Waters Xevo TQ MS Installation instructions

Waters Xevo TQ MS
Operator’s Overview and Maintenance Guide
IVD/Revision A
Copyright © Waters Corporation 2010.
All rights reserved.

ii
Copyright notice
© 2010 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND 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, UltraPerformance LC, and
Waters are registered trademarks of Waters Corporation. IntelliStart,
MassLynx, ScanWave, T-Wave, TargetLynx, “THE SCIENCE OF WHAT'S
POSSIBLE.”, UPLC, Xevo, and ZSpray are trademarks of Waters
Corporation.
Phillips is a registered trademark of Phillips Screw Company, Inc.
PEEK is a trademark of Victrex Corporation.
snoop and Swagelok are registered trademarks of Swagelok Company.
Teflon and Viton are registered trademarks of DuPont.
Varian is a trademark of Varian, Inc.
Xylan is a registered trademark of Whitford Corporation.
Other trademarks or registered trademarks are the sole property of their
respective owners.

iii
Contacting Waters
Contact Waters®with questions regarding 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, 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.
When you develop methods, follow the “Protocol for the Adoption of Analytical
Methods in the Clinical Chemistry Laboratory”, American Journal of Medical
Technology, 44, 1, pages 30–37 (1978). This protocol addresses good operating
procedures and the techniques necessary to validate system and method
performance.
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
Considerations specific to the Xevo TQ MS
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 B-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
High temperature hazard
Xevo TQ MS high temperature hazard
Warning: To avoid burn injuries, do not touch the source ion block
assembly with your hand when operating or servicing the instrument.
TP03127
TQ MS TQ MS
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. 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 (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, change its modes of
operation, and maintain it.
Intended use of the Xevo TQ MS
The Waters Xevo TQ MS can be used for general in vitro diagnostic
applications. However, only professionally trained and qualified laboratory
personnel can use the instrument for those purposes.
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
The Waters Xevo TQ MS is CE-marked according to the
European Union In Vitro Diagnostic Device Directive 98/79/EC.

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 must cover the entire range of quality-control 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
EC authorized representative information
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.
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
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iii
Considerations specific to the Xevo TQ MS....................................................... iv
Safety advisories................................................................................................. vi
Operating this instrument ................................................................................ vii
Applicable symbols ........................................................................................... vii
Audience and purpose....................................................................................... vii
Intended use of the Xevo TQ MS ..................................................................... vii
Calibrating ....................................................................................................... viii
Quality control ................................................................................................. viii
EC authorized representative information ................................................... ix
ISM classification ................................................................................................. ix
ISM Classification: ISM Group 1 Class A ......................................................... ix
1 Waters Xevo TQ MS Overview ............................................................. 1-1
Waters Xevo TQ MS .......................................................................................... 1-2
ACQUITY®Xevo TQ MS UPLC/MS systems................................................. 1-3
Non-ACQUITY devices for use with the Xevo TQ MS................................... 1-4
Software and data system ............................................................................... 1-5
Instrument Console ......................................................................................... 1-5
Ionization techniques and source probes ................................................... 1-6
Electrospray ionization (ESI).......................................................................... 1-6
IntelliStart Fluidics system ............................................................................ 1-7
Overview........................................................................................................... 1-7
System components ......................................................................................... 1-8
System operation ............................................................................................. 1-8
Table of Contents

xii Table of Contents
Ion optics ............................................................................................................. 1-9
MS operating modes ....................................................................................... 1-10
MS/MS operating modes ................................................................................ 1-11
Product (daughter) ion mode......................................................................... 1-12
Precursor (parent) ion mode.......................................................................... 1-13
Multiple reaction monitoring mode .............................................................. 1-13
Constant neutral loss mode........................................................................... 1-14
ScanWave daughter scan mode..................................................................... 1-14
Leak sensors ..................................................................................................... 1-15
Vacuum system ................................................................................................ 1-15
Rear panel ......................................................................................................... 1-16
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 ................................................. 2-5
Installing the reservoir bottles........................................................................ 2-5
Purging the infusion pump.............................................................................. 2-7
Rebooting the mass spectrometer ................................................................. 2-8
Leaving the mass spectrometer ready for operation ............................... 2-9
Emergency shutdown of the mass spectrometer ....................................... 2-9
3 Preparing the ESI Source .................................................................... 3-1
ESI mode ............................................................................................................. 3-2
Installing the ESI probe .................................................................................. 3-2
Removing the ESI probe.................................................................................. 3-6

Table of Contents xiii
4 Maintenance Procedures ..................................................................... 4-1
Maintenance schedule ..................................................................................... 4-3
Spare parts ......................................................................................................... 4-4
Troubleshooting with Connections Insight ................................................ 4-5
Safety and handling ......................................................................................... 4-6
Preparing the instrument for working on the source ............................. 4-7
Removal and refitting of the source enclosure .......................................... 4-8
Removing the source enclosure from the instrument.................................... 4-8
Fitting the source enclosure to the instrument.............................................. 4-9
Operating the source isolation valve ......................................................... 4-11
Removing O-rings and seals ......................................................................... 4-14
Cleaning the instrument case ...................................................................... 4-15
Emptying the nitrogen exhaust trap bottle .............................................. 4-15
Inspecting the Varian roughing pump oil level ....................................... 4-17
Adding oil to the Varian roughing pump .................................................. 4-18
Replacing the Varian roughing pump oil and oil mist filter ................ 4-20
Emptying the roughing pump oil.................................................................. 4-20
Replacing the oil mist filter........................................................................... 4-21
To refill the pump with oil............................................................................. 4-23
Cleaning the source components ................................................................ 4-25
Cleaning the sampling cone assembly ....................................................... 4-26
Removing the sampling cone assembly from the source ............................. 4-26
Disassembling the sampling cone assembly................................................. 4-28
Cleaning the sample cone and cone gas nozzle ............................................ 4-30
Assembling the sampling cone assembly...................................................... 4-32
Fitting the sampling cone assembly to the source ....................................... 4-33
Cleaning the extraction cone ....................................................................... 4-35
Removing the ion block assembly from the source assembly...................... 4-35

xiv Table of Contents
Removing the extraction cone from the ion block ........................................ 4-37
Cleaning the extraction cone......................................................................... 4-38
Fitting the extraction cone to the ion block.................................................. 4-40
Fitting the ion block assembly to the source assembly................................ 4-41
Cleaning the ion block assembly ................................................................. 4-42
Disassembling the source ion block assembly.............................................. 4-42
Cleaning the ion block components .............................................................. 4-49
Assembling the source ion block assembly................................................... 4-51
Cleaning the source hexapole assembly .................................................... 4-53
Removing the ion block assembly, ion block support, and hexapole from the
source assembly ....................................................................................... 4-53
Cleaning the hexapole assembly................................................................... 4-55
Fitting the hexapole assembly, PEEK ion block support, and ion block
assembly to the source assembly ............................................................ 4-57
Replacing the ESI probe tip and gasket .................................................... 4-59
Removing the ESI probe tip and gasket ....................................................... 4-59
Fitting the ESI probe tip and gasket............................................................ 4-62
Replacing the ESI probe sample capillary ............................................... 4-63
Removing the existing capillary.................................................................... 4-63
Installing the new capillary .......................................................................... 4-67
Replacing the ion block source heater ...................................................... 4-71
Replacing the source assembly seals ......................................................... 4-75
Removing the probe adjuster assembly probe and source enclosure seals. 4-75
Fitting the new source enclosure and probe adjuster assembly probe
seals .......................................................................................................... 4-77
Replacing the air filter .................................................................................. 4-79
A Safety Advisories .................................................................................. A-1
Warning symbols ............................................................................................... A-2
Task-specific hazard warnings........................................................................ A-2
Specific warnings ............................................................................................. A-3

Table of Contents xv
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 Materials of Construction and Compliant Solvents ..................... B-1
Preventing contamination ............................................................................. B-2
Items exposed to solvent ................................................................................ B-2
Solvents used to prepare mobile phases .................................................... B-3
C External Connections .......................................................................... C-1
Mass spectrometer external wiring and vacuum connections ............. C-2
Connecting the Varian oil-filled roughing pump ..................................... C-3
Making the electrical connections to the Varian oil-filled roughing pump .. C-7
Connecting the Edwards oil-free roughing pump ................................... C-8
Making the electrical connections for the Edwards oil-free roughing pump........
C-12
Connecting to the nitrogen gas supply ..................................................... C-13
Connecting to the collision cell gas supply ............................................. C-15
Connecting the nitrogen exhaust line ...................................................... C-16
Connecting the liquid waste line ............................................................... C-19
Connecting the workstation ........................................................................ C-21
Connecting Ethernet cables ........................................................................ C-22
Input/output signal connectors .................................................................. C-22
Making signal connections ............................................................................ C-25

xvi Table of Contents
Connecting to the electricity source ......................................................... C-28
D Plumbing the IntelliStart Fluidics system ..................................... D-1
Preventing contamination ............................................................................. D-2
Plumbing schematic ........................................................................................ D-2
Pipe specifications ........................................................................................... D-3
Index ..................................................................................................... Index-1

1-1
1Waters Xevo TQ MS Overview
This chapter describes the instrument, including its controls and
connections for gas and plumbing.
Contents
Topic Page
Waters Xevo TQ MS 1-2
Ionization techniques and source probes 1-6
IntelliStart Fluidics system 1-7
Ion optics 1-9
MS operating modes 1-10
MS/MS operating modes 1-11
Leak sensors 1-15
Vacuum system 1-15
Rear panel 1-16

1-2 Waters Xevo TQ MS Overview
Waters Xevo TQ MS
The Waters®Xevo™ TQ MS 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®.
The Xevo TQ MS is fitted with the electrospray ionization (ESI) source.
For mass spectrometer specifications, see the Waters Xevo TQ MS Site
Preparation Guide.
Waters Xevo TQ MS
IntelliStart technology
IntelliStart™ technology monitors LC/MS/MS performance and reports when
the mass spectrometer is ready for use.
The IntelliStart software automatically tunes and mass calibrates the mass
spectrometer and displays performance readbacks. Integrated with
MassLynx™ mass spectrometry software and Instrument Console software,
IntelliStart software enables simplified setup of the system for use in routine
TQ MSTQ MS

Waters Xevo TQ MS 1-3
analytical and open access applications. (See “Software and data system” on
page 1-5).
The IntelliStart Fluidics system is built into the mass spectrometer. It
delivers sample directly to the MS probe from the LC column or from three
integral reservoirs. The integral reservoirs can also deliver sample through
direct or combined infusion so that you can optimize instrument performance
at analytical flow rates.
Recommendation: Use reservoir A for the calibrant solution, reservoir B for
tuning compounds, and reservoir C for analyte/optimization solution.
A fourth reservoir contains solvent for automated flushing of the solvent
delivery system.
See the mass spectrometer’s online Help for further details on IntelliStart
technology.
ACQUITY®Xevo TQ MS UPLC/MS systems
The Waters Xevo TQ MS is compatible with the ACQUITY UPLC®systems; if
you are not using an ACQUITY UPLC system, refer to the documentation
relevant to your LC system. See “Non-ACQUITY devices for use with the Xevo
TQ MS” on page 1-4.
The ACQUITY Xevo TQ MS UPLC/MS system includes an ACQUITY UPLC
system and the Waters Xevo TQ MS.
ACQUITY UPLC system
The ACQUITY UPLC system includes a binary solvent manager, sample
manager, column heater, optional sample organizer, optional detectors, and a
specialized ACQUITY UPLC column. WatersMassLynx mass spectrometry
software controls the system.
For further instruction, see the ACQUITY UPLC System Operator’s Guide or
Controlling Contamination in LC/MS Systems (part number 715001307). You
can find these documents on http://www.waters.com; click Services and
Support > Support.

1-4 Waters Xevo TQ MS Overview
Waters ACQUITY Xevo TQ MS UPLC/MS system
Non-ACQUITY devices for use with the Xevo TQ MS
The following non-ACQUITY LC devices are validated for use with the Xevo
TQ MS:
• Waters Alliance 2695 separations module
• Waters Alliance 2795 separations module
• Waters 2998 PDA detector
• Waters 2487 UV detector
• Waters 1525µ binary gradient pump + 2777 autosampler
• Spark Holland Symbiosis
Sample organizer (optional)
Solvent tray
Column heater
Xevo TQ MS
Sample manager
Binary solvent manager
Access door to the fluidics pump
Access door to the fluidics valve
ESI probe high voltage connector
Probe
Source interface sliding door
Source enclosure
Source enclosure
release