Waters SYNAPT G2 Operating manual

Waters SYNAPT G2 Mass
Spectrometry System
Operator’s Overview and Maintenance Guide
Revision A
Copyright © Waters Corporation 2009
All rights reserved

ii
Copyright notice
© 2009 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS
DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY
FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use.
Trademarks
ACQUITY, ACQUITY UPLC, Connections Insight, ESCi, UPLC, and Waters
are registered trademarks of Waters Corporation. IntelliStart, LockSpray,
MassLynx, NanoFlow, NanoLockSpray, QuanTof, SYNAPT, T-Wave, “THE
SCIENCE OF WHAT'S POSSIBLE.”, Triwave, and ZSpray are trademarks of
Waters Corporation.
GELoader is a registered trademark of Cell Technology.
Swagelok and snoop are registered trademarks of Swagelok Company.
PEEK is a trademark of Victrex plc.
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].

iv
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, 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

v
Considerations specific to the SYNAPT G2 MS 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.

vi
High temperature hazard
Mass spectrometer high temperature hazard
Warning: To avoid burn injuries, avoid touching the source enclosure
with your hand when operating or servicing the instrument.
Source ion block assembly

vii
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.

viii
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
Waters designed this instrument to be used as a research tool to deliver
authenticated, exact-mass measurement. It is not for use in diagnostic
procedures.
Symbol Definition
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
This product has been tested to the requirements
of CAN/CSA-C22.2 No. 61010-1, second edition,
including Amendment 1, or a later version of the
same standard incorporating the same level of
testing requirements
ABN 49 065 444 751

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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.
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.

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

Table of Contents xi
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iv
Safety considerations .......................................................................................... iv
Considerations specific to the SYNAPT G2 MS system .................................... v
Safety advisories............................................................................................... vii
Operating this instrument .............................................................................. viii
Applicable symbols .......................................................................................... viii
Audience and purpose...................................................................................... viii
Intended use..................................................................................................... viii
Calibrating .......................................................................................................... ix
Quality control .................................................................................................... ix
ISM classification ................................................................................................. ix
ISM Classification: ISM Group 1 Class A ......................................................... ix
EC Authorized Representative .......................................................................... x
1 System Overview .................................................................................... 1-1
Waters SYNAPT G2 MS .................................................................................... 1-2
SYNAPT G2 MS UPLC/MS/MS systems ........................................................ 1-2
ACQUITY UPLC SYNAPT G2 MS UPLC/MS/MS system............................ 1-2
nanoACQUITY UPLC SYNAPT G2 MS nanoUPLC/MS/MS system ........... 1-3
Software .............................................................................................................. 1-3
IntelliStart ....................................................................................................... 1-3
MassLynx ......................................................................................................... 1-4
Instrument Console ......................................................................................... 1-4
Table of Contents

xii Table of Contents
Instrument sources ........................................................................................... 1-5
LockSpray source and ionization modes......................................................... 1-5
NanoLockSpray source .................................................................................... 1-7
Dual-mode ionization source ........................................................................... 1-9
Matrix-assisted laser desorption ionization ................................................... 1-9
IntelliStart Fluidics system ............................................................................ 1-9
Overview........................................................................................................... 1-9
IntelliStart Fluidics physical layout............................................................. 1-10
System operation ........................................................................................... 1-11
Ion optics ........................................................................................................... 1-12
Analyzers ........................................................................................................... 1-13
Quadrupole..................................................................................................... 1-13
Triwave technology........................................................................................ 1-14
TOF analyzer ................................................................................................. 1-15
Mass spectrometer configuration ............................................................... 1-17
Triwave device ............................................................................................... 1-17
TOF................................................................................................................. 1-17
Leak sensors ..................................................................................................... 1-18
Vacuum system ................................................................................................ 1-18
Controls on the instrument’s rear panel ................................................... 1-19
2 Starting Up and Shutting Down the Mass Spectrometer ............. 2-1
Starting the mass spectrometer .................................................................... 2-2
Calibration information................................................................................... 2-3
Flow rates for the ACQUITY UPLC SYNAPT G2 MS
UPLC/MS/MS system ................................................................................ 2-3
Preparing the IntelliStart Fluidics system ................................................. 2-4
Installing the vials........................................................................................... 2-4
Purging the pump ............................................................................................ 2-5
Shutting down the mass spectrometer ........................................................ 2-6
Putting the mass spectrometer in Standby mode .......................................... 2-6
Fully shutting down the mass spectrometer.................................................. 2-6

Table of Contents xiii
Rebooting the embedded PC .......................................................................... 2-7
3 Configuring the LockSpray Source ................................................... 3-1
Configuring the LockSpray source ............................................................... 3-2
Configuring for ESI mode ............................................................................... 3-2
Installing the ESI probe .................................................................................. 3-2
Removing the ESI probe.................................................................................. 3-7
Installing the ESI small bore capillary option ........................................... 3-8
Configuring for APCI mode .......................................................................... 3-14
Installing the APCI probe ............................................................................. 3-14
Installing the corona pin in the source......................................................... 3-18
Removing the corona pin from the source .................................................... 3-18
Removing the APCI probe ............................................................................. 3-18
Configuring for ESCi mode .......................................................................... 3-19
Optimizing the ESI probe for ESCi operation.............................................. 3-19
Installing the corona pin in the source......................................................... 3-19
Removing the corona pin from the source .................................................... 3-19
4 Configuring the NanoLockSpray source .......................................... 4-1
Overview of the NanoLockSpray source ..................................................... 4-2
Sample sprayer ................................................................................................ 4-3
LockSpray sprayer........................................................................................... 4-3
NanoFlow gas supply....................................................................................... 4-4
Purge gas.......................................................................................................... 4-4
Sprayer platform adjuster assembly............................................................... 4-4
Selecting and Configuring the NanoLockSpray source .......................... 4-4
Deploying the sprayer platform adjuster assembly ................................. 4-5
Adjusting the sprayer tip position ................................................................ 4-6
Setting up the camera ...................................................................................... 4-7

xiv Table of Contents
Optional glass capillary sprayer ................................................................... 4-8
Installing the glass capillary sprayer ............................................................. 4-8
Fitting and loading the glass capillary........................................................... 4-9
5 Maintenance Procedures ..................................................................... 5-1
Maintenance schedule ..................................................................................... 5-3
Spare parts ......................................................................................................... 5-4
Troubleshooting using Connections Insight .............................................. 5-5
Safety and handling ......................................................................................... 5-6
Preparing the instrument for work performed on its source ................ 5-7
Removal and refitting of the source enclosure .......................................... 5-8
Removing the source enclosure from the instrument.................................... 5-8
Fitting the source enclosure to the instrument............................................ 5-11
Installing and removing the corona pin .................................................... 5-12
Installing the corona pin in the source......................................................... 5-12
Removing the corona pin from the source .................................................... 5-14
Operating the source isolation valve ......................................................... 5-15
Removing O-rings and seals ......................................................................... 5-17
Cleaning the mass spectrometer case ........................................................ 5-18
Emptying the nitrogen exhaust trap bottle .............................................. 5-19
Cleaning the source components ................................................................ 5-21
Cleaning the sampling cone assembly ....................................................... 5-21
Removing the sampling cone assembly from the source ............................. 5-21
Disassembling the sampling cone assembly................................................. 5-23
Cleaning the sample cone and cone gas nozzle ............................................ 5-26
Assembling the sampling cone assembly...................................................... 5-28
Fitting the sampling cone assembly to the source ....................................... 5-29
Cleaning the extraction cone ....................................................................... 5-31
Removing the ion block assembly from the source assembly...................... 5-31
Removing the extraction cone from the ion block ........................................ 5-33

Table of Contents xv
Cleaning the extraction cone......................................................................... 5-34
Fitting the extraction cone to the ion block.................................................. 5-36
Fitting the ion block assembly to the source assembly................................ 5-37
Cleaning the ion block assembly ................................................................. 5-38
Disassembling the source ion block assembly.............................................. 5-38
Cleaning the ion block components .............................................................. 5-45
Assembling the source ion block assembly................................................... 5-47
Cleaning the source T-Wave ion guide assembly .................................... 5-49
Removing the T-Wave ion guide assembly from the source assembly........ 5-49
Disassembling the T-Wave ion guide assembly ........................................... 5-51
Cleaning the T-Wave ion guide assembly aperture plate............................ 5-52
Cleaning the T-Wave ion guide..................................................................... 5-52
Assembling the T-Wave ion guide assembly ................................................ 5-54
Fitting the T-Wave ion guide assembly, PEEK ion block support,
and ion block assembly to the source assembly ..................................... 5-54
Replacing the ESI probe tip and gasket .................................................... 5-55
Removing the ESI probe tip and gasket ....................................................... 5-56
Fitting the ESI probe tip and gasket............................................................ 5-58
Replacing the ESI probe sample capillary ............................................... 5-59
Removing the existing capillary.................................................................... 5-59
Installing the new capillary .......................................................................... 5-64
Cleaning the APCI probe tip ........................................................................ 5-67
Replacing the APCI probe sample capillary ............................................ 5-68
Removing the existing capillary.................................................................... 5-68
Installing the new capillary .......................................................................... 5-71
Replacing the LockSpray probe capillary ................................................ 5-74
Removing the existing capillary.................................................................... 5-74
Installing the new capillary .......................................................................... 5-77
Replacing the NanoLockSpray reference probe capillary ................... 5-78
Removing the NanoLockSpray reference probe ........................................... 5-78
Installing the new TaperTip and capillary................................................... 5-80

xvi Table of Contents
Cleaning or replacing the corona pin ........................................................ 5-83
Replacing the APCI probe heater ............................................................... 5-84
Removing the APCI probe heater ................................................................. 5-84
Fitting the new APCI probe heater .............................................................. 5-86
Replacing the ion block source heater ...................................................... 5-87
Replacing the LockSpray source assembly seals .................................... 5-91
Removing the probe adjuster assembly probe and source
enclosure seals ......................................................................................... 5-91
Fitting the new source enclosure seals......................................................... 5-93
Replacing the mass spectrometer’s air filter ........................................... 5-95
Replacing the air filter................................................................................... 5-95
Replacing the IntelliStart Fluidics tubing ............................................... 5-98
Removing the IntelliStart Fluidics tubing ................................................... 5-99
Plumbing the IntelliStart Fluidics LockSpray system ................................ 5-99
Plumbing the IntelliStart Fluidics sample delivery system...................... 5-108
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 Edwards oil-free roughing pump ................................... B-3
Making the electrical connections to the Edwards oil-free
roughing pump........................................................................................... B-7

Table of Contents xvii
Connecting to the nitrogen gas supply ....................................................... B-7
Connecting to the collision cell gas supply ............................................... B-9
Connecting the nitrogen exhaust line ...................................................... B-10
Connecting the liquid waste line ............................................................... B-13
Input/output signal connectors .................................................................. B-15
Signal connections ......................................................................................... B-18
Connecting the workstation (system without ACQUITY UPLC) ........ B-21
Connecting Ethernet cables (system with ACQUITY UPLC) .............. B-21
Connecting to the electricity source ......................................................... B-22
Connecting the NanoLockSpray source camera .................................... B-23
Installing the camera driver software .......................................................... B-23
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
Index ..................................................................................................... Index-1

xviii Table of Contents

1-1
1System Overview
This chapter describes the instrument, including its controls, sources, and
IntelliStart™ Fluidics system.
Contents
Topic Page
Waters SYNAPT G2 MS 1-2
SYNAPT G2 MS UPLC/MS/MS systems 1-2
Software 1-3
Instrument sources 1-5
IntelliStart Fluidics system 1-9
Ion optics 1-12
Analyzers 1-13
Mass spectrometer configuration 1-17
Leak sensors 1-18
Vacuum system 1-18
Controls on the instrument’s rear panel 1-19

1-2 System Overview
Waters SYNAPT G2 MS
The SYNAPT™ G2 Mass Spectrometry (MS) system is a hybrid,
quadrupole/orthogonal acceleration, time-of-flight (oa-TOF) mass
spectrometer controlled by MassLynx™ software.
Either of the following high-performance, ZSpray™, dual-orthogonal, API
sources is fitted as standard equipment:
• LockSpray™ ESI/APCI/ESCi®source (see page 1-5).
• NanoLockSpray™ ESI source (see page 1-7).
You can also use the following optional sources:
• Dual-mode APPI/APCI (see the Waters Dual-Mode (APPI/APCI) Source
for Xevo and SYNAPT G2 Instruments Operator’s Guide).
•MALDI(seetheWaters MALDI SYNAPT G2 Mass Spectrometry System
Overview and Maintenance Guide).
For the instrument’s specifications, see the Waters SYNAPT G2 MS Site
Preparation Guide.
SYNAPT G2 MS UPLC/MS/MS systems
The Waters SYNAPT G2 MS is compatible with the ACQUITY UPLC®and
nanoACQUITY UPLC®systems. If you are not using either of those systems,
refer to the documentation relevant to your LC system.
ACQUITY UPLC SYNAPT G2 MS UPLC/MS/MS system
The ACQUITY UPLC SYNAPT G2 MS UPLC®/MS/MS system includes an
ACQUITY UPLC system and the Waters SYNAPT G2 MS fitted with the
LockSpray ESI/APCI/ESCi source.
The ACQUITY UPLC system includes a binary solvent manager, sample
manager, column heater, sample organizer, detectors, and a specialized
ACQUITY UPLC column. MassLynx software controls the system.