Waters Xevo TQD Operating manual

Waters Xevo TQD
Overview and Maintenance Guide
715004387 / Revision B
Copyright © Waters Corporation 2014
All rights reserved

ii March 14, 2014, 715004387 Rev. B

March 14, 2014, 715004387 Rev. B iii
General Inform ation
Copyright notice
© 2014 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS
DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY
FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use. For the
most recent revision of this document, consult the Waters Web site
(waters.com).
Trademarks
ACQUITY, ACQUITY UltraPerformance LC, ACQUITY UPLC, Alliance,
Connections INSIGHT, ESCi, MassLynx, nanoACQUITY, nanoACQUITY
UPLC, nanoTile, “THE SCIENCE OF WHAT’S POSSIBLE”, TRIZAIC,
UNIFI, UPLC, Waters, Waters Quality Parts, and Xevo are registered
trademarks of Waters Corporation, and IntelliStart, IonSABRE, NanoFlow,
RADAR, T-Wave, and ZSpray are trademarks of Waters Corporation.
DART is a registered trademark of JEOL USA Inc.
GELoader is a registered trademark of New Brunswick Scientific, Co., Inc.
LDTD is a trademark of Phytronix Technologies Inc.
PEEK is a trademark of Victrex Corporation.
Phillips and Pozidriv are registered trademarks of Phillips Screw Company,
Inc.
snoop and Swagelok are registered trademarks of Swagelok Company.
Spark Holland and Symbiosis are trademarks of Spark-Holland BV.
Viton is a registered trademark of DuPont.
Other registered trademarks or trademarks are the sole property of their
owners.

iv March 14, 2014, 715004387 Rev. B
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.
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
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

March 14, 2014, 715004387 Rev. B v
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 TQD
Power cord replacement hazard
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 avoid electric shock, use the SVT-type power cord in the
United States and HAR-type (or better) in Europe. The main power cord
must only be replaced with one of adequate rating. For information
regarding what cord to use in other countries, contact your local Waters
distributor.
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 244),
determine whether any solvents you use that are not listed are
chemically compatible with the composition of the O-rings.

vi March 14, 2014, 715004387 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 bar, 58 psi). You must also install a
gas-fail device that interrupts the solvent flowing from the LC system in the
event the supply of nitrogen fails.
Overload hazard
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 bar, 58 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.
Warning: To prevent personal injury, ensure equipment placed on top of
the Xevo®TQD does not exceed 15kg.

March 14, 2014, 715004387 Rev. B vii
Glass-breakage hazard
High temperature hazard
Xevo TQD high temperature hazard:
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.
Warning: To avoid burn injuries, ensure the source heater is turned off
and the ion block is cool before performing maintenance on these
components. The source ion block, located behind the source enclosure
assembly, can become hot.
TP03406
Source enclosure assembly

viii March 14, 2014, 715004387 Rev. B
Hazards associated with removing an instrument from service
When you remove the instrument from use to repair or dispose of it, you must
decontaminate all of its vacuum areas. These are the areas in which you can
expect to encounter the highest levels of contamination:
• Source interior
• Waste tubing
• Exhaust system
• Rotary pump oil (where applicable)
The need to decontaminate other vacuum areas of the instrument depends on
the kinds of samples the instrument analyzed and their levels of
concentration. Do not dispose of the instrument or return it to Waters for
repair until the authority responsible for approving its removal from the
premises specifies the extent of decontamination required and the level of
residual contamination permissible. That authority must also prescribe the
method of decontamination to be used and the appropriate protection for
personnel undertaking the decontamination process.
You must handle items such as syringes, fused silica lines, and borosilicate
tips used to carry sample into the source area in accordance with laboratory
procedures for contaminated vessels and sharps. To avoid contamination by
carcinogens, toxic substances, or biohazards, you must wear
chemical-resistant gloves when handling or disposing of used oil.
Bottle placement prohibition
Warning: To avoid personal contamination with biohazards,
toxic materials, or 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.
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.

March 14, 2014, 715004387 Rev. B ix
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
Do not position the instrument so that it is difficult to operate the
disconnecting device.
Equipment misuse notice
If the equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired.
Safety advisories
Consult Appendix A for a comprehensive list of warning advisories and
notices.

x March 14, 2014, 715004387 Rev. B
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 catalog number
Serial number
Supply ratings
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
5()

March 14, 2014, 715004387 Rev. B xi
Consult instructions for use
Electrical and electronic equipment with this
symbol may contain hazardous substances and
should not be disposed of as general waste.
For compliance with the Waste Electrical and
Electronic Equipment Directive (WEEE)
2012/19/EU, contact Waters Corporation for the
correct disposal and recycling instructions.
Symbol Definition

xii March 14, 2014, 715004387 Rev. B
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. The Xevo TQD is not
intended for use in diagnostic applications.
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 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. 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.

March 14, 2014, 715004387 Rev. B xiii
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.
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 March 14, 2014, 715004387 Rev. B
EC authorized representative
Waters Corporation
Stamford Avenue
Altrincham Road
Wilmslow
SK9 4AX
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

March 14, 2014, 715004387 Rev. B xv
Copyright notice .................................................................................................. iii
Trademarks ........................................................................................................... iii
Customer comments ............................................................................................ iv
Contacting Waters ............................................................................................... iv
Safety considerations .......................................................................................... iv
Safety hazard symbol notice................................................................................ v
Considerations specific to the Xevo TQD............................................................ v
FCC radiation emissions notice ......................................................................... ix
Electrical power safety notice ............................................................................ ix
Equipment misuse notice ................................................................................... ix
Safety advisories................................................................................................. ix
Operating this instrument .................................................................................. x
Applicable symbols .............................................................................................. x
Audience and purpose....................................................................................... xii
Intended use of the Xevo TQD ......................................................................... xii
Calibrating ........................................................................................................ xii
Quality control .................................................................................................. xii
EMC considerations ......................................................................................... xiii
Canada spectrum management emissions notice .......................................... xiii
ISM Classification: ISM Group 1 Class A ...................................................... xiii
EC authorized representative ......................................................................... xiv
1 Specifications and Operating Modes ................................................. 23
Uses and compatibility ..................................................................................... 24
ACQUITY Xevo TQD UPLC/MS systems......................................................... 26
Non-ACQUITY devices for use with the Xevo TQD......................................... 29
Software and data system ................................................................................. 29
Table of Contents

xvi March 14, 2014, 715004387 Rev. B
Ionization techniques and source probes .................................................... 31
Electrospray ionization (ESI)............................................................................ 31
Combined ESI and APCI (ESCi)....................................................................... 31
Atmospheric pressure chemical ionization (APCI) .......................................... 31
Dual-mode APPI/APCI source........................................................................... 32
NanoFlow source................................................................................................ 32
Atmospheric solids analysis probe (ASAP)....................................................... 33
Atmospheric pressure gas chromatography (APGC) ....................................... 33
TRIZAIC UPLC source ...................................................................................... 33
IntelliStart Fluidics system ............................................................................. 34
Functionality...................................................................................................... 34
System operation ............................................................................................... 35
Ion optics .............................................................................................................. 36
MS operating modes .......................................................................................... 37
MS/MS operating modes ................................................................................... 38
Product (daughter) ion mode............................................................................. 39
Precursor (parent) ion mode.............................................................................. 40
Multiple reaction monitoring mode .................................................................. 40
Constant neutral loss mode............................................................................... 42
Sample inlet ......................................................................................................... 43
Leak sensors ........................................................................................................ 43
Vacuum system ................................................................................................... 43
Rear panel connections .................................................................................... 44
2 Preparing for Operation ....................................................................... 45
Starting the mass spectrometer ..................................................................... 46
Verifying the instrument’s state of readiness .................................................. 50
Monitoring the instrument LEDs ..................................................................... 50
Tuning and calibration information ................................................................. 50
Running the instrument at different flow rates............................................... 51
Preparing the IntelliStart Fluidics system .................................................. 52
Installing the reservoir bottles.......................................................................... 52

March 14, 2014, 715004387 Rev. B xvii
Purging the infusion pump................................................................................ 54
Rebooting the instrument ................................................................................ 54
Leaving the mass spectrometer ready for operation ................................ 55
Emergency shutdown of the mass spectrometer.............................................. 55
3 Changing the Mode of Operation ........................................................ 57
ESI mode .............................................................................................................. 58
Installing the ESI probe .................................................................................... 58
Removing the ESI probe.................................................................................... 61
ESCi mode ............................................................................................................ 62
Optimizing the ESI probe for ESCi operation.................................................. 62
APCI mode ........................................................................................................... 62
Installing the IonSABRE II probe .................................................................... 63
Removing the IonSABRE II probe .................................................................... 65
Combined APPI/APCI source .......................................................................... 66
APPI operation................................................................................................... 66
APCI operation................................................................................................... 67
Dual-mode operation ......................................................................................... 68
The combined APPI/APCI source components................................................. 69
Installing the combined APPI/APCI source ..................................................... 71
Removing the IonSABRE II probe and APPI/APCI source enclosure ............ 72
NanoFlow source ................................................................................................ 73
Installing the NanoFlow source ........................................................................ 74
Fitting a borosilicate glass capillary (nanovial)............................................... 77
Positioning the borosilicate glass capillary tip................................................. 80
Restarting a stalled borosilicate glass capillary electrospray ......................... 80

xviii March 14, 2014, 715004387 Rev. B
4 Maintenance Procedures ...................................................................... 81
Maintenance schedule ...................................................................................... 83
Spare parts .......................................................................................................... 85
Troubleshooting with Connections INSIGHT ............................................. 86
Safety and handling .......................................................................................... 87
Preparing the instrument for operations on or inside its source .......... 88
Removing and refitting the source enclosure ............................................. 90
Removing the source enclosure from the instrument...................................... 90
Fitting the source enclosure to the instrument................................................ 92
Installing and removing the corona pin ....................................................... 93
Installing the corona pin in the source............................................................. 93
Removing the corona pin from the source ........................................................ 95
Operating the source isolation valve ............................................................ 96
Removing O-rings and seals ............................................................................ 99
Cleaning the instrument case ....................................................................... 100
Emptying the exhaust trap bottle ................................................................ 100
Gas ballasting the roughing pump .............................................................. 102
Gas ballasting a pump fitted with a screwdriver-operated gas
ballast valve ............................................................................................... 103
Gas ballasting a pump fitted with a handle-operated gas ballast valve ...... 105
Checking the roughing pump oil level ........................................................ 106
Adding oil to the roughing pump ................................................................. 106
Cleaning the source components ................................................................. 108
Cleaning the sampling cone assembly ........................................................ 109
Removing the sampling cone assembly from the source ............................... 109
Disassembling the sampling cone assembly................................................... 111
Cleaning the sample cone and cone gas nozzle .............................................. 114
Assembling the sampling cone assembly........................................................ 116

March 14, 2014, 715004387 Rev. B xix
Fitting the sampling cone assembly to the source ......................................... 117
Cleaning the extraction cone ........................................................................ 119
Removing the ion block assembly from the source assembly........................ 119
Removing the extraction cone from the ion block .......................................... 121
Cleaning the extraction cone........................................................................... 123
Fitting the extraction cone to the ion block.................................................... 125
Fitting the ion block assembly to the source assembly.................................. 125
Cleaning the ion block assembly .................................................................. 126
Disassembling the source ion block assembly................................................ 126
Cleaning the ion block components ................................................................ 133
Assembling the source ion block assembly..................................................... 135
Cleaning the ion guide assembly .................................................................. 137
Removing the ion block assembly and ion guide from the source assembly 137
Cleaning the ion guide assembly .................................................................... 140
Removing the differential aperture from the ion guide................................. 142
Fitting the differential aperture to the ion guide assembly .......................... 144
Fitting the ion guide assembly to the source assembly ................................. 145
Fitting the ion block support to the source..................................................... 145
Replacing the ESI probe tip and gasket ..................................................... 147
Removing the ESI probe tip and gasket ......................................................... 147
Fitting the ESI probe tip and gasket.............................................................. 150
Replacing the ESI probe sample capillary ................................................ 151
Removing the existing capillary...................................................................... 151
Installing the new capillary ............................................................................ 155
Cleaning the IonSABRE II probe tip ........................................................... 159
Replacing the IonSABRE II probe sample capillary ............................... 160
Removing the existing capillary...................................................................... 160
Installing the new capillary ............................................................................ 162
Cleaning or replacing the corona pin ......................................................... 166
Replacing the IonSABRE II probe heater .................................................. 167
Removing the IonSABRE II probe heater ...................................................... 167
Fitting the new IonSABRE II probe heater.................................................... 169

xx March 14, 2014, 715004387 Rev. B
Replacing the ion block source heater ....................................................... 170
Replacing the source assembly seals .......................................................... 174
Removing the probe adjuster assembly probe and source enclosure seals... 174
Fitting the new source enclosure and probe adjuster assembly seals .......... 176
Replacing the air filter ................................................................................... 178
Replacing the roughing pump oil ................................................................ 180
Replacing the roughing pump’s oil demister element ............................ 183
APPI/APCI source—changing the UV lamp bulb ..................................... 188
APPI/APCI source—cleaning the lamp window ....................................... 189
APPI/APCI source—replacing the APPI lamp drive seals ..................... 191
Removing the APPI lamp drive assembly seals............................................. 191
Fitting the new APPI lamp drive assembly O-rings...................................... 197
Replacing the instrument’s fuses ................................................................. 199
A Safety Advisories .................................................................................. 201
Warning symbols .............................................................................................. 202
Specific warnings ............................................................................................. 203
Notices ................................................................................................................ 206
Prohibition symbol .......................................................................................... 206
Warnings that apply to all Waters instruments and devices ................. 207
Warnings that address the replacing of fuses ........................................... 212
Electrical and handling symbols .................................................................. 214
Electrical symbols ............................................................................................ 214
Handling symbols ............................................................................................ 215
B External Connections .......................................................................... 217
External wiring and vacuum connections ................................................. 218
Connecting the oil-filled roughing pump ................................................... 219
Connecting electric cables to the oil-filled roughing pump ........................... 223