5
Electrical and handling symbols ................................................................. A-12
Electrical symbols .......................................................................................... A-12
Handling symbols .......................................................................................... A-13
B External Connections .......................................................................... B-1
External wiring and vacuum connections ................................................. B-2
Connecting the oil-filled roughing pump ................................................... B-3
Making the electrical connections to the oil-filled roughing pump............... B-7
Connecting the Edwards oil-free roughing pump ................................... B-8
Making the electrical connections to the Edwards oil-free roughing pump B-11

Table of Contents xix
Connecting to the nitrogen gas supply ..................................................... B-12
Connecting to the collision cell gas supply ............................................. B-14
Connecting the nitrogen exhaust line ...................................................... B-14
Connecting the liquid waste line ............................................................... B-17
Connecting the workstation ........................................................................ B-19
Connecting Ethernet cables ........................................................................ B-19
I/O signal connectors ..................................................................................... B-20
Signal connections ......................................................................................... B-22
Connecting to the power supply ................................................................ B-25
C Materials of Construction and Compliant 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
The selector valve ............................................................................................ D-2
Plumbing schematic ........................................................................................ D-3
Tubing and connection specifications ........................................................ D-3
Index ..................................................................................................... Index-1

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