Waters Xevo TQD

Overview and Maintenance Guide

715004387 / Revision B

Copyright © Waters Corporation 2014

All rights reserved
ii March 14, 2014, 715004387 Rev. B
General Information

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.

March 14, 2014, 715004387 Rev. B iii

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 tech_comm@waters.com.

Contacting Waters
®
Contact Waters with enhancement requests or technical questions regarding
the use, transportation, removal, or disposal of any Waters product. You can
reach us via the Internet, telephone, or conventional mail.
Waters contact information:

Contacting medium Information

Internet The Waters Web site includes contact
information for Waters locations worldwide.
Visit www.waters.com.
Telephone and fax From the USA or Canada, phone
800 252-4752, or fax 508 872 1990.
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

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

iv March 14, 2014, 715004387 Rev. B

 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

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.

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 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.

March 14, 2014, 715004387 Rev. B v

 Spilled solvents 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.

Flammable solvents hazard

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.

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

Warning: To prevent personal injury, ensure equipment placed on top of

the Xevo® TQD does not exceed 15kg.

vi March 14, 2014, 715004387 Rev. B

Glass-breakage 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.

High temperature hazard

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.

Xevo TQD high temperature hazard:

Source enclosure assembly

TP03406

March 14, 2014, 715004387 Rev. B vii

 Hazards associated with removing an instrument from service

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.

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

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.

viii March 14, 2014, 715004387 Rev. B

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.

March 14, 2014, 715004387 Rev. B ix

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

5()

Serial number

Supply ratings

Authorized representative of the European

Community
Confirms that a manufactured product complies
with all applicable European Community
directives
Australia EMC Compliant

or

Confirms that a manufactured product complies

with all applicable United States and Canadian
safety requirements

x March 14, 2014, 715004387 Rev. B

Symbol Definition
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.

March 14, 2014, 715004387 Rev. B xi

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.

xii March 14, 2014, 715004387 Rev. B

 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.

March 14, 2014, 715004387 Rev. B xiii

EC authorized representative

Waters Corporation
Stamford Avenue
Altrincham Road
Wilmslow
SK9 4AX
United Kingdom

Telephone: +44-161-946-2400
Fax: +44-161-946-2480
Contact: Quality manager

xiv March 14, 2014, 715004387 Rev. B

Table of Contents
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

March 14, 2014, 715004387 Rev. B xv

 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

xvi March 14, 2014, 715004387 Rev. B

 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

March 14, 2014, 715004387 Rev. B xvii

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

xviii March 14, 2014, 715004387 Rev. B

 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

March 14, 2014, 715004387 Rev. B xix

 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

xx March 14, 2014, 715004387 Rev. B

 Connecting the Edwards oil-free roughing pump ................................... 224
Connecting electric cables to the Edwards oil-free roughing pump.............. 227

Connecting to the nitrogen gas supply ....................................................... 228

Connecting to the collision cell gas supply ............................................... 230

Connecting the nitrogen exhaust line ........................................................ 230

Connecting the liquid waste line ................................................................. 233

Connecting the workstation .......................................................................... 235

Connecting Ethernet cables .......................................................................... 236

I/O signal connectors ....................................................................................... 237

Signal connections ........................................................................................... 238

Connecting to the power supply .................................................................. 241

C Materials of Construction and Compliant Solvents ..................... 243

Preventing contamination ............................................................................. 244

Items exposed to solvent ................................................................................ 244

Solvents used to prepare mobile phases .................................................... 245

D Plumbing the IntelliStart Fluidics System .................................... 247

Preventing contamination ............................................................................. 248

The selector valve ............................................................................................ 248

Plumbing schematic ........................................................................................ 249

Tubing and connection specifications ........................................................ 250

March 14, 2014, 715004387 Rev. B xxi

xxii March 14, 2014, 715004387 Rev. B
1 Specifications and Operating
Modes
This chapter describes the instrument, including its controls and
connections for gas and plumbing.
Contents:

Topic Page
Uses and compatibility .................................................................... 24
Ionization techniques and source probes ........................................ 31
IntelliStart Fluidics system............................................................. 34
Ion optics .......................................................................................... 36
MS operating modes ........................................................................ 37
MS/MS operating modes.................................................................. 38
Sample inlet ..................................................................................... 43
Leak sensors ..................................................................................... 43
Vacuum system ................................................................................ 43
Rear panel connections .................................................................... 44

March 14, 2014, 715004387 Rev. B 23

1 Specifications and Operating Modes

Uses and compatibility

® ®
The Waters Xevo TQD 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
applications.
You can use the Xevo TQD with the following high-performance Waters
ZSpray™ sources:
• Standard multimode electrospray ionization/atmospheric pressure
chemical ionization/combined electrospray ionization and atmospheric
®
pressure chemical ionization (ESI/APCI/ESCi ) source.
Requirement: Dedicated APCI operation requires an additional probe
(IonSABRE™ II).
• Optional dual-mode APPI/APCI source
• Optional NanoFlow™ ESI source
®
• Optional TRIZAIC UPLC source
• Optional APGC source
• Optional ASAP source
For information on installing and removing the optional APGC, TRIZAIC, and
ASAP sources, refer to the operator’s guide supplements supplied with them.
You can also use the Xevo TQD with the following optional third-party
sources:
• DART®
• DESI
• LDTD™
For further details, refer to the appropriate manufacturer’s documentation.
Note: Available source options can vary depending on the software used to
operate the Xevo TQD. Refer to the MassLynx® or UNIFI® online Help for
more information about supported sources.
For mass spectrometer specifications, see the Waters Xevo TQD Site
Preparation Guide.

24 March 14, 2014, 715004387 Rev. B

 Uses and compatibility

Xevo TQD shown with visor down, and visor up:

Visor up

TP03406 TP03407

IntelliStart technology
IntelliStart™ technology monitors LC/MS/MS performance and reports when
the instrument is ready for use.
The software automatically tunes and mass calibrates the instrument,
displays performance readbacks, and enables simplified setup of the system
for use in routine analytical and open access applications. (See page 29.)

March 14, 2014, 715004387 Rev. B 25

1 Specifications and Operating Modes

1
The IntelliStart Fluidics system is built into the instrument. It delivers
sample directly to the MS probe from the LC column or from two 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. See the instrument’s online Help for further details of
IntelliStart.

ACQUITY Xevo TQD UPLC/MS systems

®
The Waters Xevo TQD is compatible with the following ACQUITY UPLC
systems:
• ACQUITY UPLC
• ACQUITY UPLC H-Class
• ACQUITY UPLC I-Class
®
• nanoACQUITY UPLC (with Nanoflow or TRIZAIC source)
If you are not using one of these systems, refer to the documentation relevant
to your LC system.
®
The ACQUITY Xevo TQD UPLC/MS system includes an ACQUITY UPLC,
ACQUITY UPLC H-Class, or ACQUITY UPLC I-Class system, and the
Waters Xevo TQD fitted with the ESI/APCI/ESCi source.
®
The nanoACQUITY Xevo TQD UPLC/MS system includes a nanoACQUITY
UPLC system and the Xevo TQD fitted with either a Nanoflow source, or a
TRIZAIC source.
If you are not using your instrument as part of an ACQUITY UPLC system,
refer to the documentation for your LC system.
Note: ACQUITY system options can vary depending on the software used to
operate the Xevo TQD.

1. In Waters product documentation, the term “fluidics” denotes plumbing

connections and components and the fluid pathways within and among
instruments or devices. It also appears in the product name “IntelliStart™
Fluidics” where it describes a mass spectrometer’s integral apparatus for
delivering sample and solvent directly to the instrument’s probe. Finally, the
term can arise in the context of a component part name, as in “fluidics
drawer”.

26 March 14, 2014, 715004387 Rev. B

 Uses and compatibility

ACQUITY system core components

Core system components for each ACQUITY system are listed below:

System Core components

ACQUITY UPLC • Binary solvent manager
• Sample manager
• Column heater
• UPLC detectors
• Solvent tray
• ACQUITY UPLC column
• Software to control the system
ACQUITY UPLC H-Class • Quaternary solvent manager
• Sample manager with flow-through needle
• Column heater-active
• UPLC detectors
• Solvent tray
• ACQUITY UPLC column
• Software to control the system
ACQUITY UPLC I-Class • Binary solvent manager
• Sample manager
• Column heater-active
• UPLC detectors
• Solvent tray
• ACQUITY UPLC column
• Software to control the system

For further instruction, see the ACQUITY UPLC System Operator’s Guide,
ACQUITY UPLC H-Class System Guide, ACQUITY UPLC I-Class System
Guide, and Controlling Contamination in UPLC/MS and HPLC/MS Systems
(part number 715001307). You can find the documents on
http://www.waters.com; click Services and Support > Support Library.

March 14, 2014, 715004387 Rev. B 27

1 Specifications and Operating Modes

Xevo TQD with ACQUITY UPLC system:

Sample organizer (optional)

Solvent tray

Column heater

Xevo TQD

Sample manager

Binary solvent
manager

Xevo TQD with nanoACQUITY UPLC system

The nanoACQUITY uses the optional NanoFlow source or TRIZAIC source, on

the Xevo TQD. It is designed for capillary-to-nano-scale separations. Its
sensitivity, resolution, and reproducibility well suit it for biomarker discovery
and proteomics applications, including protein identification and
characterization.
This system is optimized for high-resolution separations at precise nanoflow
rates. With closed-loop control, those rates range between 0.20 and
5.00 µL/min. With open-loop control and nanoACQUITY UPLC columns of
internal diameters ranging from 75 µm to 1 mm, the flow rates can extend to
100 µL/min. The column hardware and the matched outlet tubing can
withstand pressure of as much as 69,000 kPa (690 bar, 10,000 psi). The
column dimensions allow optimal MS-compatible flow rates, and matched
outlet tubing minimizes the effect of extra-column volume.
For further instruction, see the nanoACQUITY UPLC System Operator’s
Guide, TRIZAIC UPLC System Guide, and Controlling Contamination in
LC/MS Systems (part number 715001307). You can find these documents on
http://www.waters.com; click Services and Support > Support Library.

28 March 14, 2014, 715004387 Rev. B

 Uses and compatibility

Non-ACQUITY devices for use with the Xevo TQD

The following non-ACQUITY LC devices are validated for use with the Xevo
TQD:
®
• 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™ system

Software and data system

MassLynx v4.1 or UNIFI software can control the mass spectrometer. See
page 30 for more information about those applications.
Both MassLynx and UNIFI software enable these major operations:
• Configuring the system
• Creating LC and MS/MS methods that define operating parameters for a
run
• Using IntelliStart software to automatically tune and mass calibrate the
mass spectrometer
• Running samples
• Monitoring the run
• Acquiring data
• Processing data
• Reviewing data
• Printing data

March 14, 2014, 715004387 Rev. B 29

1 Specifications and Operating Modes

MassLynx v4.1
MassLynx software acquires, analyzes, manages, and distributes mass
spectrometry, ultraviolet (UV), evaporative light scattering, and analog data.
TM TM
OpenLynx and TargetLynx application managers are included as
standard software with MassLynx.
See the MassLynx v4.1 user documentation and online Help for information
about using MassLynx software.
You configure settings, monitor performance, run diagnostic tests, and
maintain the system and its modules via the MassLynx Instrument Console
application.
The Instrument Console software, which functions independently of
MassLynx software, does not recognize or control data systems.
See the online Help for the Instrument Console system for details.

UNIFI v1.6
UNIFI software integrates mass spectrometry, UPLC chromatography, and
informatics data work flows.
See UNIFI v1.6 user documentation and online Help for more information
about using UNIFI software.

30 March 14, 2014, 715004387 Rev. B

 Ionization techniques and source probes

Ionization techniques and source probes

Note: Available source options can vary depending on the software used to
operate the Xevo TQD. Refer to the MassLynx or UNIFI online Help for more
information about supported sources.

Electrospray ionization (ESI)

In electrospray ionization (ESI), a strong electrical charge is applied to the
eluent as it emerges from a nebulizer. The droplets that compose the resultant
aerosol undergo a reduction in size (solvent evaporation). As solvent continues
to evaporate, the charge density increases until the droplet surfaces eject ions
(ion evaporation). The ions can be singly or multiply charged.
The standard ESI probe accommodates eluent flow rates as high as 2 mL/min,
making it suitable for LC applications in the range 100 µL/min to 2 mL/min.
See page 58 for further details.

Combined ESI and APCI (ESCi)

Combined electrospray ionization and atmospheric pressure chemical
ionization (ESCi) is supplied as standard equipment on the mass
spectrometer. In ESCi, the standard ESI probe is used in conjunction with a
corona pin to allow alternating acquisition of ESI and APCI ionization data,
facilitating high throughput and wider compound coverage.
See page 62 for further details.

Atmospheric pressure chemical ionization (APCI)

A dedicated high-performance APCI interface is offered as an option. APCI
produces singly charged protonated or deprotonated molecules for a broad
range of nonvolatile analytes.
The APCI interface consists of the ESI/APCI/ESCi enclosure fitted with a
corona pin and an IonSABRE II probe.
See page 62 for further details.

March 14, 2014, 715004387 Rev. B 31

1 Specifications and Operating Modes

Dual-mode APPI/APCI source

The optional, combined atmospheric pressure photoionization/atmospheric
pressure chemical ionization (APPI/APCI) source comprises an IonSABRE II
probe and the APPI lamp drive assembly. The APPI lamp drive assembly
comprises a UV lamp and a repeller electrode. In addition, a specially shaped,
dual, APPI/APCI corona pin can be used. You can operate the source in APPI,
APCI, or dual mode, which switches rapidly between APPI and APCI
ionization modes.

NanoFlow source
“NanoFlow” is the name given to several techniques that use low flow rate
electrospray ionization. The NanoFlow source allows electrospray ionization
in the flow rate range 5 to 1000 nL/min. For a given sample concentration, the
ion currents observed approximate those seen in normal flow rate
electrospray. However, for similar experiments, NanoFlow’s significant
reduction in sample consumption accompanies significant increases in
sensitivity.
The following options are available for the spraying capillary:
• Universal nebulizer sprayer (Nano-LC).
This option is for flow injection or for coupling to nano-UPLC. It uses a
pump to regulate the flow rate downward to 100 nL/min. If a syringe
pump is used, a gas-tight syringe is necessary to effect correct flow rates
without leakage. A volume of 250 µL is recommended.
• Borosilicate glass capillaries (nanovials).
Metal-coated, glass capillaries allow the lowest flow rates. Usable for
one sample, they must then be discarded.
• Capillary Electrophoresis (CE) or Capillary Electrochromatography
(CEC) sprayer. This option uses a make-up liquid at the capillary tip
that provides a stable electrospray. The make-up flow rate is less than
1 µL/min.

32 March 14, 2014, 715004387 Rev. B

 Ionization techniques and source probes

Atmospheric solids analysis probe (ASAP)

The ASAP facilitates rapid analysis of volatile and semivolatile compounds in
solids, liquids, and polymers. It is particularly suited to analyzing low-polarity
compounds.The ASAP directly replaces the electrospray or IonSABRE II
probe in the instrument’s source housing and has no external gas or electrical
connections.
See the Atmospheric Solids Analysis Probe Operator’s Guide Supplement for
further details.

Atmospheric pressure gas chromatography (APGC)

The Waters APGC couples an Agilent GC with the Xevo TQD, making it
possible to perform LC and GC analyses in the same system, without
compromising performance. The APGC provides complementary information
to the LCMS instrument, enabling analysis of compounds of low molecular
weight and/or low-to-intermediate polarity.
See the Atmosheric Pressure GC Operator’s Guide Supplement for further
details.

TRIZAIC UPLC source

The TRIZAIC UPLC source accepts a nanoTile® device, which combines the
functions of an analytical column, trapping column, and nanospray emitter.
This technology simplifies the implementation of capillary-scale
chromatography and analysis of limited-volume samples.
See the TRIZAIC UPLC System Guide for further details.

March 14, 2014, 715004387 Rev. B 33

1 Specifications and Operating Modes

IntelliStart Fluidics system

Functionality
The IntelliStart Fluidics system is a solvent delivery system built into the
mass spectrometer. It delivers sample or solvent directly to the MS probe in
one of three ways:
• From the LC column.
• From two integral reservoirs. Use standard reservoir bottles (15-mL) for
instrument setup and calibration. Use 1.5-mL, low-volume vials (sold
separately) to infuse smaller volumes (see page 52.)
The reservoirs can also deliver sample through direct or combined
infusion to enable optimization at analytical flow rates.
• From a wash reservoir that contains solvent for automated flushing of
the instrument’s solvent delivery system.
The onboard system incorporates a selector valve, an infusion pump, and two
sample reservoirs mounted on the bottom, right-hand side of the instrument.
Recommendation: Use reservoir A for the calibrant solution and tuning
compounds, and reservoir B for analyte/optimization solution.

IntelliStart Fluidics system:

Selector valve

W
LC R
LC
Waste
Column S P
B
A

Reservoirs

Pump
Xevo Wash
TQD probe
A B

34 March 14, 2014, 715004387 Rev. B

 IntelliStart Fluidics system

System operation
The software automatically controls solvent and sample delivery during
auto-tuning, auto-calibration, and method development. The selector valve
systematically makes connections between the fluidics components to carry
out the operations processed by the software.
You can set IntelliStart fluidics configuration requirements in the system
console. You can edit the parameters, frequency, and extent of the
automation. See the mass spectrometer’s online Help for further details on
IntelliStart software and operation of the solvent delivery system.
For information on plumbing the IntelliStart Fluidics system, see Appendix D.

March 14, 2014, 715004387 Rev. B 35

1 Specifications and Operating Modes

Ion optics
The mass spectrometer’s ion optics operate as follows:
1. Samples from the LC or Intellistart fluidics system are introduced at
atmospheric pressure into the ionization source.
2. The ions pass through the sample cone into the vacuum system.
3. The ions pass through the transfer optics (the ion guide) to the first
quadrupole, where they can be filtered according to their mass-to-charge
ratios.
4. The mass-separated ions pass into the T-Wave™ collision cell where
they either undergo collision-induced dissociation (CID) or pass to the
second quadrupole. Any fragment ions are then mass-analyzed by the
second quadrupole.
5. The transmitted ions are detected by the photomultiplier detection
system.
6. The signal is amplified, digitized, and sent to the mass spectrometry
software.

Ion optics overview:

Sample cone
Sample inlet Transfer optics T-Wave collision Conversion dynode
cell

Isolation valve

Z-Spray ion source Quadrupole 1 Quadrupole 2 Detector

(MS1) (MS2)

36 March 14, 2014, 715004387 Rev. B

 MS operating modes

MS operating modes
The following table shows the MS operating modes.

MS operating modes:

Operating mode MS1 Collision cell MS2

MS Pass all masses Resolving
(scanning)
SIR Pass all masses Resolving
(static)

In MS mode, the instrument can acquire data at scan speeds as high as

10,000 Da/s. Use this mode for instrument tuning and calibration before
MS/MS analysis. See the mass spectrometer’s online Help for further
information.
Use the selected ion recording (SIR) mode for quantitation when you cannot
find a suitable fragment ion to perform a more specific multiple reaction
monitoring (MRM) analysis (see page 38). In SIR and MRM modes, neither
quadrupole is scanned, therefore no spectrum (intensity versus mass) is
produced. The data obtained from SIR or MRM analyses derive from the
chromatogram plot (specified mass intensity (SIR), or specified transition
(MRM) versus time).

March 14, 2014, 715004387 Rev. B 37

1 Specifications and Operating Modes

MS/MS operating modes

The following table shows the MS/MS operating modes, described in more
detail in the following pages.

MS/MS operating modes:

Operating mode MS1 Collision cell MS2

Product Static (at Fragment Scanning
(daughter) ion precursor mass) precursor ions
spectrum and pass all
Precursor Scanning masses Static (at product
(parent) ion mass)
spectrum
MRM Static (at Static (at product
precursor mass) mass)
PICS (Product Static (at Switching
Ion Confirmation precursor mass) between static
Scan) (at product mass)
and scanning
RADAR™ Static (at Switching
precursor mass) between static
(at product mass)
and scanning
Constant neutral Scanning Scanning
loss spectrum (synchronized (synchronized
with MS2) with MS1)

38 March 14, 2014, 715004387 Rev. B

 MS/MS operating modes

Product (daughter) ion mode

Product ion mode is the most commonly used MS/MS operating mode. You can
specify an ion of interest for fragmentation in the collision cell, thus yielding
structural information.

Product ion mode:

MS1 Collision cell MS2

Static (at precursor mass) Fragmenting Scanning
precursor ions and
passing all masses

Typical applications
Product ion mode is typically used for the following applications:
• Method development for MRM screening studies:
– Identifying product ions for use in MRM transitions.
– Optimizing CID tuning conditions to maximize the yield of a specific
product ion to be used in MRM analysis.
• Structural elucidation (for example, peptide sequencing)

March 14, 2014, 715004387 Rev. B 39

1 Specifications and Operating Modes

Precursor (parent) ion mode

Precursor ion mode:

MS1 Collision cell MS2

Scanning Fragmenting Static (at product mass)
precursor ions and
passing all masses

Typical application
You typically use the precursor ion mode for structural elucidation—that is, to
complement or confirm product scan data—by scanning for all the precursors
of a common product ion.

Multiple reaction monitoring mode

Multiple reaction monitoring (MRM) mode is the highly selective MS/MS
equivalent of SIR. Because both MS1 and MS2 are static, greater dwell time
on the ions of interest is possible, so the sensitivity achieved is better,
compared with scanning-mode MS/MS. This mode is the most commonly used
acquisition mode for quantitative analysis, allowing the compound of interest
to be isolated from the chemical background noise.

Multiple reaction monitoring mode:

MS1 Collision cell MS2

Static (at precursor mass) Fragmenting Static (at product mass)
precursor ions and
passing all masses

40 March 14, 2014, 715004387 Rev. B

 MS/MS operating modes

PICS mode
A variation on MRM, PICS allows you to collect a product ion spectrum from
the top of all detected peaks in MRM mode for additional confidence in your
peak assignment, activated by a single check box.

RADAR
In RADAR mode the Xevo TQD rapidly alternates between MRM and full scan
MS acquisition modes. The instrument tracks target analytes with precision
in MRM mode, while at the same time scanning (in MS mode) the background
for all other components. This enables fast characterization of potential
matrix effects, providing a platform for more robust method development

Typical application
You typically use RADAR mode during method development prior to
performing MRM or PICS to quantify known analytes in complex samples:
• Drug metabolite and pharmacokinetic studies
• Environmental, for example, pesticide and herbicide analysis
• Forensic or toxicology, for example, screening for target drugs in sports
MRM analysis with no associated RADAR or PICS operation does not produce
a spectrum because only one transition is monitored at a time. As in SIR
mode, a chromatogram is produced.

March 14, 2014, 715004387 Rev. B 41

1 Specifications and Operating Modes

Constant neutral loss mode

Constant neutral loss mode detects the loss of a specific neutral fragment or
functional group from an unspecified precursor(s).
The scans of MS1 and MS2 are synchronized. When MS1 transmits a specific
precursor ion, MS2 “looks” to see whether that precursor loses a fragment of a
certain mass. If it does, the loss registers at the detector.
In constant neutral loss mode, the spectrum shows the masses of all
precursors that actually lost a fragment of a certain mass.

Constant neutral loss mode:

MS1 Collision cell MS2

Scanning Fragmenting Scanning
(synchronized with MS2) precursor ions and (synchronized with MS1)
passing all masses

Typical application
You typically use constant neutral loss mode to screen mixtures for a specific
class of compound that is characterized by a common fragmentation pathway,
indicating the presence of compounds containing a common functional group.

42 March 14, 2014, 715004387 Rev. B

 Sample inlet

Sample inlet
Either of two methods delivers solvent and sample to the installed probe:
• An LC system, which delivers the eluent from an LC analysis.
• IntelliStart Fluidics system, which uses onboard solutions to automate
instrument optimization. You can deliver solutions by direct or
combined infusion.

Leak sensors
Leak sensors in the Xevo TQD and the drip trays of the ACQUITY UPLC
system continuously monitor system components for leaks. A leak sensor
stops system flow when its optical sensor detects about 1.5 mL of
accumulated, leaked liquid in its surrounding reservoir. At the same time, the
ACQUITY UPLC Console or UNIFI software displays an error message
alerting you that a leak has developed.
See Waters ACQUITY UPLC Leak Sensor Maintenance Instructions for
complete details.

Vacuum system
An external roughing pump and an internal split-flow turbomolecular pump
combine to create the source vacuum. The turbomolecular pump evacuates the
analyzer and ion transfer region.
Vacuum leaks and electrical or vacuum pump failures cause vacuum loss, the
damage from which is prevented by protective interlocks. The system
monitors turbomolecular pump speed and continuously measures vacuum
pressure with a built-in Pirani gauge. The gauge also serves as a switch,
stopping operation when it senses vacuum loss.
A vacuum isolation valve isolates the source from the analyzer region,
allowing routine source maintenance without venting.

March 14, 2014, 715004387 Rev. B 43

1 Specifications and Operating Modes

Rear panel connections

The following figure shows the rear panel locations of the connectors used to
operate the instrument with external devices.

Instrument rear panel:

Event inputs
and outputs

Shielded
Ethernet

Roughing pump
control

Power
Source vacuum

Turbo vacuum
Collision cell
gas inlet
(Argon)

Source vent Nitrogen inlet

44 March 14, 2014, 715004387 Rev. B

2 Preparing for Operation

This chapter describes how to start and shut down the instrument.
Contents:

Topic Page
Starting the mass spectrometer ...................................................... 46
Preparing the IntelliStart Fluidics system..................................... 52
Rebooting the instrument................................................................ 54
Leaving the mass spectrometer ready for operation...................... 55

March 14, 2014, 715004387 Rev. B 45

2 Preparing for Operation

Starting the mass spectrometer

The Waters Xevo TQD is compatible with the ACQUITY UPLC system; if you
are not using an ACQUITY UPLC system, refer to the documentation relevant
to the system you are using (see “Non-ACQUITY devices for use with Xevo
TQD” on page 29).

Notice: To avoid causing severe damage to the instrument, use

compatible solvents only. For more details, refer to the following
sources:
• See page 243 for solvent information.
• Appendix C of the ACQUITY UPLC System Operator’s Guide for
solvent compatibility with ACQUITY devices.

Starting the mass spectrometer entails powering-on the workstation, logging

in, powering-on the mass spectrometer and all other instruments, and then
starting the MassLynx or UNIFI software.
Requirement: You must power-on and log in to the workstation first to ensure
that it obtains the IP addresses of the system instruments.
See the mass spectrometer’s online help for details on MassLynx, IntelliStart,
and UNIFI software.

To start the mass spectrometer:

Warning: To avoid igniting flammable solvents, never let the nitrogen

supply pressure fall below 400 kPa (4.0 bar, 58 psi).

1. On the rear panel, ensure the nitrogen supply is connected to the

instrument’s nitrogen inlet connection (see the figure on page 44).
Requirement: The nitrogen must be dry and oil-free, with a purity of at
least 95% or, for APGC use, at least 99.999%. Regulate the supply at 600
to 690 kPa (6.0 to 6.9 bar, 90 to 100 psi).
For more information on connections, see the figure on page 44.
2. Ensure that the collision gas supply is connected to the instrument’s
collison cell gas inlet.
Requirement: The collision gas is argon; it must be dry and of high
purity (99.997%). Regulate the supply at 50 kPa (0.5 bar, 7 psi).

46 March 14, 2014, 715004387 Rev. B

 Starting the mass spectrometer

3. Power-on the workstation, and log in.

4. Press the power switch on the top, right-hand side of the mass
spectrometer and the switches on the top, left-hand sides of the
ACQUITY instruments.
Result: Each system instrument runs a series of startup tests.
5. Allow 3 minutes for the embedded PC (located inside the mass
spectrometer) to initialize and to sound an alert indicating that the PC is
ready.
Tip: The power and status LEDs change as follows:
• Each system instrument’s power LED shows green.
• During initialization, the binary or quaternary solvent manager’s
and sample manager’s status LED flashes green.
• After the instruments successfully power-on, all power LEDs show
steady green. The binary solvent manager’s flow LED, the sample
manager’s run LED, and the mass spectrometer’s Operate LED
remain off.
6. Start the MassLynx or UNIFI software, and monitor the Instrument
Console software for messages and LED indications.

March 14, 2014, 715004387 Rev. B 47

2 Preparing for Operation

7. To evacuate (pump down) the mass spectrometer, follow the procedure

below for MassLynx software or UNIFI software.

MassLynx software:
a. Click IntelliStart in the MassLynx main window’s lower left-hand
corner.
Result: The mass spectrometer’s console appears. The mass
spectrometer is in Standby mode.
b. Click Control > Pump, to start the roughing pump.
Tip: After a 20-second delay, during which the turbopump is
starting, the roughing pump starts. IntelliStart displays
“Instrument in standby”, and the Operate LED remains off.
c. Wait a minimum of 2 hours for the instrument to be fully pumped
down (evacuated).
Tip: In the Instrument Console, the System Ready indicator shows
green when the instrument is fully pumped down (evacuated).

d. Click Resolve or Operate .

Result: When the mass spectrometer is in good operating condition,
IntelliStart software displays “Ready” in the Instrument Console.
Tip: If clicking Resolve fails to put the instrument into Operate
mode, IntelliStart software displays corrective actions in the
Instrument Console.

48 March 14, 2014, 715004387 Rev. B

 Starting the mass spectrometer

UNIFI software:
a. From the Xevo TQD console, in the Maintain pane, click Vacuum.
b. On the Status page, click Pump.
Tip: After a 20-second delay, during which the turbopump is starting,
the roughing pump starts. The Instrument System pane shows that
the instrument is in Standby mode, and the Operate LED remains off.
c. Wait a minimum of 2 hours for the instrument to be fully pumped
down (evacuated).
Tip: In the Instrument Summary pane, the Status indicator shows
green when the instrument is fully pumped down (evacuated).

d. Click Instrument Operate Mode .

Result: When the mass spectrometer is in good operating condition,
UNIFI software displays status “Running” in the Instrument
Summary pane.
Tip: If clicking Instrument Operate Mode fails to put the instrument
into Operate mode, UNIFI software displays corrective actions.

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2 Preparing for Operation

Verifying the instrument’s state of readiness

When the instrument is in good operating condition, the power and Operate
LEDs show constant green. You can view any error messages in IntelliStart
software (MassLynx), or UNIFI software.

Monitoring the instrument LEDs

Light-emitting diodes on the instrument indicate its operational status.

Power LED
The power LED, to the top, right-hand side of the mass spectrometer’s front
panel, indicates when the instrument is powered-on or powered-off.

Operate LED
The Operate LED, on the right-hand side of the power LED, indicates the
operating condition.
See the instrument’s online Help for details of the Operate LED indications.

Tuning and calibration information

You must tune and, if necessary, calibrate the instrument prior to use. You
can perform these tasks using IntelliStart (MassLynx software) or UNIFI
software. For further instruction, see the mass spectrometer’s online Help.

50 March 14, 2014, 715004387 Rev. B

 Starting the mass spectrometer

Running the instrument at different flow rates

The ACQUITY UPLC system runs at high flow rates. To optimize desolvation,
and thus sensitivity, run the ACQUITY Xevo TQD system at appropriate gas
flows and desolvation temperatures. IntelliStart software automatically sets
these parameters when you enter a flow rate, according to the following table.

Flow rate versus temperature and gas flow:

Flow rate Desolvation Desolvation gas

Source temp (°C)
(mL/min) temp (°C) flow (L/h)
0.000 to 0.020 150 200 800
0.021 to 0.100 150 300 800
0.101 to 0.500 150 500 1000
>0.500 150 600 1000

If you are using an APCI interface, IntelliStart software automatically sets

the parameters according to the following table.

Flow rate versus IonSABRE II probe temperature and gas flow:

IonSABRE II
Flow rate Desolvation gas
probe
(mL/min) flow (L/h)
temperature (°C)
0.000 to 0.020 400 800
0.021 to 0.500 500 1000
>0.500 600 1000

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2 Preparing for Operation

Preparing the IntelliStart Fluidics system

For additional information, see page 233 and Appendix D.

Notice: To avoid damaging the mass spectrometer by accidentally

spilling solvent on it, do not store large-volume solvent reservoirs on top
of the instrument.

Installing the reservoir bottles

Use standard reservoir bottles (15-mL) for instrument setup and calibration.
Use the Low-volume Adaptor Kit (sold separately) to infuse smaller volumes.
The low-volume vials have a volume of 1.5 mL.

Required material
Chemical-resistant, powder-free gloves

52 March 14, 2014, 715004387 Rev. B

 Preparing the IntelliStart Fluidics system

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while installing reservoir bottles.

To install the reservoir bottles:

1. Remove the reservoir bottle caps.
2. Screw the reservoir bottles onto the instrument, as shown below.

TP03410

3. For each reservoir bottle, ensure that the end of the solvent delivery
tube is positioned so that it is close to, but does not touch, the bottom of
the bottle.

To install low-volume vials:

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while installing low-volume vials.

1. If a standard reservoir bottle is fitted, remove it.

2. Screw the low-volume adaptor into the manifold and tighten it.
3. Screw the low-volume vial into the adaptor.
4. For each low-volume vial, ensure that the end of the solvent delivery
tube is positioned so that it is close to, but does not touch, the bottom of
the vial.

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2 Preparing for Operation

Purging the infusion pump

Whenever you replace a solution bottle, purge the infusion pump with the
solution that you are going to use next. See the mass spectrometer’s online
Help for details.
Requirement: Ensure that the end of the tubing is fully submerged in the
solvent in the wash reservoir.
Tip: Depending on the solutions used, the instrument’s solvent delivery
system can require more than one purge cycle to minimize carryover.

Rebooting the instrument

The reset button causes the mass spectrometer to reboot.
Reboot the instrument when either of these conditions applies:
• Immediately following a software upgrade.
• The mass spectrometer software fails to initialize.

To reboot the instrument:

1. Ensure that the mass spectrometer software is closed.
2. Insert a short length (7.5 cm) of PEEK™ tubing, or similar object, into
the reset button aperture at the top, right-hand side of the instrument’s
front panel.
Reset button aperture

TP03415

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 Leaving the mass spectrometer ready for operation

3. Remove the PEEK tubing from the reset button aperture.

4. Wait until the reboot sequence ends before starting the mass
spectrometer software.
Tip: An audible alert sounds when the reboot sequence is complete.

Leaving the mass spectrometer ready for operation

Leave the mass spectrometer in Operate mode except in the following cases:
• When performing routine maintenance
• When changing the source
• When leaving the mass spectrometer unused for a long period
In these instances, put the mass spectrometer in Standby mode. See the
online Help for details.

Emergency shutdown of the mass spectrometer

To shut down the instrument in an emergency:

Warning: To avoid electric shock, isolate the instrument observing the

procedure outlined below. The instrument’s power switch does not
isolate it from the main power supply.

Notice: To avoid losing data, reboot the instrument as described on

page 54. Data can be lost when you perform an emergency shutdown.

1. Operate the power button on the front of the instrument.

2. Disconnect the power cable from the instrument’s rear panel.

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2 Preparing for Operation

56 March 14, 2014, 715004387 Rev. B

3 Changing the Mode of Operation

This chapter describes how to prepare the mass spectrometer for the
following modes of operation:
• ESI (electrospray ionization)
• ESCi (combined electrospray and atmospheric pressure chemical
ionization)
• APCI (atmospheric pressure chemical ionization)
• Combined Atmospheric Pressure Photoionization (APPI/APCI)
• NanoFlow
For details about other Waters and third-party source options, refer to
the documentation supplied with the source.

Note: Available source options can vary depending on the software used
to operate the Xevo TQD. Refer to the MassLynx or UNIFI online Help
for more information about supported sources.

Contents:

Topic Page
ESI mode .......................................................................................... 58
ESCi mode ........................................................................................ 62
APCI mode........................................................................................ 62
Combined APPI/APCI source .......................................................... 66
NanoFlow source .............................................................................. 73

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3 Changing the Mode of Operation

ESI mode
The following sections explain how to install and remove an ESI probe. For
further details on running ESI applications, see page 31.

Installing the ESI probe

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The LC
system connections, ESI probe, and source can be contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To install the ESI probe:

1. Prepare the instrument for installing the probe according to the
procedure on page 88, “Preparing the instrument for operations on or
inside its source”.

Warning: To avoid puncture wounds, handle the ESI probe with

care; the probe tip is sharp.

2. Remove the protective sleeve, if fitted, from the ESI probe tip.

58 March 14, 2014, 715004387 Rev. B

 ESI mode

3. With the probe label facing you, carefully slide the ESI probe into the
hole in the probe adjuster assembly, ensuring that the probe location
dowel aligns with the location hole of the probe adjuster assembly.
Probe label

Probe locking ring

Probe location dowel

Location hole of the probe

adjuster assembly

TP03129

4. Tighten the probe locking ring to secure the probe in place.

Requirement: Fully tighten the probe locking ring. Doing so ensures a
successful result on the automatic pressure test, which runs when the
probe is correctly seated, and the source enclosure door is closed.
5. Connect the ESI probe’s cable to the high-voltage connector.

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3 Changing the Mode of Operation

Warning: To avoid electric shock, do not use stainless steel tubing

or stainless steel “finger tight” screws to connect the selector valve
to the ESI probe; use the PEEK tubing and natural (beige) colored
PEEK “finger tight” screws supplied with the instrument.

6. Using PEEK tubing equal to 0.004-inch ID, connect port S of the selector
valve to the ESI probe.
Recommendation: To reduce peak broadening, use 0.004-inch ID tubing
for sample flow rates ≤1.2 mL/min; use 0.005-inch ID tubing for sample
flow rates >1.2 mL/min.
Requirements:
• If you are replacing the tubing between the selector valve and the
probe, minimize the length to reduce peak broadening.
• When cutting the tubing to length, cut it squarely (that is,
perpendicular to its horizontal axis).

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 ESI mode

Removing the ESI probe

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The LC
system connections, ESI probe, and source can be contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To remove the ESI probe:

1. Prepare the instrument for removing the probe according to the
procedure on page 88, “Preparing the instrument for operations on or
inside its source”.
2. Disconnect the tubing from the ESI probe.
3. Disconnect the ESI probe cable from the high-voltage connector.
4. Unscrew the probe locking ring.

Warning: To avoid puncture wounds, handle the ESI probe with

care; the probe tip is sharp.

5. Carefully remove the ESI probe from the probe adjuster assembly.
6. If available, fit the protective sleeve to the ESI probe tip.

March 14, 2014, 715004387 Rev. B 61

3 Changing the Mode of Operation

ESCi mode
To run ESCi applications, you must fit an ESI probe and corona pin to the
ESI/APCI/ESCi source enclosure.
See “Installing the ESI probe” on page 58, “Installing the corona pin in the
source” on page 93, and “IntelliStart Fluidics System” on page 34.

Optimizing the ESI probe for ESCi operation

See the mass spectrometer’s online Help for details on how to optimize the ESI
probe for ESCi operation.

APCI mode
APCI mode, an option for the mass spectrometer, produces singly charged
protonated or deprotonated molecules for a broad range of nonvolatile
analytes.
The APCI interface consists of the ESI/APCI/ESCi enclosure fitted with a
corona pin and an IonSABRE II probe. Mobile phase from the LC column
enters the probe, where it is pneumatically converted to an aerosol, rapidly
heated, and vaporized or gasified at the probe tip.

APCI mode:

IonSABRE II probe

Sample cone Corona pin

Hot gas from the IonSABRE II probe passes between the sample cone and the
corona pin, which is typically operated with a discharge current of 5 µA.
Mobile phase molecules rapidly react with ions generated by the corona

62 March 14, 2014, 715004387 Rev. B

 APCI mode

discharge to produce stable reagent ions. Analyte molecules introduced into

the mobile phase react with the reagent ions at atmospheric pressure and
typically become protonated (in the positive ion mode) or deprotonated (in the
negative ion mode). The sample and reagent ions then pass through the
sample cone and into the mass spectrometer.

Installing the IonSABRE II probe

Required materials
• Chemical-resistant, powder-free gloves
• Sharp knife or PEEK tubing cutter

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The LC
system connections, IonSABRE II probe, and source can be
contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To install the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 88).
2. With the probe label facing toward you, carefully slide the IonSABRE II
probe into the hole in the probe adjuster assembly, ensuring that the
probe location dowel aligns with the probe adjuster assembly location
hole.

March 14, 2014, 715004387 Rev. B 63

3 Changing the Mode of Operation

Probe label
Probe locking ring
Probe location dowel

Location hole of the probe

adjuster assembly

TP03129

3. Tighten the probe locking ring to secure the probe in place.

Requirement: Fully tighten the probe locking ring. Doing so ensures a
successful result on the automatic pressure test, which runs when the
probe is correctly seated, and the source enclosure door is closed.

Warning: To avoid electric shock, do not use stainless steel tubing

or stainless steel “finger tight” screws to connect the selector valve
to the IonSABRE II probe; use the PEEK tubing and natural
(beige) colored PEEK “finger tight” screws supplied with the
instrument.

4. Using tubing equal to 0.004-inch ID, connect port S of the selector valve
to the IonSABRE II probe.
Recommendation: To reduce peak broadening, use 0.004-inch ID tubing
for sample flow rates ≤1.2 mL/min; use 0.005-inch ID tubing for sample
flow rates >1.2 mL/min.
Requirements:
• If you are replacing the tubing between the selector valve and the
probe, minimize the length to reduce peak broadening.
• When cutting the tubing to length, cut it squarely (that is,
perpendicular to its horizontal axis).
5. Install the corona pin (see page 93).

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 APCI mode

Removing the IonSABRE II probe

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The LC
system connections, IonSABRE II probe, and source can be
contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To remove the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 88).
2. Remove the corona pin (see page 93).
3. Disconnect the selector valve tubing from the IonSABRE II probe.
4. Unscrew the probe locking ring.
5. Carefully remove the probe from the probe adjuster assembly.

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3 Changing the Mode of Operation

Combined APPI/APCI source

Operate this optional, replacement source enclosure in APPI, APCI, or dual
APPI/APCI mode. Dual-mode APPI/APCI performs rapid switching between
ionization modes.

APPI operation
In atmospheric pressure photoionization (APPI) mode, the source is fitted
with an IonSABRE II probe and the APPI lamp drive assembly is advanced
into the source.

APPI mode:

IonSABRE II probe
Sample ions
Sample molecules

Sample cone APPI lamp drive assembly

Photons from UV lamp Repeller electrode

the UV lamp

The IonSABRE II probe introduces vaporized sample into the source where
photons generated by an ultraviolet (UV) lamp (mounted in the APPI lamp
drive assembly) produce sample ions. Direct photoionization of a sample
molecule occurs when the photon energy exceeds the ionization potential of
the sample molecule.
A repeller electrode (mounted on the APPI lamp drive assembly) deflects and
focuses the sample ions toward the sample cone.

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 Combined APPI/APCI source

APCI operation
The atmospheric pressure chemical ionization (APCI) mode produces singly
charged protonated or deprotonated molecules for a large range of nonvolatile
analytes. In APCI mode, the source is fitted with an APCI corona pin. Unused,
the APPI lamp drive assembly is retracted from the source.

APCI mode:

IonSABRE II probe

Sample cone Retracted APPI lamp drive

assembly

APCI corona pin

The IonSABRE II probe introduces vaporized sample into the source. The
sample passes between the sample cone and the corona pin, which typically
operates with a discharge current of 5 µA. The corona discharge generates
ions that react with the mobile phase molecules to produce stable reagent
ions. Analyte molecules in the mobile phase react with the reagent ions at
atmospheric pressure and become protonated (in the positive ion mode) or
deprotonated (in the negative ion mode). The sample and reagent ions pass
through the sample cone.

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3 Changing the Mode of Operation

Dual-mode operation
Dual-mode operation enables rapid switching between APPI and APCI
ionization modes and allows high-throughput operations (for example, for
sample screening).
You replace the standard corona pin with a specially shaped APPI/APCI
corona pin, so that the APPI lamp holder can be advanced into the source for
dual operation.
When the source is configured for dual operation in APCI mode, current is
applied to the corona pin, but the repeller electrode is inactive.

Dual operation in APCI mode:

IonSABRE II probe Repeller electrode inactive

Sample cone

Corona pin with current applied

Photons from the UV lamp

When the source is configured for dual operation in APPI mode, the corona pin
is inactive, and a voltage is applied to the repeller electrode.

Dual operation in APPI mode:

IonSABRE II probe Repeller electrode with

voltage applied

Sample cone

Photons from the UV lamp Corona pin inactive

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 Combined APPI/APCI source

The combined APPI/APCI source components

The combined APPI/APCI source comprises the standard IonSABRE II probe
and a source enclosure with an APPI lamp drive incorporated.

The combined APPI/APCI source enclosure:

APPI lamp drive assembly

Notice: To prevent damage to the corona pin and lamp assembly, ensure
that the lamp assembly does not touch the corona pin when the source
enclosure door is closed.

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3 Changing the Mode of Operation

The UV lamp, which you ignite via a control in the MassLynx Tune window,
provides a constant photon output. You vary the intensity of incident
radiation upon the sample molecules by adjusting the distance between the
UV lamp and probe tip.

APPI lamp drive assembly inside the source enclosure:

APPI lamp drive

assembly
Source enclosure

IonSABRE II probe

UV lamp and
repeller electrode

TP03201

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 Combined APPI/APCI source

Installing the combined APPI/APCI source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The source
components can be contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To install the combined APPI/APCI source:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the probe and source; these components can be hot.

2. Remove the probe from the currently installed source.

• If you are removing an ESI probe, see page 61.
• If you are removing an IonSABRE II probe, see page 65.
3. Remove the existing source enclosure (see page 90).
4. Install the combined APPI/APCI source enclosure (see page 92).
5. Install the corona pin (see page 93).
6. Connect the APPI drive cable to the instrument’s front panel connector.

March 14, 2014, 715004387 Rev. B 71

3 Changing the Mode of Operation

7. Connect the HT cable to the instrument’s front panel connector.

Notice: To prevent damage to the corona pin and lamp assembly,

ensure that the lamp assembly does not touch the corona pin when
the source enclosure door is closed.

8. Install the IonSABRE II probe to the source, and ensure that it is

working correctly (see page 63).
Tip: An automatic pressure test runs each time you close the source
enclosure and when the instrument starts.

Removing the IonSABRE II probe and APPI/APCI source

enclosure
Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The source
components can be contaminated.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To remove the combined APPI/APCI source:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the probe and source; these components can be hot.

2. Remove the IonSABRE II probe (see page 65).

3. Disconnect the HT cable from the instrument’s front panel.
4. Disconnect the APPI drive cable from the instrument’s front panel.
5. Remove the source enclosure (see page 90).

72 March 14, 2014, 715004387 Rev. B

 NanoFlow source

6. Remove the corona pin (see page 95).

7. Fit the blanking plug to the pin’s mounting contact.

NanoFlow source
The NanoFlow source enclosure comprises the NanoFlow stage (for x-axis,
y-axis, and z-axis adjustment), the sprayer-enclosure, and a microscope
camera.

NanoFlow source, stage and microscope camera:

Microscope Camera

Sprayer enclosure

X, Y, Z stage

A sprayer is mounted on an X, Y, Z stage (three-axis manipulator) that slides

on a pair of guide rails that allow its withdrawal from the source enclosure for
maintenance and changes.

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3 Changing the Mode of Operation

A light within the source provides illumination for the spray, which you can
observe using the microscope camera mounted on the corner of the source
housing.
The low flow rates involved with operating the NanoFlow source prohibit its
use with the instrument’s solvent delivery system.

Installing the NanoFlow source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The source
components can be contaminated.

Warning: To avoid electric shock, ensure that the instrument is

prepared for working on the source before commencing this
procedure.

Warning: To avoid burn injuries, ensure that the source heater is

turned off and the block is cool before opening the source. The ion
block, which can be hot, is exposed when you fit the NanoFlow
source.

To install the NanoFlow source:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the probe and source; these components can be hot.

2. Remove the probe from the currently installed source.

• If you are removing an ESI probe, see page 61.
• If you are removing an IonSABRE II probe, see page 65.
3. Remove the existing source enclosure (see page 90).

74 March 14, 2014, 715004387 Rev. B

 NanoFlow source

Notice: To prevent the sprayer from colliding with the cone and
breaking, always retract the stage before installing the source
enclosure or closing the door.

4. On the NanoFlow source, loosen the stage retaining screw, pull the stop
screw, and slide the stage fully out of the enclosure.

Retaining screw
Stop screw

5. Using both hands, fit the NanoFlow source enclosure to the two
supporting studs on the source adaptor housing.
6. Close the source enclosure door.
7. Connect a 1/16-inch PTFE tube between the mass-flow controller output
(mounted beneath the stage on the front of the NanoFlow source) and
your sprayer.
Tip: For details regarding how to fit each sprayer, see the corresponding
reference:
• Waters Universal NanoFlow Sprayer Installation and Maintenance
Guide (part number 71500110107)
• “Fitting a borosilicate glass capillary (nanovial)” on page 77
• Capillary Electrophoresis/Capillary Electrochromatography
Sprayer User's Guide (part number 6666522)

March 14, 2014, 715004387 Rev. B 75

3 Changing the Mode of Operation

8. Connect the probe cable to the high-voltage connector.

9. Connect the high-voltage cable to the instrument’s HV connection.

High-voltage cable

Tip: The NanoFlow stage contains a high-voltage interlock, so the

capillary voltage (the voltage applied to the sprayer assembly) and the
sampling cone voltage remain disabled until the sprayer is pushed fully
forward in the source.
10. Slide closed the instrument’s source interface door.

76 March 14, 2014, 715004387 Rev. B

 NanoFlow source

Fitting a borosilicate glass capillary (nanovial)

Required materials
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• Borosilicate glass capillary
• Fused silica syringe needle or GELoader® tip
• Fused silica cutter

Warning: To avoid lacerations, puncture injuries, and

possible contamination with biohazardous and toxic samples,
do not touch the sharp end of the capillary.

Notice: To avoid damaging capillaries, take great care when

handling them. Capillaries are extremely fragile; always
hold their blunt end, never the sharp end, which can easily
be damaged.

Warning: To avoid electric shock, ensure that the NanoFlow

stage is fully retracted from the source before beginning this
procedure.

To fit a borosilicate glass capillary (nanovial):

1. Loosen the stage retaining screw.
2. Pull the stop screw to release the stage.
3. Slide the stage out of the NanoFlow source enclosure and remove the
magnetic cover.
4. Unscrew the retaining screw, and lift the sprayer from the stage.

March 14, 2014, 715004387 Rev. B 77

3 Changing the Mode of Operation

5. Unscrew the union from the end of the sprayer assembly.

Capillary
Union

6. Remove the existing capillary from the sprayer.

7. Carefully remove the new borosilicate glass capillary from its case by
lifting vertically while pressing on the foam with two fingers.

Foam

Capillary

8. Load sample into the capillary using a fused silica syringe needle or a
GELoader tip, minimizing any bubbles between the capillary tip and the
sample.

78 March 14, 2014, 715004387 Rev. B

 NanoFlow source

Recommendation: When using a GELoader tip, break the glass

capillary in half, scoring it with a fused silica cutter so that the
GELoader can reach the capillary’s tip.
9. Thread the knurled nut and approximately 5 mm of conductive
elastomer over the blunt end of the capillary.
10. Fit the capillary into the holder (probe).
11. Finger-tighten the nut so that 5 mm of glass capillary protrude from its
end.
Tip: Measure the protrusion from the end of the nut to the shoulder of
the glass capillary.

Sprayer assembly:

PTFE tubing

Ferrule

Union
Knurled nut
Blue conductive elastomer

5 mm Glass capillary

12. Screw the sprayer back into the assembly.

13. Replace the sprayer cover.
14. On the ES+/- Source tab of the MassLynx MS Tune window, ensure that
the Capillary parameter is set to 0 kV.

March 14, 2014, 715004387 Rev. B 79

3 Changing the Mode of Operation

Notice: To prevent the capillary tip from colliding with the cone or
the side of the source, adjust the sprayer tip position before you
push the sprayer inside the NanoFlow source enclosure.

15. Carefully push the stage back into the NanoFlow source enclosure, using
the stop and handle.

Positioning the borosilicate glass capillary tip

Having obtained a signal, you must adjust the tip position to maximize it.
Using the three-axis manipulator, you can adjust the tip position up and
down, left and right, forward and backward. As a starting point, set the tip so
that it is on the center line of the sampling cone and at a distance between two
and three times the diameter of the cone aperture. Typically this distance is
approximately 2 mm.

Capillary tip position:

3d

2d

Cone aperture diameter d

For tuning instructions, see the instrument’s online help.

Restarting a stalled borosilicate glass capillary electrospray

Should the spray stop, you can restart it. To do so, in the MassLynx Tune
window, set Capillary to 0 kV. Then adjust the three-axis manipulator so that,
viewed under magnification, the capillary tip touches the sample cone, and a
small piece of the borosilicate glass capillary shears off.
If necessary, you can also apply some NanoFlow gas pressure, to force a drop
of liquid from the capillary. Apply as much as 1.4 bar (20 psi). Doing so
induces the drop’s appearance unless the capillary is blocked.

80 March 14, 2014, 715004387 Rev. B

4 Maintenance Procedures

This chapter provides the maintenance guidelines and procedures

necessary to maintain the instrument’s performance.
Keep to a maintenance schedule, and perform maintenance as required
and described in this chapter.
Contents:

Topic Page
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
Installing and removing the corona pin.......................................... 93
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
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
Cleaning the extraction cone ........................................................... 119
Cleaning the ion block assembly ..................................................... 126
Cleaning the ion guide assembly..................................................... 137
Replacing the ESI probe tip and gasket ......................................... 147
Replacing the ESI probe sample capillary...................................... 151

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4 Maintenance Procedures

Contents:

Topic Page
Cleaning the IonSABRE II probe tip .............................................. 159
Replacing the IonSABRE II probe sample capillary ...................... 160
Cleaning or replacing the corona pin .............................................. 166
Replacing the IonSABRE II probe heater....................................... 167
Replacing the ion block source heater............................................. 170
Replacing the source assembly seals .............................................. 174
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
Replacing the instrument’s fuses .................................................... 199

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 Maintenance schedule

Maintenance schedule
The following table lists periodic maintenance schedules that ensure optimum
instrument performance.
The maintenance frequencies shown apply to instruments that normally
receive moderate use.

Maintenance schedule:

Procedure Frequency For information...

Clean the instrument case. As required. See page 100.
Empty the exhaust trap bottle Check daily, empty as See page 100.
in the instrument exhaust required.
line.
Replace the oil-free (scroll) Annually. See Edwards
pump’s seals. document XDS35i
Instruction Manual
A730-01-880.
Gas ballast the roughing ESI – weekly. See page 102.
pump.
Inspect and adjust the Weekly. See page 106.
roughing pump oil level.
Clean the source components. When they are visibly See page 108.
fouled, the background
or high-peak
contaminants are
unacceptably high, or
sensitivity decreases to
unacceptable levels.
Clean or replace the ESI When sensitivity See page 177.
probe tip. decreases to
unacceptable levels.
Replace the ESI probe When sensitivity See page 151.
capillary. decreases to
unacceptable levels or
sample flow is
inconsistent.

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4 Maintenance Procedures

Maintenance schedule:

Procedure Frequency For information...

Clean the IonSABRE II probe When sensitivity See page 159.
tip. (Options using the decreases to
IonSABRE II probe only.) unacceptable levels or
when significant
chemical interference
is present.
Replace the IonSABRE II When sensitivity See page 160.
probe capillary. (Options decreases to
using the IonSABRE II probe unacceptable levels or
only.) sample flow is
inconsistent.
Clean or replace the corona When the corona pin is See page 166.
pin (APCI and ESCi modes). corroded or black, or
the sensitivity
decreases to
unacceptable levels.
Replace the IonSABRE II If the heater fails to See page 167
probe heater. (Options using heat when the
the IonSABRE II probe only.) instrument is pumped
down (evacuated).
Replace the ion block heater If the heater fails to See page 170.
cartridge. heat when the
instrument is pumped
down (evacuated).
Replace the source assembly Annually. See page 174.
seals.
Replace the instrument’s air Annually. See page 178.
filters.
Change the roughing pump Annually. See page 180.
oil.

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 Spare parts

Maintenance schedule:

Procedure Frequency For information...

Replace the roughing pump’s Annually. See page 183.
demister element. Tip: Applications that
contaminate the
roughing pump oil
reduce this period,
which must be
determined from
experience.
Clean the APPI/APCI source When the window See page 189.
UV lamp window. becomes visibly dirty
or when the sensitivity
decreases to
unacceptable levels.
Change the APPI/APCI source When the bulb fails. See page 188.
UV lamp bulb.
Replace the APPI lamp drive Annually. See page 191.
assembly O-rings.

Spare parts
Replace only spare parts, which are the parts mentioned in this document. For
details about spare parts, use the Waters Quality Parts® Locator on the
Waters Web site’s Services & Support page.

March 14, 2014, 715004387 Rev. B 85

4 Maintenance Procedures

Troubleshooting with Connections INSIGHT

®
Connections INSIGHT is an “intelligent” device management (IDM) Web
service that enables Waters to provide proactive service and support for the
ACQUITY UPLC system. To use Connections INSIGHT, you must install its
service agent software on your workstation. In a client/server system, the
service agent must also be installed on the computer from which you control
the system. The service agent software automatically and securely captures
and sends information about the support needs of your system directly to
Waters.
If you encounter a performance issue when using the Instrument Console, you
can manually submit a Connections INSIGHT request to Waters customer
support. Alternatively, you can use Remote Desktop, a real-time collaboration
option that controls the two-way connection with the ACQUITY UPLC system
by enabling the Connections INSIGHT iAssist service level.
Consult these sources for more information about Connections INSIGHT and
Connections INSIGHT iAssist:
• http://www.waters.com
• Connections INSIGHT Installation Guide (part number 715001399)
• Connections INSIGHT User's Guide (part number 715001400)
• Your sales representative
• Your local Waters subsidiary
• Waters Customer Support

To submit a Connections INSIGHT request:

1. Open the Connections INSIGHT software tray application, and select
the iHelp tab.
2. In the Connections INSIGHT Request dialog box, type your name,
telephone number, e-mail address, and a description of the problem.
3. Click Submit, and allow approximately 5 minutes to save the service
profile.
Result: A .zip file containing your Connections INSIGHT profile is
forwarded to Waters customer support for review.
Note: Saving a service profile or plot file from the Instrument Console
can require as much as 150 MB of file space.

86 March 14, 2014, 715004387 Rev. B

 Safety and handling

Safety and handling

Bear in mind the following safety considerations when performing
maintenance procedures:

Warning: To avoid personal contamination, always wear

chemical-resistant, powder-free gloves while handling instrument
components. The components can be contaminated with
biohazards or toxic materials.

Warning: To prevent injury, always observe Good Laboratory

Practice when handling solvents, changing tubing, or operating
the instrument. Know the physical and chemical properties of the
solvents used (see the Material Safety Data Sheets for the solvents
in use).

Warning: To avoid electric shock,

• do not remove the instrument’s panels. There are no
user-serviceable parts inside the instrument.
• ensure that the instrument is in Standby mode before
commencing any maintenance.

Warning: To avoid burn injuries, take great care while working

with the probe and source; they can be hot.

Warning: To avoid injury, ensure that these criteria are met when
performing maintenance inside the source enclosure:
• The instrument is in Standby mode.
• LC flow is diverted to waste or set to Off.
• Desolvation gas flow is stopped.

See Appendix A for safety advisory information.

March 14, 2014, 715004387 Rev. B 87

4 Maintenance Procedures

Preparing the instrument for operations on or inside its

source
For safety reasons, you must follow this procedure before working on the
source (for example, when changing the probe, operating the source isolation
valve, and maintaining the source).
Follow the procedure for the software that controls your mass spectrometer:
MassLynx software, or UNIFI software.

To use MassLynx software to prepare the instrument for operations on or

inside its source:

1. In the Instrument Console, click Stop Flow to stop the LC flow or, if
column flow is required, divert the LC flow to waste as follows:
a. In the Instrument Console system tree, expand Xevo TQD,
Interactive Fluidics.

b. Click Control .
c. Select Waste as the flow state.

2. In the Instrument Console, click Standby , and confirm that the

Operate indicator is not illuminated.
3. Wait 3 minutes to allow the desolvation gas flow to cool the probe and
source.

4. In the Instrument Console, click API to stop the desolvation gas

flow.
5. Lift the visor on the front of the instrument so that it is clear of all the
source components and probe.

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 Preparing the instrument for operations on or inside its source

To use UNIFI software to prepare the instrument for operations on or inside

its source:

1. On the System Console tool bar, click Stop Flow to stop the LC flow
or, if column flow is required, divert the LC flow to waste as follows:
a. On the Setup pane, click Fluidics.
b. On the Sample Fluidics page, from the Flow Path menu, select
Waste.

2. Click Instrument Standby Mode , and confirm that the Operate

indicator is not illuminated.
3. Wait 3 minutes to allow the desolvation gas flow to cool the probe and
source.

4. Stop the API gas by clicking .

(If the API gas is already stopped, is shown on the tool bar.)
5. Lift the visor on the front of the instrument so that it is clear of all the
source components and probe.

March 14, 2014, 715004387 Rev. B 89

4 Maintenance Procedures

Removing and refitting the source enclosure

The optional combined APPI/APCI, NanoFlow, and TRIZAIC sources are
supplied as a complete source enclosure. To fit them, you must first remove
the standard source enclosure.

Removing the source enclosure from the instrument

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazardous

and/or toxic materials, always wear chemical-resistant,
powder-free gloves while performing this procedure. The source
components can be contaminated.

To remove the source enclosure:

1. Prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

Warning: To avoid burn injuries, take great care while working

with the probe and source; they can be hot.

2. Remove the probe from the source.

• If you are removing an ESI probe, see page 61.
• If you are removing an IonSABRE II probe, see page 65.
3. Disconnect the probe adjuster and options cables from the instrument’s
connectors.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if a corona pin is fitted.
The corona pin tip is sharp.

4. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.

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 Removing and refitting the source enclosure

5. Using both hands, grasp the source enclosure and lift it vertically off the
two supporting studs on the source adaptor housing.
Cable storage positions Supporting stud

TP03164

Source enclosure

6. Store the cables neatly by plugging them into the cable-storage positions
on the rear of the source enclosure.

March 14, 2014, 715004387 Rev. B 91

4 Maintenance Procedures

Fitting the source enclosure to the instrument

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, and to avoid spreading
contamination to uncontaminated surfaces, wear clean,
chemical-resistant, powder-free gloves when working with the
source components.

Warning: To avoid puncture wounds, take great care while fitting

the source enclosure to the source if a corona pin is fitted (the pin
tip is sharp).

To fit the source enclosure:

1. Using both hands, fit the source enclosure to the two supporting studs
on the source adaptor housing.

Notice: To prevent the sprayer from colliding with the cone and,
consequently, breaking when you use a NanoFlow source, always
retract the stage before closing the source enclosure door.

2. Close the source enclosure.

3. Connect the probe adjuster and options cables to the instrument’s
connectors.

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 Installing and removing the corona pin

Installing and removing the corona pin

For ESCi, APCI, and dual-mode APCI/APPI operation, you must fit a corona
pin.

Installing the corona pin in the source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, and to avoid spreading
contamination to uncontaminated surfaces, wear clean,
chemical-resistant, powder-free gloves while performing this
procedure. The LC system connections, ESI probe, and source can
be contaminated.

Warning: To avoid electric shock, ensure that the instrument is

prepared for working on the source before commencing this
procedure.

To install the corona pin in the source:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the source enclosure open; the source can be hot.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if an ESI probe is fitted;
the ESI probe tip is sharp.

2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.

March 14, 2014, 715004387 Rev. B 93

4 Maintenance Procedures

3. Remove the blanking plug from the corona pin mounting contact.
Tip: Store the blanking plug in a safe location.

Corona pin mounting contact:

Corona pin mounting

contact blanking plug

TP03130

Warning: To avoid puncture wounds, handle the corona pin with

care; the tip is sharp.

4. Fit the corona pin to the mounting contact, ensuring that the corona pin
is securely mounted.

Corona pin:

Corona pin

TP03130

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 Installing and removing the corona pin

5. Close the source enclosure.

6. Look through the source window, and use the vernier probe adjuster to
position the probe tip so that it is pointing approximately midway
between the tips of the sample cone and corona pin.

Removing the corona pin from the source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, and to avoid spreading contamination
to uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves while performing this procedure. The LC system
connections, ESI probe, and source can be contaminated.

Warning: To avoid electric shock, ensure that the instrument is

prepared for working on the source before commencing this
procedure.

To remove the corona pin from the source:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the instrument’s source enclosure open; the source can be hot.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if an ESI probe is fitted;
the ESI probe tip is sharp.

2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.
3. Remove the corona pin from its mounting contact (see the figure on page 95).
Tip: Store the corona pin in a safe location.
4. Fit the blanking plug to the corona pin mounting contact (see the figure
on page 94).
5. Close the source enclosure.

March 14, 2014, 715004387 Rev. B 95

4 Maintenance Procedures

Operating the source isolation valve

You must close the source isolation valve to isolate the source from the
instrument vacuum system for certain maintenance procedures.

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid electric shock, before beginning this procedure,

prepare the instrument according to the procedure on page 88,
“Preparing the instrument for operations on or inside its source”.

To close the source isolation valve before starting a maintenance

procedure:
1. Prepare the instrument according the procedure on page 88, “Preparing
the instrument for operations on or inside its source”.

Warning: To avoid burn injuries, take great care while working

with the instrument’s source enclosure open; the source can be hot.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.

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 Operating the source isolation valve

3. Close the source isolation valve by moving its handle counterclockwise,

to the vertical position.

Isolation valve handle

in closed position

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

To open the source isolation valve after completing a maintenance

procedure:
1. Open the source isolation valve by moving its handle clockwise to the
horizontal position.

March 14, 2014, 715004387 Rev. B 97

4 Maintenance Procedures

Isolation valve handle

in open position

TP03130

2. Close the source enclosure.

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 Removing O-rings and seals

Removing O-rings and seals

When performing certain maintenance procedures, you must remove O-rings
or seals from instrument components. An O-ring removal kit can be purchased
separately.

O-ring removal kit:

Tool 1

Tool 2

Notice: To avoid scratching the O-ring or seal, take care while using the
removal tools to remove it from components.

To remove an O-ring:
1. Use the forked end of tool 1 to impale the O-ring or seal.
2. Pull the O-ring or seal from its groove; if necessary, use tool 2 as an aid.

Warning: To avoid spreading contamination, dispose of the

O-ring or seal in accordance with local environmental
regulations.

3. Dispose of the O-ring or seal in accordance with local environmental

regulations.

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4 Maintenance Procedures

Cleaning the instrument case

Notice: To avoid damaging the instrument, do not use abrasives or

solvents to clean the instrument’s case.

Use a soft cloth, dampened with water, to clean the outside surfaces of the
instrument.

Emptying the exhaust trap bottle

Inspect the exhaust trap bottle in the instrument’s exhaust line daily, and
empty it before it is more than 10% full.

Nitrogen exhaust trap bottle:

From instrument
waste (12-mm)
To laboratory
exhaust (12-mm)

Valve control
cable (from
instrument)

100 March 14, 2014, 715004387 Rev. B

 Emptying the exhaust trap bottle

Required material
Chemical-resistant, powder-free gloves

To empty the nitrogen exhaust trap bottle:

1. To stop the LC flow, follow the action below for your software:

Software Action

MassLynx In the instrument console, click Stop Flow .

UNIFI On the System Console tool bar, click Stop Flow .

2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, wear clean,
chemical-resistant, powder-free gloves when handling the
nitrogen exhaust trap bottle. The waste liquid in the bottle
comprises ACQUITY UPLC solvents and analytes.

3. Unscrew and remove the nitrogen exhaust trap bottle from the cap and
associated fittings.

Warning: To avoid spreading contamination, dispose of the

waste liquid in accordance with local environmental
regulations.

4. Dispose of the waste liquid in accordance with local environmental

regulations.
5. Fit and fully tighten the nitrogen exhaust trap bottle to the cap.
6. Secure the nitrogen exhaust trap bottle in the upright position.
7. Close the source enclosure.
Tip: A leak test runs automatically. If the test results in a failure, ensure
that the nitrogen exhaust trap bottle is fully tightened to the cap.

March 14, 2014, 715004387 Rev. B 101

4 Maintenance Procedures

8. To start the LC flow, follow the action below for your software:

Software Action

MassLynx In the instrument console, click Start Flow .

UNIFI On the System Console tool bar, click Start Flow .

Gas ballasting the roughing pump

The roughing pump draws large quantities of solvent vapors. The vapors tend
to condense in the pump oil, diminishing pumping efficiency. Gas ballasting
purges condensed contaminants from the oil.
Note: This procedure is not required for an oil-free roughing pump.

Roughing pump:

Exhaust port flange

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

Gas ballast valve

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 Gas ballasting the roughing pump

Notice: To avoid shortening the oil life and pump life, routinely gas
ballast the roughing pump according to the guidelines below.

Gas ballast the roughing pump when these conditions apply:

• With ESI operation, once a week
• When the roughing pump oil appears cloudy
• When the vacuum pressure is higher than normal
• When condensate forms in the roughing pump exhaust line
• When you change the roughing pump oil
The roughing pump can be fitted with either of the following:
• A screwdriver-operated gas ballast valve. See page 103.
• A handle-operated gas ballast valve. See page 105.

Gas ballasting a pump fitted with a screwdriver-operated gas

ballast valve
Required material
Flat-blade screwdriver

Warning: To avoid burn injuries, take great care while working with the
roughing pump; it can be hot.

Notice: To avoid damage, follow these guidelines:

• Do not vent the instrument when the roughing pump is gas
ballasting.
• Do not gas ballast the roughing pump while the instrument is in
Operate mode.
• Avoid gas ballasting the roughing pump for more than 2 hours.

March 14, 2014, 715004387 Rev. B 103

4 Maintenance Procedures

To gas ballast the roughing pump:

1. Use the flat-blade screwdriver to turn the gas ballast valve on the pump
a quarter-turn to the open position .

TP02654

2. Run the pump for 30 to 60 minutes.

Tip: It is normal for the roughing pump temperature to increase during
ballasting. To maintain an ambient temperature of less than 40 °C in
the space where the pump is located, ensure the space is adequately
ventilated.
3. Use the flat-blade screwdriver to turn the gas ballast valve to the closed

position .

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 Gas ballasting the roughing pump

Gas ballasting a pump fitted with a handle-operated gas ballast

valve
Warning: To avoid burn injuries, take great care while working with the
roughing pump; it can be hot.

Notice: To avoid damage, follow these guidelines:

• do not vent the instrument when the roughing pump is gas
ballasting.
• do not gas ballast the roughing pump while the instrument is in
Operate mode.
• avoid gas ballasting the roughing pump for more than 2 hours.

To gas ballast the roughing pump:

1. Move the gas ballast valve handle on the pump counterclockwise, from
the horizontal position to the vertical position.

TP02654

2. Run the pump for 30 to 60 minutes.

Tip: It is normal for the roughing pump temperature to increase during
ballasting. To maintain an ambient temperature of less than 40 °C in
the space where the pump is located, ensure the space is adequately
ventilated.
3. Move the gas ballast valve handle on the pump clockwise, from the
vertical position to the horizontal position.

March 14, 2014, 715004387 Rev. B 105

4 Maintenance Procedures

Checking the roughing pump oil level

To ensure correct operation of the roughing pump, do not operate it with the
oil level at less than 30% of the maximum level, as indicated in the pump’s
sight glass.
Note: This procedure is not required for an Edwards oil-free roughing pump.
The roughing pump oil level appears in the roughing pump’s oil level sight
glass. Check the oil level weekly; you must maintain the oil level at or near
the indicated maximum level when the pump is not operating.
Requirement: You must check the oil level while the roughing pump is
running. Note that the oil level in the sight glass is lower when the pump is
running than when it is stopped. When the pump is running, the oil level is
typically at 30% to 60% of the maximum level.

Adding oil to the roughing pump

If the roughing pump’s oil level is low, you must add oil to the pump.

Required materials
• Chemical-resistant, powder-free gloves
• 8-mm Allen wrench
• Container to catch used oil
• Funnel
• Anderol vacuum oil, type GS 495

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, and to avoid spreading
contamination to uncontaminated surfaces, wear clean,
chemical-resistant, powder-free gloves when adding or
replacing oil. The pump oil can be contaminated with analyte
accumulated during normal operation.

Warning: To avoid burn injuries, take great care while

working with the roughing pump; it can be hot.

106 March 14, 2014, 715004387 Rev. B

 Adding oil to the roughing pump

To add oil to the roughing pump:

1. Vent and shut down the mass spectrometer (see the instrument’s online
Help for details).
2. Use the 8-mm Allen wrench to unscrew and remove the roughing pump’s
oil filler plug (see the figure on page 102).
Requirement: To maintain pump performance, use only Anderol
vacuum oil, type GS 495.
3. Using the funnel, add Anderol vacuum oil, type GS 495, into the oil filler
aperture until the oil reaches the oil level sight glass MAX level.
4. Ensure that the O-ring on the oil filler plug is clean and properly seated.

Notice: To avoid oil leakage, and consequent damage to the pump,

when refitting the oil filler plug, ensure that:
• the plug is not cross-threaded;
• the O-ring is not pinched;
• the plug is not overtightened.

5. Use the 8-mm Allen wrench to fit and tighten the roughing pump’s oil
filler plug.
Tip: When the oil filler plug is tightened, the plug seals by means of an
O-ring. Compression is controlled by the O-ring groove depth in the plug.
Overtightening does not improve the plug seal; it merely makes the plug
difficult to remove.
Tip: After you add oil to the pump, the following situations can occur:
• The oil level drops slightly during the first month of operation.
• The oil darkens in color over time.
• After running the pump for 12 to 48 hours, it is common to see a few
drops of oil near the filler plug. Excess oil around the lip of the filler
plug will run down and drip off the pump when the pump reaches
operating temperature.
• When the pump begins to run at normal operating temperature, the
spilled oil produces a slight odor.

March 14, 2014, 715004387 Rev. B 107

4 Maintenance Procedures

Cleaning the source components

Clean the sample cone and cone gas nozzle when these conditions apply:
• The sample cone and cone gas nozzle are visibly fouled.
• You dismissed LC and sample-related causes for decreased signal
intensity.
See page 109.
If cleaning the sample cone and cone gas nozzles fails to increase signal
sensitivity, also clean the extraction cone. See page 119.
If cleaning the extraction cone fails to increase signal sensitivity, clean the ion
block and isolation valve. See page 126.
If cleaning the ion block and isolation valve fails to increase signal sensitivity,
also clean the ion guide assembly. See page 137.

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 Cleaning the sampling cone assembly

Cleaning the sampling cone assembly

You can remove the sampling cone assembly (the sample cone, O-ring, and
cone gas nozzle) for cleaning without venting the instrument.

Removing the sampling cone assembly from the source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid electric shock, before beginning this

procedure, prepare the instrument according the procedure on
page 88, “Preparing the instrument for operations on or inside its
source”.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

Warning: To avoid burn injuries, take great care while working

with the source enclosure open; the source can be hot.

March 14, 2014, 715004387 Rev. B 109

4 Maintenance Procedures

To remove the sampling cone assembly from the source:

1. Close the source isolation valve (see page 96).
2. Grasp the cone gas nozzle handle, and use it to rotate the sampling cone
assembly 90 degrees, moving the handle from the vertical to the
horizontal position.

Sampling cone
assembly
Cone gas nozzle
handle

TP03131

Notice: To avoid damaging the instrument by sudden venting, do

not open the isolation valve at any time while the sampling cone
assembly is removed from the ion block assembly.

3. Slide the sampling cone assembly out of the ion block assembly.

Ion block assembly

TP03132

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 Cleaning the sampling cone assembly

Disassembling the sampling cone assembly

Required material
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the sampling cone
assembly.

To disassemble the sampling cone assembly:

1. Slide the collar to the end of the combined 2.5-mm Allen wrench and
cone extraction tool.

Collar

March 14, 2014, 715004387 Rev. B 111

4 Maintenance Procedures

2. Insert the collar in the sample cone.

Notice: To avoid damaging the fragile sample cone, do not place

it on its tip; instead, place it on its flanged base.

3. Rotate the tool and collar counter-clockwise and then lift them to remove
the sample cone from the cone gas nozzle.

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 Cleaning the sampling cone assembly

4. Remove the O-ring from the sample cone.

Cone gas nozzle

Cone gas nozzle handle

O-ring

Warning: To avoid spreading contamination, dispose of the

O-ring or seal in accordance with local environmental
regulations.

5. If the O-ring shows signs of deterioration or damage, dispose of it in

accordance with local environmental regulations.
6. Unscrew and remove the PEEK cone gas nozzle handle from the cone
gas nozzle.

March 14, 2014, 715004387 Rev. B 113

4 Maintenance Procedures

Cleaning the sample cone and cone gas nozzle

Required materials
• Chemical-resistant, powder-free gloves.
• Appropriately sized glass vessels in which to completely immerse
components when cleaning. Use only glassware not previously cleaned
with surfactants.
• HPLC-grade (or better) methanol.
• HPLC-grade (or better) water.
• Formic acid.
• Ultrasonic bath.
• Source of oil-free, inert gas (nitrogen or argon) for drying (air-drying
optional).
• Wash bottle containing HPLC-grade (or better) 1:1 methanol/water.
• Large beaker.

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the sample cone and cone
gas nozzle.

Warning: To avoid injury, work with extreme care. Use a fume

hood, and suitable protective equipment. Formic acid is
extremely corrosive and toxic.

Notice: To avoid damaging the fragile sample cone, do not place

it on its tip; instead, place it on its flanged base.

To clean the sample cone and cone gas nozzle:

1. If the sample cone contains debris, place a drop of formic acid on its
aperture.
2. Immerse the sample cone, cone gas nozzle, and cone gas nozzle handle in
separate glass vessels containing 1:1 methanol/water.
Tip: If the components are obviously contaminated, use 45:45:10
methanol/water/formic acid.

114 March 14, 2014, 715004387 Rev. B

 Cleaning the sampling cone assembly

3. Place the vessels in the ultrasonic bath for 30 minutes.

4. If you used formic acid in the cleaning solution, do as follows:
a. Rinse the components by immersing them in separate glass vessels
containing water and then place the vessels in the ultrasonic bath
for 20 minutes.
b. Remove any residual water from the extraction cone by immersing
it in a glass vessel containing methanol and then place the vessel in
the ultrasonic bath for 10 minutes.

Notice: To avoid recontaminating the components, wear clean,

chemical-resistant, powder-free gloves for the rest of this
procedure.

5. Carefully remove the components from the vessels, and blow-dry them
with inert, oil-free gas.
6. Inspect each component for persisting contamination. If contamination
is present, do as follows:
a. Use the wash bottle containing 1:1 methanol/water to rinse the
component over the large beaker.
b. Blow-dry the component with inert, oil-free gas.
7. Inspect each component for persisting contamination. If contamination
is present, dispose of the component, and obtain a new one before
reassembling the sampling cone assembly.

March 14, 2014, 715004387 Rev. B 115

4 Maintenance Procedures

Assembling the sampling cone assembly

Required material
Clean, chemical-resistant, powder-free gloves

Notice:
• To avoid recontaminating the sampling cone assembly, wear clean
chemical-resistant, powder-free gloves during this procedure.
• To avoid damaging the fragile sample cone, do not place it on its tip;
instead, place it on its flanged base.

To assemble the sampling cone assembly:

1. Fit the cone gas nozzle handle onto the cone gas nozzle and turn the
handle clockwise to tighten.

O-ring

Sample cone

Cone gas nozzle

Cone gas nozzle handle TP02663

2. Carefully fit the sample cone into the cone gas nozzle.
3. Fit the O-ring into the groove created between the sample cone and cone
gas nozzle. (Fit a new O-ring if the old one has been disposed of.)

116 March 14, 2014, 715004387 Rev. B

 Cleaning the sampling cone assembly

Fitting the sampling cone assembly to the source

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

Notice: To avoid damaging the instrument by sudden venting, do

not open the source isolation valve before fitting the sampling
cone assembly to the ion block assembly.

March 14, 2014, 715004387 Rev. B 117

4 Maintenance Procedures

To fit the sampling cone assembly to the source:

1. Ensure that the source isolation valve is in the closed position (see
page 96).
2. Hold the sampling cone assembly so that the cone gas nozzle handle is
oriented horizontally and at the top, and then slide the sampling cone
assembly into the ion block assembly.

Ion block assembly

TP03132

Sampling cone assembly

3. Grasp the cone gas nozzle handle and use it to rotate the sampling cone
assembly 90 degrees, moving the handle downward from the horizontal
to the vertical position.
4. Open the source isolation valve (see page 97).
5. Close the source enclosure.

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 Cleaning the extraction cone

Cleaning the extraction cone

Clean the ion block and extraction cone when cleaning the sample cone and
cone gas nozzle fails to increase signal sensitivity. You must remove the ion
block assembly from the source assembly to clean the extraction cone.

Removing the ion block assembly from the source assembly

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

To remove the ion block assembly:

1. Vent and shut down the mass spectrometer (see the mass spectrometer’s
online Help for details).

Warning: To avoid burn injuries, allow the source to cool for at

least 30 minutes before proceeding; the source can be hot.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

2. Close the source isolation valve (see page 96).

March 14, 2014, 715004387 Rev. B 119

4 Maintenance Procedures

3. Use the combined 2.5-mm Allen wrench and cone extraction tool to
unscrew the 4 captive screws that secure the ion block assembly.

Screws securing the

Ion block

TP03130

4. Remove the ion block assembly from the PEEK ion block support.

PEEK ion block

support

Ion block assembly

TP03130

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 Cleaning the extraction cone

Removing the extraction cone from the ion block

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the ion block components.

To remove the extraction cone from the ion block:

1. On the rear of the ion block, use the combined 2.5-mm Allen wrench and
cone extraction tool to loosen the captive screws securing the 2 PEEK
extraction cone retainer clips, and then rotate the retainer clips clear of
the extraction cone.
Extraction cone handle insulator

Retainer clip
rotated clear of the
extraction cone

Securing screw Extraction cone

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4 Maintenance Procedures

Notice:
• To avoid damaging the extraction cone aperture, take great
care when removing it from the ion block.
• To avoid damaging the fragile extraction cone, do not place it
on its tip; instead, place it on its flanged base.

2. Remove the extraction cone from the ion block.

Extraction cone aperture

3. Remove the extraction cone handle insulator from the extraction cone
handle.

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 Cleaning the extraction cone

Cleaning the extraction cone

Required materials
• Chemical-resistant, powder-free gloves.
• Appropriately sized glass vessel in which to completely immerse the
extraction cone when cleaning. Use only glassware not previously
cleaned with surfactants.
• HPLC-grade (or better) methanol.
• HPLC-grade (or better) water.
• Formic acid.
• Ultrasonic bath.
• Source of oil-free, inert gas (for example, nitrogen) for drying (air-drying
optional).
• Wash bottle containing HPLC-grade (or better) 1:1 methanol/water.
• Large beaker.

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the extraction cone.

Warning: To avoid injury, work with extreme care. Use a fume

hood, and suitable protective equipment. Formic acid is
extremely corrosive and toxic.

Notice: To avoid damaging the fragile extraction cone, do not

place it on its tip; instead, place it on its flanged base.

March 14, 2014, 715004387 Rev. B 123

4 Maintenance Procedures

To clean the extraction cone:

1. Immerse the extraction cone in the glass vessel containing 1:1
methanol/water.
Tip: If the extraction cone is obviously contaminated, use 45:45:10
methanol/water/formic acid.
2. Place the vessel in the ultrasonic bath for 30 minutes.
3. If you used formic acid in the cleaning solution, do as follows:
a. Rinse the extraction cone by immersing it in a glass vessel
containing water and then placing the vessel in the ultrasonic bath
for 20 minutes.
b. Dry the components by immersing them in separate glass vessels
containing methanol and then placing the vessels in the ultrasonic
bath for 10 minutes.

Notice: To avoid recontaminating the extraction cone, wear

clean, chemical-resistant, powder-free gloves for the rest of this
procedure.

4. Carefully remove the extraction cone from the vessel, and blow-dry it
using inert, oil-free gas.
5. Inspect the extraction cone for persisting contamination. If
contamination is present, do as follows:
a. Use the wash bottle containing 1:1 methanol/water to rinse the
extraction cone over the large beaker.
b. Blow-dry the extraction cone with inert, oil-free gas.

Warning: To avoid spreading contamination, dispose of the

extraction cone in accordance with local environmental
regulations.

6. Inspect the extraction cone for persisting contamination. If

contamination is present, dispose of the extraction cone, and obtain a
new one.

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 Cleaning the extraction cone

Fitting the extraction cone to the ion block

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the ion block.

To fit the extraction cone onto the ion block:

1. Fit the extraction cone handle insulator onto the extraction cone handle.
2. Fit the extraction cone onto the ion block.
3. Rotate the 2 PEEK extraction cone retainer clips to secure the extraction
cone, then use the combined 2.5-mm Allen wrench and cone extraction
tool to tighten the retainer clip securing screws.

Fitting the ion block assembly to the source assembly

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid puncture wounds, take great care while

working with the source enclosure open if one or both of these
conditions apply:
• An ESI probe is fitted (the probe tip is sharp).
• A corona pin is fitted (the pin tip is sharp).

March 14, 2014, 715004387 Rev. B 125

4 Maintenance Procedures

Notice: To avoid recontaminating the ion block assembly, wear

clean chemical-resistant, powder-free gloves during this
procedure.

To fit the ion block assembly to the source assembly:

1. Fit the ion block assembly to the PEEK ion block support.
2. Use the combined 2.5-mm Allen wrench and cone extraction tool to fit
and then slowly tighten the 4 ion block assembly securing screws
sequentially and in small increments.
3. Open the source isolation valve (see page 96).
4. Close the source enclosure.

Cleaning the ion block assembly

Clean the ion block assembly when cleaning the sample cone, cone gas nozzle,
and extraction cone fails to increase signal sensitivity.

Disassembling the source ion block assembly

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
• O-ring removal kit
• Needle-nose pliers

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the ion block assembly.

To disassemble the ion block assembly:

1. Remove the ion block assembly from the source assembly (see page 119).

126 March 14, 2014, 715004387 Rev. B

 Cleaning the ion block assembly

2. Ensure that the isolation valve is closed.

Isolation valve handle

in closed position

Sampling cone
assembly retaining
blocks

Cone gas nozzle

handle

3. Grasp the cone gas nozzle handle and use it to rotate the sampling cone
assembly through 90 degrees.

Notice: To ensure correct operation of the ion block assembly

after reassembly, follow these guidelines:
• Do not remove the sampling cone assembly retaining blocks.
• Do not adjust the screws securing the sampling cone assembly
retaining blocks.

4. Slide the sampling cone assembly out of the ion block assembly.

March 14, 2014, 715004387 Rev. B 127

4 Maintenance Procedures

5. Use the combined 2.5-mm Allen wrench and cone extraction tool to
loosen the 2 ion block cover plate captive securing screws.

Ion block cover plate securing screw

Ion block cover plate

6. Remove the ion block cover plate.

7. Grasp the isolation valve and pull it out of the ion block.

Isolation valve

O-ring

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 Cleaning the ion block assembly

8. Use the O-ring removal kit to carefully remove the isolation valve O-ring
(see page 99).

Warning: To avoid spreading contamination, dispose of the

isolation valve O-ring in accordance with local
environmental regulations.

9. If the isolation valve O-ring shows signs of deterioration or damage,

dispose of it in accordance with local environmental regulations.
10. Use the combined 2.5-mm Allen wrench and cone extraction tool to
loosen the captive PEEK terminal block securing screw.

PEEK terminal
block securing
screw

Notice: To avoid damaging the heater cartridge assembly wires,

do not bend or twist them when removing the assembly from the
ion block.

11. Use the needle-nose pliers to grasp the PEEK terminal block and
partially lift it out of the ion block.

March 14, 2014, 715004387 Rev. B 129

4 Maintenance Procedures

12. Holding the PEEK ion block gently, use the needle-nose pliers to gently
grasp the heat-shrink tubing on the heater cartridge assembly, and
carefully slide it and the PEEK terminal block out of the ion block.

Heat-shrink tubing PEEK terminal block

Heater cartridge assembly

13. Use the O-ring removal kit to carefully remove the cover seal from the
ion block (see also page 99).

Cover seal

Cone gas O-ring

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 Cleaning the ion block assembly

14. Use the O-ring removal kit to carefully remove the cone gas O-ring from
the ion block.

Warning: To avoid spreading contamination, dispose of the

cover seal and cone gas O-ring in accordance with local
environmental regulations.

15. If the cover seal or cone gas O-ring shows signs of deterioration or
damage, dispose of it in accordance with local environmental
regulations.
16. Insert the combined 2.5-mm Allen wrench and cone extraction tool
through the hole in the ion block blanking plug, and then unscrew and
remove the ion block blanking plug and associated seal.

Blanking plug

Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid spreading contamination, dispose of the

blanking plug seal in accordance with local environmental
regulations.

17. If the blanking plug seal shows signs of deterioration or damage, dispose
of it in accordance with local environmental regulations.

March 14, 2014, 715004387 Rev. B 131

4 Maintenance Procedures

18. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the captive screws securing the 2 PEEK extraction cone retainer
clips.

Securing screw
Retainer clip

Extraction cone

Notice:
• To avoid damaging the extraction cone aperture, take great
care when removing the extraction cone from the ion block.
• To avoid damaging the fragile extraction cone, do not place it
on its tip; instead, place it on its flanged base.

19. Remove the extraction cone from the ion block.

Extraction cone aperture

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 Cleaning the ion block assembly

20. Remove the extraction cone handle insulator from the extraction cone
handle.
21. Remove the extraction cone seal from the ion block.

Extraction cone seal

Cleaning the ion block components

Required materials
• Chemical-resistant, powder-free gloves.
• Appropriately sized glass vessels in which to completely immerse
components when cleaning. Use only glassware not previously cleaned
with surfactants.
• HPLC-grade (or better) methanol.
• HPLC-grade (or better) water.
• Formic acid.
• Ultrasonic bath.
• Source of oil-free, inert gas (for example, nitrogen) for drying (air-drying
optional).
• Wash bottle containing HPLC-grade (or better) 1:1 methanol/water.
• Large beaker.

March 14, 2014, 715004387 Rev. B 133

4 Maintenance Procedures

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the ion block components.

Warning: To avoid injury, work with extreme care. Use a fume

hood, and suitable protective equipment. Formic acid is
extremely corrosive and toxic.

To clean the ion block components:

1. Immerse the ion block and isolation valve in separate glass vessels
containing 1:1 methanol/water.
Tip: If the components are obviously contaminated, use 45:45:10
methanol/water/formic acid.
2. Place the vessels in the ultrasonic bath for 30 minutes.
3. If you used formic acid in the cleaning solution, do as follows:
a. Rinse the components by immersing them separately in glass
vessels containing water and then place the vessels in the ultrasonic
bath for 20 minutes.
b. Dry the components by immersing them in separate glass vessels
containing methanol, and then place the vessels in the ultrasonic
bath for 10 minutes.

Notice: To avoid recontaminating the components, wear clean,

chemical-resistant, powder-free gloves for the rest of this
procedure.

4. Carefully remove the components from the vessels, and blow-dry them
using inert, oil-free gas.
Inspect each component for persisting contamination.
Requirement: If contamination is present, do as follows:
a. Use the wash bottle containing 1:1 methanol/water to rinse the
component over the large beaker.
b. Blow-dry the component with inert, oil-free gas.

134 March 14, 2014, 715004387 Rev. B

 Cleaning the ion block assembly

Warning: To avoid spreading contamination, dispose of the

components in accordance with local environmental
regulations.

5. Inspect each component for persisting contamination.

Requirement: If contamination is present, dispose of the component, and
obtain a new one before reassembling the ion block.

Assembling the source ion block assembly

Required materials
• Clean, chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
• Needle-nose pliers
• Isopropyl alcohol in a small container

Notice:
• To avoid recontaminating the ion block assembly, wear clean
chemical-resistant, powder-free gloves during this procedure.
• To avoid damaging the fragile extraction cone, do not place it on its
tip; instead, place it on its flanged base.

To assemble the ion block assembly:

1. Fit the extraction cone seal to the ion block.

Notice: To avoid damaging the extraction cone aperture, take

great care when fitting the extraction cone to the ion block.

2. Fit the extraction cone handle’s insulator onto the extraction cone
handle.
3. Fit the extraction cone onto the ion block.
4. Fit the 2 PEEK extraction cone retainer clips onto the ion block.

March 14, 2014, 715004387 Rev. B 135

4 Maintenance Procedures

5. Use the combined 2.5-mm Allen wrench and cone extraction tool to
tighten the captive screw securing each extraction cone retainer clip to
the ion block.
6. Fit the blanking plug seal onto the ion block blanking plug.
Requirement: Fit a new seal if the old one was discarded.
7. Fit the blanking plug onto the ion block and finger tighten it.
8. Insert the combined 2.5-mm Allen wrench and cone extraction tool
through the hole in the blanking plug, and use the tool to fully tighten
the plug.

Notice: To avoid damaging the heater cartridge assembly wires,

do not bend or twist them when fitting the assembly to the ion
block.

9. Using the needle-nose pliers to gently grasp the heat-shrink tubing on

the heater cartridge assembly, slide the assembly and the PEEK
terminal block into the ion block.
10. Use the combined 2.5-mm Allen wrench and cone extraction tool to
tighten the captive PEEK terminal block securing screw.
11. Ensure that the grooves for the cover seal, cone gas O-ring, and isolation
valve O-ring are free of dirt and debris.
Tip: If contamination is present, use 1:1 methanol/water, applied to a
lint-free cloth, to carefully clean the grooves.
12. Fit the cover seal onto the ion block, ensuring that it is correctly seated.
Requirement: Fit a new seal if the old one was discarded.
13. Fit the cone gas O-ring onto the ion block, ensuring that it is correctly
seated.
Requirement: Fit a new O-ring if the old one was discarded.
14. If the old isolation valve O-ring has been disposed of, soak a new O-ring
in isopropyl alcohol for a few minutes.
Rationale: Doing so lubricates the O-ring and aids fitting the O-ring to
the isolation valve.
15. Fit the O-ring onto the isolation valve.

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 Cleaning the ion guide assembly

16. Fit the isolation valve onto the ion block assembly, so that it is in the
closed position.
17. Fit the ion block cover plate onto the ion block assembly, and then use
the combined 2.5-mm Allen wrench and cone extraction tool to tighten
the 2 captive securing screws on the ion block’s cover plate.
18. Hold the sampling cone assembly so that the cone gas nozzle handle is
oriented horizontally and at the top.
19. Slide the sampling cone assembly into the ion block assembly.
20. Grasp the sampling cone assembly handle, and use it to rotate the
sampling cone assembly through 90 degrees.
21. Fit the ion block assembly to the source assembly (see page 125).

Cleaning the ion guide assembly

Clean the ion guide assembly if cleaning the ion block and isolation valve fails
to increase signal sensitivity.

Removing the ion block assembly and ion guide from the source
assembly
Required materials
• Chemical-resistant, powder-free gloves
• 3-mm Allen wrench
• O-ring removal kit

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source
components.

To remove the ion block assembly and ion guide:

1. Remove the source enclosure from the instrument (see page 90).

March 14, 2014, 715004387 Rev. B 137

4 Maintenance Procedures

2. Remove the ion block assembly from the PEEK ion block support (see
page 119).
3. Use the 3-mm Allen wrench to unscrew and remove the 4 screws
securing the PEEK ion block support to the adaptor housing, and
remove the ion block support.

Ion guide
assembly

Securing screws PEEK ion block Adaptor housing

support

Warning: To avoid spreading contamination, dispose of the

O-rings in accordance with local environmental regulations.
The O-rings can be contaminated with biohazards or toxic
materials.

4. If any of the O-rings show signs of deterioration or damage, dispose of

them in accordance with local environmental regulations.

138 March 14, 2014, 715004387 Rev. B

 Cleaning the ion guide assembly

Notice: To avoid damaging the ion guide assembly when removing

it from the source assembly, do not grasp the ion guide by its metal
lens plates. Instead, grasp the circuit boards on the top and bottom
of the device.

5. Carefully grasp the circuit boards on the top and bottom of the ion guide,
and remove the guide from the adaptor housing.

Source assembly

Ion guide circuit boards

TP03413

March 14, 2014, 715004387 Rev. B 139

4 Maintenance Procedures

Cleaning the ion guide assembly

Required materials
• Chemical-resistant, powder-free gloves.
• Glass-fiber pen.
• 500-mL measuring cylinder or appropriately sized glass vessel in which
to completely immerse the ion guide when cleaning. Use only glassware
not previously cleaned with surfactants.
• Length of small diameter PEEK or PTFE tubing appropriately sized for
suspending the ion guide in the glass vessel when cleaning.
• HPLC-grade (or better) methanol.
• Formic acid.
• Ultrasonic bath.
• Source of oil-free, inert gas (for example, nitrogen) for drying (air-drying
optional).
• HPLC-grade (or better) 1:1 methanol/water.
• Wash-bottle containing HPLC-grade (or better) 1:1 methanol/water.
• Large beaker.

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when handling the ion guide PCB assemblies,
and throughout this procedure.

Notice: To avoid damaging the ion guide assembly, use only

methanol and water as solvents. Do not use acetone, chlorinated
solvents, or acid.

To clean the ion guide assembly:

1. Bend a PEEK or PTFE tube into a hook shape.
2. Insert one end of the hook into one of the holes in the ion guide’s rear
circuit board carrier.

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 Cleaning the ion guide assembly

Notice: To avoid vibration-caused damage to the ion guide

assembly, ensure that the bottom of the assembly is not in contact
with the bottom of the glass vessel.

3. Use the hook to carefully suspend the ion guide assembly in the glass
vessel so that the bottom of the assembly does not touch the bottom of
the vessel.

Hook

Rear circuit board

carrier

TP03412

4. Add 1:1 methanol/water to the glass vessel until the ion guide assembly
is immersed completely.
5. Place the vessel in the ultrasonic bath for 30 minutes.

Notice: To avoid recontaminating the ion guide assembly, wear

clean, chemical-resistant, powder-free gloves for the rest of this
procedure.

6. Carefully remove the ion guide assembly from its vessel, and blow-dry it
using inert, oil-free gas.
7. Inspect the ion guide assembly for persisting contamination.
Requirement: If contamination is present, do as follows:
a. Use the wash bottle containing methanol to rinse the ion guide
assembly over the large beaker.
b. Blow-dry the ion guide assembly with inert, oil-free gas.

March 14, 2014, 715004387 Rev. B 141

4 Maintenance Procedures

Removing the differential aperture from the ion guide

Required material
Small, flat-blade screwdriver

Notice: To avoid a reduction in sensitivity, remove and clean the

differential aperture only when cleaning the ion guide assembly
fails to remove all visible contamination from the differential
aperture. Sensitivity can diminish if the differential aperture fails
to correctly align with the ion guide during refitting.

To remove the ion guide differential aperture:

1. Use the small, flat-blade screwdriver to remove the 3 slotted screws that
secure the differential aperture to the 3 supporting rods.

Differential
aperture

Slotted screws

Supporting rods

2. Remove the differential aperture from the ion guide.

142 March 14, 2014, 715004387 Rev. B

 Cleaning the ion guide assembly

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when handling the differential pumping
aperture, and throughout this procedure.

To clean the differential aperture:

1. Use the glass-fiber pen to remove gross contamination from the
differential aperture by gentle abrasion.
2. Using 1:1 methanol/water from the wash bottle, flush the differential
aperture.
Rationale: Doing so removes residual fibers displaced from the
glass-fiber pen.
3. Completely immerse the differential aperture in a glass vessel
containing 1:1 methanol/water.
Requirement: If the differential aperture is still contaminated after
using the glass-fiber pen, use 45:45:10 methanol/water/formic acid.
4. Place the vessel in the ultrasonic bath for 30 minutes.
5. If you used formic acid in the cleaning solution, rinse the differential
aperture by immersing it in a glass vessel containing water and then
place the vessel in the ultrasonic bath for 20 minutes.

Notice: To avoid recontaminating the differential aperture, wear

clean, chemical-resistant, powder-free gloves for the following
step.

6. Carefully remove the differential aperture from the vessel, and blow it
dry using inert, oil-free gas.

March 14, 2014, 715004387 Rev. B 143

4 Maintenance Procedures

Fitting the differential aperture to the ion guide assembly

Required materials
• Clean, chemical-resistant, powder-free gloves
• Small, flat-blade screwdriver

To fit the differential aperture onto the ion guide assembly:

1. Hold the differential aperture against the support rods so that the rods
align with the 3 holes in the differential aperture’s base.

Notice: To avoid a reduction in sensitivity, ensure that the

differential aperture aligns correctly with the ion guide during
refitting.

2. To ensure the differential aperture aligns correctly with the ion guide
assembly, sight along the central axis of the ion guide, from the ion entry
side, and confirm that the hole at the centre of the differential aperture
is concentric with lens plates of the ion guide.
3. Use the small flat-blade screwdriver to fit and tighten the 3 slotted
screws that secure the differential aperture to the support rods.
Requirement: While tightening the screws, ensure that the differential
aperture aligns correctly with the lens plates of the ion guide (see
step 2).

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 Cleaning the ion guide assembly

Fitting the ion guide assembly to the source assembly

Required material
Clean, chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Notice: To avoid damaging the ion guide assembly when fitting it

to the source assembly, avoid pushing on the metal ion guide lens
plates. Instead, handle the ion guide assembly using the circuit
boards on both sides of the assembly.

To fit the ion guide assembly to the source assembly:

1. Slide a short length of the ion guide assembly’s differential aperture end
into the adaptor housing, with the arrows on the front circuit board
carrier pointing upward.
2. Carefully slide the assembly fully into place.

Fitting the ion block support to the source

Required materials
• Chemical-resistant, powder-free gloves
• 3-mm Allen wrench
• New seals and O-rings

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

To fit the PEEK ion block support onto the source:

1. Ensure that the grooves for the PEEK ion block support O-rings are free
from dirt and debris.

March 14, 2014, 715004387 Rev. B 145

4 Maintenance Procedures

Tip: If contamination is present, use 1:1 methanol/water, applied to a

lint-free cloth, to carefully clean the grooves.
2. Fit the O-rings (new ones if you disposed of the old) to the PEEK ion
block support.
Tip: To fit an O-ring in its groove, start fitting the O-ring at the notch in
the groove, and then progressively work the ring into the groove, in
either direction from the notch.
3. Fit the PEEK ion block support onto the instrument’s housing.
4. Use the 3-mm Allen wrench to fit and tighten the 4 screws securing the
PEEK ion block support.
5. Fit the ion block assembly to the PEEK ion block support (see page 125).
6. Fit the source enclosure to the instrument (see page 92).

146 March 14, 2014, 715004387 Rev. B

 Replacing the ESI probe tip and gasket

Replacing the ESI probe tip and gasket

Replace the ESI probe tip if a blockage occurs in the internal metal sheathing
through which the stainless steel capillary passes or if the probe tip is
damaged.

Removing the ESI probe tip and gasket

Required materials
• Chemical-resistant, powder-free gloves
• 7-mm wrench
• 10-mm wrench

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid burn injuries, take great care while performing

this procedure; the probe and source can be hot.

Warning: To avoid puncture wounds, handle the probe with care;

the ESI probe tip is sharp.

To remove the ESI probe tip and gasket:

1. Remove the ESI probe from the source (see page 61).

March 14, 2014, 715004387 Rev. B 147

4 Maintenance Procedures

2. Use the 10-mm wrench to remove the probe tip.

10-mm wrench

Probe tip

Tip: If the probe tip is difficult to remove, use the 7-mm wrench in
conjunction with the 10-mm wrench.

7-mm wrench

10-mm wrench

Probe tip

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 Replacing the ESI probe tip and gasket

3. Remove the metal gasket from the probe tip.

Metal gasket

Warning: To avoid spreading contamination, dispose of the

probe tip and metal gasket in accordance with local
environmental regulations. They can be contaminated with
biohazards or toxic materials.

4. Dispose of the metal gasket in accordance with local environmental

regulations.
5. If the probe tip is damaged, dispose of it in accordance with local
environmental regulations.

March 14, 2014, 715004387 Rev. B 149

4 Maintenance Procedures

Fitting the ESI probe tip and gasket

Required materials
• Chemical-resistant, powder-free gloves
• 7-mm wrench
• New metal gasket

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid puncture wounds, handle the probe with care;

the ESI probe tip is sharp.

To fit the ESI probe tip and gasket:

1. Fit the new metal gasket into the probe tip.
2. Fit the probe tip (a new one if you disposed of the old) over the capillary,
and screw the tip onto the probe assembly.

Notice: To avoid gas leakage, fully tighten the probe tip.

3. Use the 7-mm wrench to tighten the probe tip.

4. Use the nebulizer adjuster knob to adjust the capillary so that it
protrudes by approximately 0.5 mm from the end of the probe.
5. Fit the ESI probe onto the source (see page 58).

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 Replacing the ESI probe sample capillary

Replacing the ESI probe sample capillary

Replace the stainless steel sample capillary in the ESI probe if it becomes
blocked and cannot be cleared, or if it becomes contaminated or damaged.

Removing the existing capillary

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
• 7-mm wrench
• 8-mm wrench
• 10-mm wrench
• Needle-nose pliers

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid burn injuries, take great care while performing

this procedure; the probe and source can be hot.

Warning: To avoid puncture wounds, handle the probe with care;

the ESI probe tip is sharp.

To remove the existing capillary:

1. Remove the probe from the source (see page 61).
2. Retrieve the combined 2.5-mm Allen wrench and cone extraction tool
from its storage location on the source adaptor housing.

March 14, 2014, 715004387 Rev. B 151

4 Maintenance Procedures

3. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the 3 screws retaining probe end-cover.

End-cover retaining screws

4. Remove the end cover and gasket from the probe assembly.

Nebulizer adjuster knob

Gasket

End cover

5. Unscrew and remove the nebulizer adjuster knob.

152 March 14, 2014, 715004387 Rev. B

 Replacing the ESI probe sample capillary

6. Use the 10-mm wrench to remove the probe tip.

10-mm wrench

Probe tip

Tip: If the probe tip is difficult to remove, use the 7-mm wrench in
conjunction with the 10-mm wrench.

7-mm wrench

10-mm wrench

Probe tip

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4 Maintenance Procedures

7. Remove the metal gasket from the probe tip.

Metal gasket

8. Remove the PEEK union/UNF coupling assembly and capillary from the
probe.
PEEK union/UNF
coupling assembly

Capillary

9. Unscrew and remove the knurled collar from the UNF coupling.
PEEK union UNF coupling

Locknut Knurled collar

Conductive sleeve

10. Remove the knurled collar and conductive sleeve from the capillary.
11. Use the 7-mm wrench to loosen the locknut.
Tip: Use the 8-mm wrench to steady the UNF coupling when loosening
the locknut.

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 Replacing the ESI probe sample capillary

12. Unscrew the finger-tight PEEK union from the UNF coupling.
Ferrule

PTFE liner sleeve

13. Remove the ferrule and PTFE liner sleeve from the capillary.
14. Remove the capillary from the UNF coupling.

Warning: To avoid spreading contamination, dispose of the

capillary, PTFE liner sleeve, and ferrule in accordance with
local environmental regulations. The used components can
be contaminated with biohazardous or toxic materials.

15. Dispose of the capillary, PTFE liner sleeve, and ferrule in accordance
with local environmental regulations.

Installing the new capillary

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
• 10-mm wrench
• Needle-nose pliers
• LC pump
• HPLC-grade (or better) 1:1 acetonitrile/water
• Ferrule
• Seal
• PTFE liner tubing
• Conductive sleeve
• Red PEEK tubing
• Sharp knife or PEEK tubing cutter
• Metal gasket for the probe tip
• Safety goggles

March 14, 2014, 715004387 Rev. B 155

4 Maintenance Procedures

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid puncture wounds, handle the probe with care;

the ESI probe tip is sharp.

To install the new capillary:

1. Use the sharp knife or PEEK tubing cutter to cut a piece of red PEEK
tubing approximately 60 cm (24 inches) long.
Requirement: Cut the tubing squarely (that is, perpendicular to its
horizontal axis).
2. Insert one end of the red PEEK tubing in the probe inlet connector, and
screw the connector into the PEEK union so that it is finger-tight.
Rationale: Doing so ensures a minimum dead volume when fitting the
capillary.
Probe inlet connector

TP02671

PEEK tubing

3. Fit the UNF coupling to the new capillary.

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 Replacing the ESI probe sample capillary

4. Use the needle-nose pliers to slide a new liner sleeve and ferrule onto
the capillary.
5. Insert the capillary in the PEEK union, and ensure that it is fully
seated.
6. Screw the UNF coupling into the PEEK union, finger-tight only.
7. Gently tug on the capillary, testing to ensure that it stays in place.
8. Use the 7-mm wrench to tighten the locknut against the PEEK union
until the union can no longer be twisted.
9. Slide a new conductive sleeve and the knurled collar over the capillary.
10. Tighten the knurled collar onto the UNF coupling.

Warning: To avoid eye injury from high-pressure liquid jet spray,

wear safety goggles when performing the leak test.

11. Perform a leak test by attaching the free end of the PEEK tubing to an
LC pump and pumping 50:50 acetonitrile/water through it at 1 mL/min.
• If leakage occurs, disassemble and remake the connection, and then
repeat the leak test.
• If the backpressure on the LC pump is high, replace the capillary,
and repeat the leak test.
12. When no leakage occurs and the backpressure on the LC pump is
normal, disconnect the PEEK tubing from the LC pump.
13. Remove the probe inlet connector and PEEK tubing from the PEEK
union.
14. Carefully thread the capillary through the probe assembly.

March 14, 2014, 715004387 Rev. B 157

4 Maintenance Procedures

15. Carefully push the PEEK union/UNF coupling assembly and capillary
into the probe assembly so that the locating pin on the UNF coupling is
fully engaged in the locating slot at the head of the probe assembly.
UNF coupling locating pin

Probe assembly locating slot

16. Fit the nebulizer adjuster knob onto the PEEK union/UNF coupling
assembly.
17. Finger-tighten the nebulizer adjuster knob onto the probe assembly.
18. Fit the gasket and end cover onto the probe assembly.
19. Use the combined 2.5-mm Allen wrench and cone extraction tool to fit
and tighten the 3 screws retaining the probe end-cover.
20. Return the combined 2.5-mm Allen wrench and cone extraction tool to
its storage location on the source adaptor housing.
21. Fit the metal gasket onto the probe tip.
22. Fit the probe tip over the capillary, and screw the tip onto the probe
assembly.

Notice: To avoid gas leakage, fully tighten the probe tip.

23. Use the 10-mm wrench to tighten the probe tip.

24. Use the nebulizer adjuster knob to adjust the capillary so that it
protrudes by approximately 0.5 mm from the end of the probe tip.
25. Fit the ESI probe into the source (see also page 58).

158 March 14, 2014, 715004387 Rev. B

 Cleaning the IonSABRE II probe tip

Cleaning the IonSABRE II probe tip

Clean the IonSABRE II probe tip when you detect buffer buildup on the probe
tip or when the signal intensity weakens. See the mass spectrometer’s online
Help for further details.

To clean the IonSABRE II probe tip:

1. On the Instrument Console system tree, click Xevo TQD > Manual
optimization.

2. On the Manual Optimization page, click to stop the liquid flow.

3. Click Gas to start the desolvation gas.

4. Set Desolvation Gas to 650 L/hr.
5. Set IonSABRE II probe Temp to 650 °C.

6. Click Operate .
7. Wait 10 minutes.
Rationale: The high IonSABRE II probe heater temperature removes
any chemical contamination from the probe tip.

8. Click Standby .

March 14, 2014, 715004387 Rev. B 159

4 Maintenance Procedures

Replacing the IonSABRE II probe sample capillary

Replace the stainless steel sample capillary in the IonSABRE II probe if it
becomes blocked and you cannot clear it, or if it becomes contaminated or
damaged.

Removing the existing capillary

Required materials
• Chemical-resistant, powder-free gloves
• 7-mm wrench
• Combined 2.5-mm Allen wrench and cone extraction tool

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid burn injuries, take great care while performing

this procedure; the probe and source can be hot.

To remove the existing capillary:

1. Remove the probe from the source (see page 65).
2. Retrieve the combined 2.5-mm Allen wrench and cone extraction tool
from its storage location on the source adaptor housing.
3. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the 3 screws retaining the probe end-cover.

End-cover retaining screws

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 Replacing the IonSABRE II probe sample capillary

4. Remove the end cover and gasket.

Nebulizer adjuster knob

Gasket

End-cover

5. Unscrew and remove the nebulizer adjuster knob.

6. Remove the PEEK union/UNF coupling assembly and capillary from the
probe.
Tip: The PEEK union used with the IonSABRE II probe is notched on
one of its flats, a feature that distinguishes it from the PEEK union used
with the ESI probe (see “Replacing the ESI probe sample capillary” on
page 151).
PEEK union/UNF coupling assembly

Notch Capillary

Locknut

March 14, 2014, 715004387 Rev. B 161

4 Maintenance Procedures

7. Use the 7-mm wrench to loosen the locknut.

8. Unscrew the finger-tight PEEK union from the UNF coupling.
Ferrule

9. Remove the ferrule from the capillary.

10. Remove the capillary from the UNF coupling.

Warning: To avoid spreading contamination, dispose of the

capillary and ferrule in accordance with local environmental
regulations. The used components can be contaminated with
biohazardous or toxic materials.

11. Dispose of the capillary and ferrule in accordance with local

environmental regulations.

Installing the new capillary

Required materials
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• 7-mm wrench
• Combined 2.5-mm Allen wrench and cone extraction tool
• Red PEEK tubing
• LC pump
• HPLC-grade (or better) 1:1 acetonitrile/water
• Capillary
• Sharp knife or PEEK tubing cutter
• Safety goggles

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 Replacing the IonSABRE II probe sample capillary

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

To install the new capillary:

1. Use the sharp knife or PEEK tubing cutter to cut a piece of red PEEK
tubing approximately 60 cm (24 inches) long.
Requirement: Cut the tubing squarely (that is, perpendicular to its
horizontal axis).
2. Insert one end of the red PEEK tubing in the probe inlet connector, and
screw the connector, finger-tight, into the PEEK union.
Rationale: Doing so ensures a minimum dead volume when fitting the
capillary.
Probe inlet connector

TP02671

PEEK tubing

3. Fit the UNF coupling to the new capillary.

Requirement: Use a UNF coupling with no grooves, which is appropriate
for the IonSABRE II probe.

March 14, 2014, 715004387 Rev. B 163

4 Maintenance Procedures

4. Use the needle-nose pliers to slide a new ferrule onto the capillary.
5. Insert the capillary in the PEEK union, and ensure that it is fully
seated.
6. Screw the UNF coupling into the PEEK union, finger-tight only.
7. Gently tug on the capillary, testing to ensure that it stays in place.
8. Use the 7-mm wrench to tighten the locknut against the PEEK union.

Warning: To avoid eye injury from high-pressure liquid jet spray,

wear safety goggles when performing the leak test.

9. Perform a leak test by attaching the free end of the PEEK tubing to an
LC pump and pumping 50:50 acetonitrile/water through it at 1 mL/min.
• If leakage occurs, disassemble and remake the connection, and
repeat the leak test.
• If the backpressure on the LC pump is high, replace the capillary,
and repeat the leak test.
10. When no leakage occurs and the backpressure on the LC pump is
normal, disconnect the PEEK tubing from the LC pump.
11. Remove the probe inlet connector and PEEK tubing from the PEEK
union.
12. Remove the probe heater (see step 2 on page 167).
13. Fit the PEEK union/UNF coupling assembly to the nebulizer adjuster
knob.
14. Carefully thread the capillary through the probe assembly.

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 Replacing the IonSABRE II probe sample capillary

15. Carefully push the PEEK union/UNF coupling assembly and capillary
into the probe assembly so that the locating pin on the UNF coupling is
fully engaged in the locating slot at the head of the probe assembly.
Probe assembly locating slot

UNF coupling locating pin

16. Fit the nebulizer adjuster knob to the PEEK union/UNF coupling
assembly.
17. Finger-tighten the nebulizer adjuster knob onto the probe assembly.
18. Fit the probe gasket and end-cover to the probe assembly.
19. Use the combined 2.5-mm Allen wrench and cone extraction tool to fit
and tighten the 3 screws retaining the probe end-cover.
20. Return the combined 2.5-mm Allen wrench and cone extraction tool in
its storage location on the source adaptor housing.

Notice:
• To avoid damaging the probe heater, take great care to grip the
heater so as not to damage its electrical wiring.
• To avoid damaging the probe heater’s electrical connections,
capillary sleeve, or capillary, take great care when fitting the
heater over the capillary sleeve.

21. Fit the probe heater (see step 1 through step 3 on page 169).
22. Fit the probe to the instrument (see page 63).

23. In the Instrument Console, click API to start the probe and
desolvation gas flows.

March 14, 2014, 715004387 Rev. B 165

4 Maintenance Procedures

Cleaning or replacing the corona pin

Required materials
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• HPLC-grade (or better) methanol
• Lint-free tissue
• Lapping film
• Corona pin

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid burn injuries, take great care while performing

this procedure; the probe and source can be hot.

Warning: To avoid electric shock, ensure that the instrument is in

Standby mode before commencing this procedure.

Warning: To avoid puncture wounds, handle the corona pin with

care; the corona pin tip is sharp.

To clean or replace the corona pin:

1. Remove the corona pin from the source (see page 95) and inspect the pin
for damage.
2. Replace the corona pin if it is damaged; otherwise clean its tip with the
lapping film and a methanol-saturated tissue.
3. Install the corona pin in the source (see page 93).

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 Replacing the IonSABRE II probe heater

Replacing the IonSABRE II probe heater

Replace the IonSABRE II probe heater if it fails to heat the probe.

Removing the IonSABRE II probe heater

Required material
Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

To remove the IonSABRE II probe heater:

1. Remove the probe from the source (see page 65).

Probe heater

March 14, 2014, 715004387 Rev. B 167

4 Maintenance Procedures

Notice: To avoid damaging the probe heater’s electrical

connections, do not twist the heater when removing it from the
probe assembly.

2. Gripping the probe heater as shown, carefully pull it off the probe
assembly.

Probe heater

Warning: To avoid spreading contamination, dispose of the

probe heater in accordance with local environmental
regulations. The probe heater can be contaminated with
biohazardous or toxic materials.

3. Dispose of the probe heater in accordance with local environmental

regulations.

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 Replacing the IonSABRE II probe heater

Fitting the new IonSABRE II probe heater

Required materials
• Chemical-resistant, powder-free gloves
• IonSABRE II probe heater

Notice: To avoid damaging the probe heater’s electrical

connections, capillary sleeve, or capillary, take great care when
fitting the heater over the capillary sleeve.

To fit the new IonSABRE II probe heater:

1. Use the probe adjuster knob to adjust the capillary so that it protrudes
approximately 0.5 mm from the end of the probe.

Probe heater connections

0.5 mm

Capillary Capillary sleeve

2. Carefully slide the probe heater over the capillary sleeve on the probe
assembly.

Notice: To avoid damaging the probe heater’s electrical

connections, do not twist the heater when fitting it to the probe
assembly.

3. Fit the probe heater to the probe assembly, ensuring that the heater is
fully seated on the probe assembly.
4. Fit the probe to the instrument (see page 63).

5. In the Instrument Console, click API to start the desolvation gas.

March 14, 2014, 715004387 Rev. B 169

4 Maintenance Procedures

Replacing the ion block source heater

Replace the ion block source heater if it fails to heat when the instrument is
pumped down (evacuated).

Required materials
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• Combined 2.5-mm Allen wrench and cone extraction tool
• Ion block source heater

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the ion block assembly.

To replace the ion block source heater:

1. Remove the ion block assembly from the instrument (see page 119).
2. Ensure that the isolation valve is closed.

Isolation valve handle

in closed position

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 Replacing the ion block source heater

3. Use the combined 2.5-mm Allen wrench and cone extraction tool to
loosen the 2 captive screws securing the ion block cover plate.
Ion block cover plate securing screw

Ion block cover plate

4. Remove the ion block cover plate.

March 14, 2014, 715004387 Rev. B 171

4 Maintenance Procedures

5. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the 2 screws securing the heater wires to the PEEK terminal
block.

Heater cartridge wire

securing screws

PEEK terminal block

6. Use the needle-nose pliers to carefully swing the ring terminal tags out
of the terminal block.
Ring terminal tag

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 Replacing the ion block source heater

7. Use the needle-nose pliers to gently grasp the heat-shrink tubing on the
heater cartridge assembly and slide the assembly out of the ion block.
Heat-shrink tubing

Heater cartridge assembly

8. Dispose of the heater cartridge assembly.

Notice: To avoid damaging the heater cartridge assembly wires,

do not bend or twist them when fitting the assembly to the ion
block.

9. Use the needle-nose pliers to gently grasp the heat-shrink tubing on the
new heater cartridge assembly and slide the assembly into the ion block.

Notice: To avoid a short circuit to the ion block cover, ensure that
the 2 heater cartridge ring tags are pushed fully down on the
PEEK block terminals.

10. Use the needle-nose pliers to position the 2 heater wire ring tags fully
down on the PEEK block terminals.
11. Use the combined 2.5-mm Allen wrench and cone extraction tool to fit
and tighten the 2 screws securing the heater wires to the PEEK
terminal block.
12. Fit the ion block cover plate onto the ion block assembly, and then use
the combined 2.5-mm Allen wrench and cone extraction tool to tighten
the 2 captive screws securing ion block cover plate.
13. Fit the ion block assembly onto the instrument (see page 137).

March 14, 2014, 715004387 Rev. B 173

4 Maintenance Procedures

Replacing the source assembly seals

Warning: To avoid solvent vapors of biohazards and toxic

materials leaking into the laboratory atmosphere, replace the
seals listed below exactly as described in this section.

Warning: To avoid solvent vapors of biohazards and toxic

materials leaking into the laboratory atmosphere, replace the
seals listed below at intervals not exceeding one year.

To avoid solvent vapors of biohazards and toxic materials leaking into the
laboratory atmosphere, replace the following seals at intervals not exceeding
one year:
• Probe adjuster assembly probe seal
• Probe adjuster assembly nebulization gas seal
• Source enclosure seal
• Nebulizer gas seal
• Desolvation gas seal

Removing the probe adjuster assembly probe and source

enclosure seals
Required materials
• Chemical-resistant, powder-free gloves
• O-ring removal kit

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 Replacing the source assembly seals

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

To remove the probe adjuster assembly probe and source enclosure seals:
1. Remove the source enclosure from the instrument (see page 90).
2. Use the O-ring removal kit to carefully remove the following seals from
the probe adjuster assembly (see page 99):
• Probe seal
• Nebulizer gas seal

Probe adjuster nebulizer gas seal

Probe adjuster assembly probe seal

3. Use the O-ring removal kit to carefully remove the following seals from
the source enclosure:
• Source enclosure seal
• Nebulizer gas seal
• Desolvation gas seal

March 14, 2014, 715004387 Rev. B 175

4 Maintenance Procedures

Nebulizer gas seal

Desolvation gas seal

Source enclosure seal

TP03164

Warning: To avoid spreading contamination, dispose of the

seals in accordance with local environmental regulations.
The seals can be contaminated with biohazardous or toxic
materials.

4. Dispose of all the seals in accordance with local environmental

regulations.

Fitting the new source enclosure and probe adjuster assembly

seals
Required materials
• Chemical-resistant, powder-free gloves
• Wash bottle containing HPLC-grade (or better) 1:1 methanol/water
• New seals

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 Replacing the source assembly seals

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

To fit the new source enclosure and probe adjuster assembly probe seals:
1. Ensure that all the grooves for seals are free from dirt and debris.
Tip: If contamination is present, use 1:1 methanol/water, applied to a
lint-free cloth, to carefully clean the grooves.
Requirement: Ensure that the tails of the source enclosure seals are
correctly located in the groove when fitting them to the source enclosure.
2. Fit the new source enclosure seal to the source enclosure.
Tip: Start by feeding the seal into the groove at the bottom right-hand
corner, and then working around the seal in a counterclockwise
direction.
3. Fit the following new seals to the source enclosure:
• Nebulizer gas seal
• Desolvation gas seal
Requirement: These seals have a special cross-section; fit them in the
groove as shown.
Seal

Groove

4. Fit the following new seals to the probe adjuster assembly:

• Probe seal
• Nebulizer gas seal
5. Refit the source enclosure to the instrument (see page 92).

March 14, 2014, 715004387 Rev. B 177

4 Maintenance Procedures

Replacing the air filter

You must replace the air filter annually.

Required material
New air filter

To replace the air filter:

1. Lift the instrument’s visor so that the source probe is fully exposed.
2. Fully open the source enclosure.
3. Disconnect the probe cable from the high-voltage connector, and leave
the cable in a position that does not obstruct the air filter grill.

Air filter grill

Probe cable

TP03403

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 Replacing the air filter

4. Open the air filter grill by pulling the tab at the top of the grill toward
you.

Air filter grill tab Air filter grill

TP03405

5. Remove and dispose of the old filter.

6. Place the new filter flat on the inside part of the grill, with its edges
beneath the metal lip.
7. Close the air filter grill.
8. Connect the probe cable to the high-voltage connector.
9. Close the source enclosure.
10. Lower the instrument’s visor.

March 14, 2014, 715004387 Rev. B 179

4 Maintenance Procedures

Replacing the roughing pump oil

Change the roughing pump oil annually.
Note: This procedure is not required for an Edwards oil-free roughing pump.

Required materials
• Chemical-resistant, powder-free gloves
• 8-mm Allen wrench
• Flat-blade screwdriver
• Container to catch used oil
• Funnel
• 1-L container of Anderol vacuum oil, type GS 495

To replace the roughing pump oil:

1. Gas ballast the roughing pump for 1 hour, to reduce the oil’s viscosity
(see page 102).
Rationale: Gas ballasting helps to circulate and mix the oil through the
pump before draining.
2. Vent and shut down the instrument (see the mass spectrometer’s online
Help for details).
3. Allow the roughing pump to cool.

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when adding or replacing oil. The
roughing pump oil can be irritant, or contaminated with
biohazardous or toxic analyte accumulated during normal
operation.

Warning: To avoid burn injuries, take great care while

working with the roughing pump; it can be hot.

4. Place the container for used oil under the pump’s drain plug.

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 Replacing the roughing pump oil

5. Use the 8-mm Allen wrench to remove the oil filler plug.

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

6. Use the 8-mm Allen wrench to remove the oil drain plug.
7. Tip the pump toward the drain plug aperture and allow the oil to drain
completely into the container.

Warning: To avoid spreading contamination, dispose of the

roughing pump oil in accordance with local environmental
regulations. It can be an irritant, or it can be contaminated
with biohazards or toxic materials.

8. Dispose of the roughing pump oil in accordance with local environmental

regulations.
9. Ensure that the O-ring on the oil drain plug is clean and properly
seated.

Notice: To avoid oil leakage when fitting the oil drain plug to the
roughing pump, observe these precautions:
• Ensure that the plug is not cross-threaded.
• Ensure that the O-ring is not pinched.
• Do not overtighten the plug.

10. Use the 8-mm Allen wrench to fit and tighten the roughing pump’s oil
drain plug.

March 14, 2014, 715004387 Rev. B 181

4 Maintenance Procedures

Tip: When the oil drain plug is tightened, the plug seals by means of an
O-ring. Compression is controlled by the O-ring groove depth in the plug.
Increased torque does not improve the plug seal; it only makes the plug
difficult to remove later.
Requirement: To maintain pump performance, use only Anderol
vacuum oil, type GS 495.
11. Using the funnel, pour all the oil from the 1-L container into the oil filler
aperture.
12. Wait a few minutes, and then recheck the oil level.
13. Ensure that the O-ring on the oil filler plug is clean and properly seated.

Notice: To avoid oil leakage when fitting the oil filler plug to the
roughing pump, observe these precautions:
• Ensure that the plug is not cross-threaded.
• Ensure that the O-ring is not pinched.
• Do not overtighten the plug.

14. Use the 8-mm Allen wrench to refit the oil filler plug.
15. Gas ballast the roughing pump (see page 102).
Tip: After you add oil to the pump, the following situations can occur:
• The oil level drops slightly during the first month of operation.
• The oil changes color (darkens) over time.
• After the pump runs for 12 to 48 hours, a few drops of oil often
appear near the filler plug. Excess oil around the lip of the filler plug
runs down and drips off the pump when the pump reaches operating
temperature.
• When the pump begins to run at normal operating temperature, the
spilled oil produces a slight odor.

182 March 14, 2014, 715004387 Rev. B

 Replacing the roughing pump’s oil demister element

Replacing the roughing pump’s oil demister element

Replace the roughing pump’s oil demister element annually.
Note: This procedure is not required for an Edwards oil-free roughing
pump.

Required materials
• Chemical-resistant, powder-free gloves
• 6-mm Allen wrench
• 10-mm wrench

To remove the roughing pump oil demister element:

1. Vent and shut down the instrument (see the mass spectrometer’s online
Help for details).
2. Allow the roughing pump to cool.

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when adding or replacing oil. The
roughing pump oil can be irritant, or contaminated with
biohazardous or toxic analyte accumulated during normal
operation.

Warning: To avoid burn injuries, take great care while

working with the roughing pump; it can be hot.

3. Use the 6-mm Allen wrench to remove the 4 bolts securing the exhaust
flange to the roughing pump.

Securing bolt

Exhaust flange

March 14, 2014, 715004387 Rev. B 183

4 Maintenance Procedures

4. Carefully remove the exhaust flange and oil demister element from the
roughing pump.

Oil demister element

TP02693

5. Use the 10-mm wrench to remove the nut that secures the oil demister
element to the exhaust flange.

Spring
Securing nut

TP02686

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 Replacing the roughing pump’s oil demister element

6. Holding the oil demister element slightly elevated to prevent the loss of
the spring, remove the exhaust flange from the oil demister element.

TP02692

7. Remove the spring from the oil demister element.

Warning: To avoid spreading contamination, dispose of the

oil demister element in accordance with local environmental
regulations. It can be contaminated with irritant oil, or with
biohazardous or toxic materials.

8. Dispose of the oil demister element in accordance with local

environmental regulations.

March 14, 2014, 715004387 Rev. B 185

4 Maintenance Procedures

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when replacing the oil demister element. The
pump oil can be irritant, or contaminated with biohazardous or
toxic analyte accumulated during normal operation.

To fit the new oil demister element:

1. Fit the spring onto the new oil demister element.

TP02682

2. Holding the oil demister element slightly elevated to prevent the loss of
the spring, fit the exhaust flange to the oil demister element.

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 Replacing the roughing pump’s oil demister element

Notice: To avoid damage, do not overtighten the nut that secures

the oil demister element onto the exhaust flange; ensure that only
approximately 1 mm of thread is exposed beyond the nut when it
is tightened.

3. Use the 10-mm wrench to fit and tighten the nut that secures the oil
demister element to the exhaust flange.

1 mm exposed thread
after tightening

TP02686

4. Ensure that the inscription “TOP” is at the top of the oil demister
element, and, using both hands, carefully fit the oil demister element
and exhaust flange to the roughing pump.
Requirement: The bolts securing the source exhaust flange to the
roughing pump must each be sequentially and incrementally tightened
until they are all fully tight.
5. Use the 6-mm Allen wrench to fit the 4 bolts securing the exhaust flange
to the roughing pump.

March 14, 2014, 715004387 Rev. B 187

4 Maintenance Procedures

APPI/APCI source—changing the UV lamp bulb

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
®
• Small Phillips (cross-head) screwdriver
• 20-cm (8-inch) length of 4-mm nylon tube

Warning: To avoid personal contamination with biohazards or

toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the source components.

Warning: To avoid electric shock, ensure that the instrument is

suitably prepared before commencing this procedure.

To change the UV lamp bulb:

1. Prepare the instrument for working on the source (see page 88).

Warning: To avoid burn injuries, take great care while working

with the probe, source, and lamp bulb; these components can be
hot.

Warning: To avoid eye injury from UV radiation, ensure that the

APPI lamp is extinguished before carrying out this procedure.

2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.
3. Retrieve the combined 2.5-mm Allen wrench and cone extraction tool
from its storage location on the source adaptor housing.
4. Hook the short-end of the Allen wrench through the ring on the back of
the bulb extraction plug, and tug to remove it.

188 March 14, 2014, 715004387 Rev. B

 APPI/APCI source—cleaning the lamp window

Notice: To avoid breaking the bulb, do not use a screwdriver to

push the bulb forward in the lamp drive assembly.

5. Insert the length of 4-mm nylon tube through the back of the lamp drive
assembly, and push the bulb forward.
6. Remove the bulb from the lamp drive assembly.
7. Insert the new bulb into the lamp drive assembly.
Tip: The lamp glass is magnesium fluoride. Avoid touching it because
dirt or other contaminants on the window significantly reduce UV
transmission.
8. Refit the lamp bulb access plug.
9. Return the combined 2.5-mm Allen wrench and cone extraction tool to
its storage location on the source adaptor housing.
10. Close the source enclosure.
11. Slide closed the instrument’s source interface door.

APPI/APCI source—cleaning the lamp window

The transmission of the high-energy photons responsible for APPI relies on
the cleanliness of the magnesium fluoride lamp window. Clean the window to
keep the surface clear of contamination and thus avoid reduced sensitivity.

Required materials
• Chemical-resistant, powder-free gloves
• Lint-free cloth
• Methanol or isopropyl alcohol

Warning: To avoid burn injuries, take great care while working

with the probe, source, and lamp bulb; these components can be
hot.

Warning: To avoid eye injury from UV radiation, ensure that the

APPI lamp is extinguished before carrying out this procedure.

March 14, 2014, 715004387 Rev. B 189

4 Maintenance Procedures

To clean the lamp window:

1. Prepare the instrument for working on the source (see page 88).
2. Pull the source enclosure release (located at the bottom, right-hand side)
outward, and swing open the enclosure.
3. Use methanol or isopropyl alcohol, applied to the lint-free cloth, to
carefully clean the lamp window.
4. Close the source enclosure.
5. Slide closed the instrument’s source interface door.

190 March 14, 2014, 715004387 Rev. B

 APPI/APCI source—replacing the APPI lamp drive seals

APPI/APCI source—replacing the APPI lamp drive seals

Warning: To avoid leaking of biohazardous or toxic materials,

ensure the integrity of the source exhaust system. The APPI lamp
drive assembly O-rings listed below must be renewed at intervals
not exceeding 1 year, exactly as described in this section.

The following APPI lamp drive assembly O-rings must be renewed at

intervals of no greater than 1 year:
• UV lamp bulb sealing O-ring
• Mounting shaft O-rings
• UV lamp mounting flange O-ring
Tip: An automatic pressure test runs each time you close the source enclosure
and when the instrument starts.

Removing the APPI lamp drive assembly seals

Required materials
• Chemical-resistant, powder-free gloves
• Combined 2.5-mm Allen wrench and cone extraction tool
• 3-mm Allen wrench
• Small Phillips (cross-head) screwdriver
®
• Small Pozidriv screwdriver
• 20-cm (8-inch) length of 4-mm nylon tube
• O-ring removal kit
• The mounting-shaft insertion tool
• A suitable, clear working area on a bench
• A soft cloth or mat to protect the source enclosure window as it is laid on
its face

March 14, 2014, 715004387 Rev. B 191

4 Maintenance Procedures

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the probe and source
components.

Warning: To avoid electric shock, ensure that the instrument

is in Standby mode before commencing this procedure.

To remove the APPI lamp drive assembly seals:

1. Remove the IonSABRE II probe and combined APPI/APCI source
enclosure (see page 72).

Notice: To avoid damaging the UV bulb, handle it with care; the

bulb is fragile.

2. Remove the UV bulb from the lamp drive assembly, and store it in a
secure place (see page 188).
3. Retrieve the combined 2.5-mm Allen wrench and cone extraction tool
from its storage location on the source adaptor housing.
4. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the 2 lamp-drive cover screws (located above the bulb-extraction
plug-aperture).

Notice: To avoid damaging the source enclosure’s glass window,

take care to lay it on a smooth surface. Laying it face-first on a
hard object or other protrusion can break the glass window.

5. Clear an area, lay out the soft cloth or mat, and lay the source enclosure
on its face.

192 March 14, 2014, 715004387 Rev. B

 APPI/APCI source—replacing the APPI lamp drive seals

6. Use the Phillips (cross-head) screwdriver to remove the 2 source

enclosure, release-handle screws, and remove the handle.

Source enclosure
cover screws

Lamp-drive cover
screws

Release handle

TP03204

7. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the remaining 2 lamp-drive cover screws, which were hidden by
the release handle.
8. Slide the cover off the lamp drive.
9. Use the 3-mm Allen wrench to remove the 4 source enclosure cover
screws.
10. Ease the source enclosure cover over the lamp drive assembly.
11. Use the combined 2.5-mm Allen wrench and cone extraction tool to
unscrew the 4 mounting-flange screws.

March 14, 2014, 715004387 Rev. B 193

4 Maintenance Procedures

Tip: Take care not to drop the screws inside the lower cover.

Lamp mounting flange

Mounting-flange screw

TP03205

12. Slide the lamp assembly, shaft, and flange out of the APPI source
enclosure.
Tip: The cables remain attached to the shaft, which you fully withdraw
and lay on the bench beside the source enclosure.

PEEK insulator

Repeller electrode
Electrode screw

Insulator retaining screw

194 March 14, 2014, 715004387 Rev. B

 APPI/APCI source—replacing the APPI lamp drive seals

13. Using the small Phillips screwdriver, remove the electrode screw and
repeller electrode.
14. Use the combined 2.5-mm Allen wrench and cone extraction tool to
remove the two insulator screws.
15. Remove the PEEK insulator from the end of the mounting shaft.
16. Slide the shaft mounting flange off the shaft, and note the correct
orientation, for its reassembly.
17. Use the O-ring removal kit to carefully remove the O-ring sealing the
lamp bulb from inside the bulb holder (see page 99).

Lamp bulb sealing O-ring

18. Use the O-ring removal kit to carefully remove the two O-rings from
inside the lamp mounting flange.

Mounting shaft O-rings

Lamp mounting flange

March 14, 2014, 715004387 Rev. B 195

4 Maintenance Procedures

19. Use the O-ring removal kit to carefully remove the shaft mounting
flange O-ring from the APPI source enclosure side.

Lamp mounting flange O-ring

Warning: To avoid spreading contamination, dispose of the

O-rings in accordance with local environmental regulations.
They can be contaminated with irritant oil, or with
biohazardous or toxic materials.

20. Dispose of the O-rings in accordance with local environmental

regulations.

196 March 14, 2014, 715004387 Rev. B

 APPI/APCI source—replacing the APPI lamp drive seals

Fitting the new APPI lamp drive assembly O-rings

Required materials
• Chemical-resistant, powder-free gloves
• 3-mm Allen wrench
• Small Phillips (cross-head) screwdriver
• Small Pozidriv screwdriver
• 1:1 methanol/water
• Lint-free cloth

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the lamp drive
assembly.

Notice: To avoid causing damage, take care when fitting the

APPI lamp drive assembly O-rings. Small nicks, tears, dirt,
and dust can compromise their performance, leading to rapid
deterioration in the assembly’s operation.

To fit the new APPI lamp drive assembly O-rings:

1. Ensure that all the grooves for the O-rings are free from dirt and hair.
Tips:
• If contamination is present, use 1:1 methanol/water, applied to the
lint-free cloth, to carefully clean the grooves.
• For the asymmetric O-ring seals, first seat the O-ring in the small
radius at the bottom of the groove. Then use a suitable tool, one with
a circular cross-section, to “roll” the remainder of the O-ring into the
groove.
2. Fit the lamp bulb sealing O-ring in the lamp aperture.
3. Fit the two new O-rings inside the lamp mounting flange.
4. Fit the new lamp mounting flange O-ring to the APPI source enclosure
side.

March 14, 2014, 715004387 Rev. B 197

4 Maintenance Procedures

5. Fit the mounting shaft insertion tool to the mounting shaft.

Mounting shaft
insertion tool

Notice: To prevent damage to the mounting shaft O-rings, fit the

mounting shaft insertion tool to the mounting shaft before fitting
the shaft to the lamp mounting flange.

6. Slide the lamp mounting flange onto the shaft, taking care to align it
correctly.
7. Reinsert the shaft through the side of the source enclosure, and fit the
lamp mounting flange to the APPI source enclosure side.
Tip: Tighten the securing screws sequentially and by small increments
until they are all fully tight. Doing so ensures that the lamp mounting
flange is uniformly seated on the APPI source enclosure side plate.
8. Use the combined 2.5-mm Allen wrench and cone extraction tool to
tighten the four mounting-flange securing screws.
9. Remove the mounting shaft insertion tool from the mounting shaft.
10. Fit the PEEK insulator to the end of the mounting shaft.
11. Use the combined 2.5-mm Allen wrench and cone extraction tool to fit
and tighten the two insulator retaining screws.
12. Fit the repeller electrode to the PEEK insulator.

198 March 14, 2014, 715004387 Rev. B

 Replacing the instrument’s fuses

13. Use the small Phillips screwdriver to fit and tighten the repeller
electrode retaining screw.
14. Insert the UV bulb into the lamp drive assembly and push it fully home.
15. Fully retract the lamp mounting shaft from the source enclosure.
16. Refit the lamp-assembly collar-cover, and secure it on its base with the 4
screws.
17. Refit the lamp assembly cover, and secure it on its base (2 screws) and
above the bulb extraction aperture (2 screws).
18. Refit the source enclosure release handle, and secure it with the 2
screws.
Refit and reconnect the source enclosure to the machine, refit the corona
pin and probe. Refer to page 71 for instructions.

Replacing the instrument’s fuses

Warning: To avoid electrical shock, disconnect the mass spectrometer

from the power supply before replacing fuses. The mass spectrometer
has two fuses, and uses double pole/neutral fusing circuitry. Thus
circuits can remain live even when one fuse has blown.

Warning: To protect against fire, replace fuses with those of the type
and rating specified below, and printed on panels adjacent to the
instrument’s fuse covers.

If one or both of the mass spectrometer’s fuses blow, the instrument will shut
down immediately. If this occurs, disconnect the power cord from the rear
panel, and replace the fuses, located at the bottom left-hand-side of the
instrument’s rear panel, with T10AH250V, 6x32mm fuses.

March 14, 2014, 715004387 Rev. B 199

4 Maintenance Procedures

200 March 14, 2014, 715004387 Rev. B

A Safety Advisories

Waters instruments and devices display hazard symbols that alert you
to the hidden dangers associated with a product’s operation and
maintenance. The symbols also appear in product manuals where they
accompany statements describing the hazards and advising how to avoid
them. This appendix presents the safety symbols and statements that
apply to all of the products that Waters offers.

Contents:

Topic Page
Warning symbols.............................................................................. 202
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

March 14, 2014, 715004387 Rev. B 201

A Safety Advisories

Warning symbols
Warning symbols alert you to the risk of death, injury or seriously adverse
physiological reactions associated with an instrument’s use or misuse. Heed
all warnings when you install, repair, or operate any Waters instrument or
device. Waters accepts no liability in cases of injury or property damage
resulting from the failure of individuals to comply with any safety precaution
when installing, repairing, or operating any of its instruments or devices.
The following symbols warn of risks that can arise when you operate or
maintain a Waters instrument or device, or a component of an instrument or
device. When one of these symbols appear in a manual’s narrative sections or
procedures, an accompanying statement identifies the applicable risk and
explains how to avoid it.

Warning: (General risk of danger. When this symbol appears on an

instrument, consult the instrument’s user documentation for important
safety-related information before you use the instrument.)

Warning: (Risk of burn injury from contacting hot surfaces.)

Warning: (Risk of electric shock.)

Warning: (Risk of fire.)

Warning: (Risk of sharp-point puncture injury.)

Warning: (Risk of hand crush injury.)

Warning: (Risk of injury caused by moving machinery.)

Warning: (Risk of exposure to ultraviolet radiation.)

Warning: (Risk of contacting corrosive substances.)

Warning: (Risk of exposure to a toxic substance.)

Warning: (Risk of personal exposure to laser radiation.)

202 March 14, 2014, 715004387 Rev. B

 Warning symbols

Warning: (Risk of exposure to biological agents that can pose a serious

health threat.)

Warning: (Risk of tipping.)

Warning: (Risk of explosion.)

Warning: (Risk of eye injury.)

Specific warnings
The following warnings (both symbols and text) can appear in the user
manuals of particular instruments and devices and on labels affixed to them
or their component parts.

Burst warning
This warning applies to Waters instruments and devices fitted with
nonmetallic tubing.

Warning: To avoid injury from bursting, nonmetallic tubing, heed these

precautions when working in the vicinity of such tubing when it is
pressurized:
• Wear eye protection.
• Extinguish all nearby flames.
• Do not use tubing that is, or has been, stressed or kinked.
• Do not expose nonmetallic tubing to incompatible compounds like
tetrahydrofuran (THF) and nitric or sulfuric acids.
• Be aware that some compounds, like methylene chloride and
dimethyl sulfoxide, can cause nonmetallic tubing to swell,
significantly reducing the pressure at which the tubing can rupture.

March 14, 2014, 715004387 Rev. B 203

A Safety Advisories

Mass spectrometer shock hazard

The following warning applies to all Waters mass spectrometers.

Warning: To avoid electric shock, do not remove the mass spectrometer’s

protective panels. The components they cover are not user-serviceable.

The following warning applies to certain mass spectrometers when they are in
Operate mode.

Warning: To avoid nonlethal electric shock, ensure the mass

spectrometer is in Standby mode before you touch any of its external
surfaces that are marked with this high voltage warning symbol.

Mass spectrometer flammable solvents warning

This warning applies to mass spectrometers performing an analysis that
requires the use of flammable solvents.

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.

204 March 14, 2014, 715004387 Rev. B

 Warning symbols

Biohazard warning
The following warning applies to Waters instruments and devices that can
process material containing biohazards, which are substances that contain
biological agents capable of producing harmful effects in humans.

Warning: To avoid infection with potentially infectious, human-sourced

products, inactivated microorganisms, and other biological materials,
assume that all biological fluids that you handle are infectious.
Specific precautions appear in the latest edition of the US National
Institutes of Health (NIH) publication, Biosafety in Microbiological and
Biomedical Laboratories (BMBL).
Observe Good Laboratory Practice (GLP) at all times, particularly when
working with hazardous materials, and consult your the biohazard
safety representative for your organization regarding the proper use and
handling of infectious substances.

Biohazard and chemical hazard warning

This warning applies to Waters instruments and devices that can process
biohazards, corrosive materials, or toxic materials.

Warning: To avoid personal contamination with biohazards,

toxic materials, or corrosive materials, you must understand
the hazards associated with their handling.
Guidelines prescribing the proper use and handling of such
materials appear in the latest edition of the National
Research Council's publication, Prudent Practices in the
Laboratory: Handling and Disposal of Chemicals.
Observe Good Laboratory Practice (GLP) at all times,
particularly when working with hazardous materials, and
consult the safety representative for your organization
regarding its protocols for handling such materials.

March 14, 2014, 715004387 Rev. B 205

A Safety Advisories

Notices
Notices appear where an instrument or device can be subject to use or misuse
that can damage it or compromise a sample’s integrity. The exclamation point
symbol and its associated statement alert you to such risk.

Notice: To avoid damaging the instrument’s case, do not clean it with

abrasives or solvents.

Bottles Prohibited symbol

The Bottles Prohibited symbol alerts you to the risk of instrument damage
caused by solvent spills.

Prohibited: To avoid equipment damage caused by spilled solvent, do

not place reservoir bottles directly atop an instrument or device or on its
front ledge. Instead, place bottles in the bottle tray, which serves as a
secondary containment in the event of spills.

206 March 14, 2014, 715004387 Rev. B

 Warnings that apply to all Waters instruments and devices

Warnings that apply to all Waters instruments and

devices
When operating this device, follow standard quality-control procedures and
the equipment guidelines in this section.
Attention: Changes or modifications to this unit not expressly approved by the
party responsible for compliance could void the user’s authority to operate the
equipment.

Important: Toute modification sur cette unité n’ayant pas été expressément
approuvée par l’autorité responsable de la conformité à la réglementation peut
annuler le droit de l’utilisateur à exploiter l’équipement.

Achtung: Jedwede Änderungen oder Modifikationen an dem Gerät ohne die

ausdrückliche Genehmigung der für die ordnungsgemäße Funktionstüchtigkeit
verantwortlichen Personen kann zum Entzug der Bedienungsbefugnis des
Systems führen.

Avvertenza: qualsiasi modifica o alterazione apportata a questa unità e non

espressamente autorizzata dai responsabili per la conformità fa decadere il
diritto all'utilizzo dell'apparecchiatura da parte dell'utente.

Atencion: cualquier cambio o modificación efectuado en esta unidad que no

haya sido expresamente aprobado por la parte responsable del cumplimiento
puede anular la autorización del usuario para utilizar el equipo.

注意：未經有關法規認證部門允許對本設備進行的改變或修改,可能會使使用者喪失操作該設
備的權利。

注意：未经有关法规认证部门明确允许对本设备进行的改变或改装，可能会使使用者丧失操
作该设备的合法性。

주의: 규정 준수를 책임지는 당사자의 명백한 승인 없이 이 장치를 개조 또는 변경할 경우,

이 장치를 운용할 수 있는 사용자 권한의 효력을 상실할 수 있습니다.

注意：規制機関から明確な承認を受けずに本装置の変更や改造を行うと、本装置のユー
ザーとしての承認が無効になる可能性があります。

March 14, 2014, 715004387 Rev. B 207

A Safety Advisories

Warning: Use caution when working with any polymer tubing under pressure:
• Always wear eye protection when near pressurized polymer tubing.
• Extinguish all nearby flames.
• Do not use tubing that has been severely stressed or kinked.
• Do not use nonmetallic tubing with tetrahydrofuran (THF) or concentrated
nitric or sulfuric acids.
• Be aware that methylene chloride and dimethyl sulfoxide cause nonmetallic
tubing to swell, which greatly reduces the rupture pressure of the tubing.
Attention: Manipulez les tubes en polymère sous pression avec precaution:
• Portez systématiquement des lunettes de protection lorsque vous vous
trouvez à proximité de tubes en polymère pressurisés.
• Eteignez toute flamme se trouvant à proximité de l’instrument.
• Evitez d'utiliser des tubes sévèrement déformés ou endommagés.
• Evitez d'utiliser des tubes non métalliques avec du tétrahydrofurane (THF)
ou de l'acide sulfurique ou nitrique concentré.
• Sachez que le chlorure de méthylène et le diméthylesulfoxyde entraînent le
gonflement des tuyaux non métalliques, ce qui réduit considérablement leur
pression de rupture.
Vorsicht: Bei der Arbeit mit Polymerschläuchen unter Druck ist besondere
Vorsicht angebracht:
• In der Nähe von unter Druck stehenden Polymerschläuchen stets
Schutzbrille tragen.
• Alle offenen Flammen in der Nähe löschen.
• Keine Schläuche verwenden, die stark geknickt oder überbeansprucht sind.
• Nichtmetallische Schläuche nicht für Tetrahydrofuran (THF) oder
konzentrierte Salpeter- oder Schwefelsäure verwenden.
• Durch Methylenchlorid und Dimethylsulfoxid können nichtmetallische
Schläuche quellen; dadurch wird der Berstdruck des Schlauches erheblich
reduziert.

208 March 14, 2014, 715004387 Rev. B

 Warnings that apply to all Waters instruments and devices

Attenzione: fare attenzione quando si utilizzano tubi in materiale polimerico

sotto pressione:
• Indossare sempre occhiali da lavoro protettivi nei pressi di tubi di polimero
pressurizzati.
• Spegnere tutte le fiamme vive nell'ambiente circostante.
• Non utilizzare tubi eccessivamente logorati o piegati.
• Non utilizzare tubi non metallici con tetraidrofurano (THF) o acido solforico
o nitrico concentrati.
• Tenere presente che il cloruro di metilene e il dimetilsolfossido provocano
rigonfiamenti nei tubi non metallici, riducendo notevolmente la pressione di
rottura dei tubi stessi.
Advertencia: se recomienda precaución cuando se trabaje con tubos de polímero
sometidos a presión:
• El usuario deberá protegerse siempre los ojos cuando trabaje cerca de tubos
de polímero sometidos a presión.
• Si hubiera alguna llama las proximidades.
• No se debe trabajar con tubos que se hayan doblado o sometido a altas
presiones.
• Es necesario utilizar tubos de metal cuando se trabaje con tetrahidrofurano
(THF) o ácidos nítrico o sulfúrico concentrados.
• Hay que tener en cuenta que el cloruro de metileno y el sulfóxido de dimetilo
dilatan los tubos no metálicos, lo que reduce la presión de ruptura de los
tubos.

警告：當在有壓力的情況下使用聚合物管線時，小心注意以下幾點。
• 當接近有壓力的聚合物管線時一定要戴防護眼鏡。
• 熄滅附近所有的火焰。
• 不要使用已經被壓癟或嚴重彎曲管線。
• 不要在非金屬管線中使用四氫呋喃或濃硝酸或濃硫酸。
• 要了解使用二氯甲烷及二甲基亞楓會導致非金屬管線膨脹，大大降低管線的耐壓能力。

March 14, 2014, 715004387 Rev. B 209

A Safety Advisories

警告：当有压力的情况下使用管线时，小心注意以下几点：
• 当接近有压力的聚合物管线时一定要戴防护眼镜。
• 熄灭附近所有的火焰。
• 不要使用已经被压瘪或严重弯曲的管线。
• 不要在非金属管线中使用四氢呋喃或浓硝酸或浓硫酸。
• 要了解使用二氯甲烷及二甲基亚枫会导致非金属管线膨胀，大大降低管线的耐压能力。

경고: 가압 폴리머 튜브로 작업할 경우에는 주의하십시오.

• 가압 폴리머 튜브 근처에서는 항상 보호 안경을 착용하십시오.
• 근처의 화기를 모두 끄십시오.
• 심하게 변형되거나 꼬인 튜브는 사용하지 마십시오.
• 비금속(Nonmetallic) 튜브를 테트라히드로푸란(Tetrahydrofuran: THF) 또는
농축 질산 또는 황산과 함께 사용하지 마십시오.
• 염화 메틸렌(Methylene chloride) 및 디메틸술폭시드(Dimethyl sulfoxide)는
비금속 튜브를 부풀려 튜브의 파열 압력을 크게 감소시킬 수 있으므로 유의하십시오.

警告：圧力のかかったポリマーチューブを扱うときは、注意してください。
• 加圧されたポリマーチューブの付近では、必ず保護メガネを着用してください。
• 近くにある火を消してください。
• 著しく変形した、または折れ曲がったチューブは使用しないでください。
• 非金属チューブには、テトラヒドロフラン(THF)や高濃度の硝酸または硫酸などを流
さないでください。
• 塩化メチレンやジメチルスルホキシドは、非金属チューブの膨張を引き起こす場合が
あり、その場合、チューブは極めて低い圧力で破裂します。

210 March 14, 2014, 715004387 Rev. B

 Warnings that apply to all Waters instruments and devices

Warning: The user shall be made aware that if the equipment is used in a
manner not specified by the manufacturer, the protection provided by the
equipment may be impaired.

Attention: L’utilisateur doit être informé que si le matériel est utilisé d’une
façon non spécifiée par le fabricant, la protection assurée par le matériel risque
d’être défectueuses.

Vorsicht: Der Benutzer wird darauf aufmerksam gemacht, dass bei

unsachgemäßer Verwenddung des Gerätes die eingebauten
Sicherheitseinrichtungen unter Umständen nicht ordnungsgemäß
funktionieren.

Attenzione: si rende noto all'utente che l'eventuale utilizzo

dell'apparecchiatura secondo modalità non previste dal produttore può
compromettere la protezione offerta dall'apparecchiatura.

Advertencia: el usuario deberá saber que si el equipo se utiliza de forma

distinta a la especificada por el fabricante, las medidas de protección del equipo
podrían ser insuficientes.

警告：使用者必須非常清楚如果設備不是按照製造廠商指定的方式使用，那麼該設備所提供
的保護將被消弱。

警告：使用者必须非常清楚如果设备不是按照制造厂商指定的方式使用，那么该设备所提供
的保护将被削弱。

경고: 제조업체가 명시하지 않은 방식으로 장비를 사용할 경우 장비가 제공하는 보호 수단이

제대로 작동하지 않을 수 있다는 점을 사용자에게 반드시 인식시켜야 합니다.

警告： ユーザーは、製造元により指定されていない方法で機器を使用すると、機器が提供
している保証が無効になる可能性があることに注意して下さい。

March 14, 2014, 715004387 Rev. B 211

A Safety Advisories

Warnings that address the replacing of fuses

The following warnings pertain to instruments equipped with
user-replaceable fuses.

If the fuse types and ratings appear on the instrument:

Warning: To protect against fire, replace fuses with those of the type
and rating printed on panels adjacent to instrument fuse covers.
Attention: pour éviter tout risque d'incendie, remplacez toujours les
fusibles par d'autres du type et de la puissance indiqués sur le panneau
à proximité du couvercle de la boite à fusible de l'instrument.
Vorsicht: Zum Schutz gegen Feuer die Sicherungen nur mit
Sicherungen ersetzen, deren Typ und Nennwert auf den Tafeln neben
den Sicherungsabdeckungen des Geräts gedruckt sind.
Attenzione: per garantire protezione contro gli incendi, sostituire i
fusibili con altri dello stesso tipo aventi le caratteristiche indicate sui
pannelli adiacenti alla copertura fusibili dello strumento.
Advertencia: Para evitar incendios, sustituir los fusibles por aquellos
del tipo y características impresos en los paneles adyacentes a las
cubiertas de los fusibles del instrumento.
警告 ：為了避免火災，更換保險絲時，請使用與儀器保險絲蓋旁面板上所印刷之相同
類型與規格的保險絲。

警告：为了避免火灾，应更换与仪器保险丝盖旁边面板上印刷的类型和规格相同的
保险丝。

경고: 화재의 위험을 막으려면 기기 퓨즈 커버에 가까운 패널에 인쇄된 것과 동일한

타입 및 정격의 제품으로 퓨즈를 교체하십시오.

警告：火災予防のために、ヒューズ交換では機器ヒューズカバー脇のパネルに記
載されているタイプおよび定格のヒューズをご使用ください。

212 March 14, 2014, 715004387 Rev. B

 Warnings that address the replacing of fuses

If the fuse types and ratings do not appear on the instrument:

Warning: To protect against fire, replace fuses with those of the type
and rating indicated in the “Replacing fuses” section of the Maintenance
Procedures chapter.
Attention: pour éviter tout risque d'incendie, remplacez toujours les
fusibles par d'autres du type et de la puissance indiqués dans la
rubrique "Remplacement des fusibles" du chapitre traitant des
procédures de maintenance.
Vorsicht: Zum Schutz gegen Feuer die Sicherungen nur mit
Sicherungen ersetzen, deren Typ und Nennwert im Abschnitt
"Sicherungen ersetzen" des Kapitels "Wartungsverfahren" angegeben
sind.
Attenzione: per garantire protezione contro gli incendi, sostituire i
fusibili con altri dello stesso tipo aventi le caratteristiche indicate nel
paragrafo "Sostituzione dei fusibili" del capitolo "Procedure di
manutenzione".
Advertencia: Para evitar incendios, sustituir los fusibles por aquellos
del tipo y características indicados en la sección "Sustituir fusibles".

警告 ：為了避免火災，更換保險絲時，應使用「維護步驟」章節中「更換保險絲」所指
定之相同類型與規格的保險絲。

警告：为了避免火灾，应更换 “ 维护步骤 ” 一章的 “ 更换保险丝 ” 一节中介绍的相同类

型和规格的保险丝。

경고: 화재의 위험을 막으려면 유지관리 절차 단원의 “퓨즈 교체” 절에 설명된 것과

동일한 타입 및 정격의 제품으로 퓨즈를 교체하십시오.

警告： 火災予防のために、ヒューズ交換ではメンテナンス項目の「ヒューズの交換」
に記載されているタイプおよび定格のヒューズをご使用ください。

March 14, 2014, 715004387 Rev. B 213

A Safety Advisories

Electrical and handling symbols

Electrical symbols
The following electrical symbols and their associated statements can appear
in instrument manuals and on an instrument’s front or rear panels.

Electrical power on

Electrical power off

Standby

Direct current

Alternating current

Protective conductor terminal

Frame, or chassis, terminal

Fuse

214 March 14, 2014, 715004387 Rev. B

 Electrical and handling symbols

Handling symbols
The following handling symbols and their associated statements can appear
on labels affixed to the packaging in which instruments, devices, and
component parts are shipped.

Keep upright!

Keep dry!

Fragile!

Use no hooks!

March 14, 2014, 715004387 Rev. B 215

A Safety Advisories

216 March 14, 2014, 715004387 Rev. B

B External Connections

Warning: To avoid skeletal or muscle injury associated with lifting

heavy objects, use suitable machinery and the supplied harness to
lift the mass spectrometer.

Notice: To avoid damaging the mass spectrometer, observe the

following precautions:
• Contact Waters Technical Service before moving it.
• If you must transport the instrument, or remove it from service,
contact Waters Technical Service for recommended cleaning,
flushing, and packaging procedures.
See page 87.

Contents:

Topic Page
External wiring and vacuum connections ...................................... 218
Connecting the oil-filled roughing pump ........................................ 219
Connecting the Edwards oil-free roughing pump .......................... 224
Connecting to the nitrogen gas supply ........................................... 228
Connecting to the collision cell gas supply ..................................... 230
Connecting the nitrogen exhaust line............................................. 230
Connecting the liquid waste line..................................................... 233
Connecting the workstation ............................................................ 235
Connecting Ethernet cables............................................................. 236
I/O signal connectors........................................................................ 237
Connecting to the power supply ...................................................... 241

March 14, 2014, 715004387 Rev. B 217

B External Connections

External wiring and vacuum connections

Rear panel connections appear in the figure below. Note that the connectors
and controls not identified are for use by Waters engineers only.

Rear panel:

Event inputs
and outputs

Shielded
Ethernet

Roughing pump
control

Power
Source vacuum

Turbo vacuum
Collision cell
gas inlet
(argon)

Source vent Nitrogen inlet

218 March 14, 2014, 715004387 Rev. B

 Connecting the oil-filled roughing pump

Connecting the oil-filled roughing pump

Note: To connect the alternative dry roughing pump, see page 224.

Exhaust port flange

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

Gas ballast valve

Required materials:
• Chemical-resistant, powder-free gloves
• 7-mm nut driver
• 8-mm Allen wrench
• Sharp knife
• NW25 tee (included in the installation kit)
• NW25 center rings (included in the installation kit)
• NW25 clamps (included in the installation kit)
• 10-mm reducer fitting (included in the installation kit)
• 10-mm ID nylon tube (included in the installation kit)
• PVC exhaust tubing (included in the Waters Rough Pump Connect Kit)
• PVC hose clamps (included in the Waters Rough Pump Connect Kit)
• 1-inch ID vacuum hose (included in the Waters Rough Pump Connect
Kit)

March 14, 2014, 715004387 Rev. B 219

B External Connections

Bear in mind these requirements when connecting the roughing pump:

• The pump must be horizontal, or within one degree of horizontal.
• The ambient temperature of the area in which you place the pump must
range between 15 and 40 ºC.
• The pump must be oriented so that it permits easy access to the gas
ballast valve and oil-level sight glass.
For proper ventilation, the following minimum clearances must apply:
Left-side minimum clearance Back-side minimum clearance
is 15.24 cm (6 inches) is 15.24 cm (6 inches)

TP02689

Front-side minimum clearance Right-side minimum clearance

is 35.56 cm (14 inches) is 15.24 cm (6 inches)

To connect the roughing pump:

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the pump and its
connections.

1. Place the PTFE drip tray on the floor, within 5 feet of the instrument.

Warning: To avoid skeletal or muscle injury, at least two people

must lift the roughing pump.

2. Place the pump on the PTFE drip tray.

220 March 14, 2014, 715004387 Rev. B

 Connecting the oil-filled roughing pump

3. Attach the NW25 tee to the inlet of the pump using the NW25 center
ring, and then secure the connection with a clamp.

1-inch ID
vacuum hose

Clamps

Flange 10-mm nylon tube

NW25 tee

10-mm reducer
Pump inlet fitting

TP03414

4. Using the NW25 center rings and clamp, and the 7-mm nut driver,
attach the flanged end of a length of 1-inch ID vacuum hose to the top
port on the NW25 tee, and the 10-mm reducer fitting and a length of
10-mm ID nylon tubing to the middle (perpendicular) port on the tee.
5. Using 2 hose clamps, connect the opposite end of the length of 1-inch
vacuum hose in step 4 to the 1-inch OD straight vacuum port on the
instrument’s rear panel.
6. Connect the opposite end of the 10-mm nylon tube to the 10-mm source
vent port on the instrument’s rear panel.

Notice: To prevent serious damage to the instrument, two

separate exhaust systems are required: one for nitrogen, the other
for the roughing pump. Vent the exhausts to atmosphere through
separate lines. Oil mist can seriously damage the instrument if the
nitrogen exhaust line connects with the roughing pump exhaust
line. Your warranty does not cover damage caused by routing
exhaust lines incorrectly.

7. Using 1 hose clamp, connect a length of 12.7-mm clear PVC exhaust

tubing to the roughing pump exhaust port NW25 nozzle fitting.
Requirement: Use the sharp knife to cut the PVC exhaust tubing
squarely (that is, perpendicularly to its horizontal axis).

March 14, 2014, 715004387 Rev. B 221

B External Connections

8. Route the open end of the exhaust tubing to a suitable exhaust vent.
9. Check the oil level in the pump (see “Checking the roughing pump oil
level” on page 106, and, if needed, “Adding oil to the roughing pump” on
page 106).
Requirement: To ensure correct operation of the roughing pump, do not
operate it when its oil level is less than 30% of the MAX level.
10. Connect electric cables to the roughing pump (see page 223).

222 March 14, 2014, 715004387 Rev. B

 Connecting the oil-filled roughing pump

Connecting electric cables to the oil-filled roughing pump

Roughing pump electrical connections:

Detector rear panel

Roughing pump d.c. connector

Roughing pump main

power connector

To power source

To make the electrical connections to the roughing pump:

1. Connect the relay cable from the roughing pump d.c. connector to the
pump connector on the instrument’s rear panel.
2. Connect the roughing pump power cord to the main power source.

March 14, 2014, 715004387 Rev. B 223

B External Connections

Connecting the Edwards oil-free roughing pump

Warning: To avoid electric shock, shut down the mass spectrometer, and
disconnect all power cables from the oil-free roughing pump before
performing maintenance procedures on the pump. Always carry out
maintenance in accordance with the operator’s guide supplied with the
roughing pump.

The oil-free roughing pump is an alternative to the oil-filled roughing pump.

To connect the oil-filled roughing pump, see page 219.
Inlet flange

Exhaust port flange

TP03165

Required materials
• Chemical-resistant, powder-free gloves
• 7-mm nut driver
• Sharp knife
• NW25 tee (included in the installation kit)
• NW25 center rings (included in the installation kit)
• NW25 clamps (included in the installation kit)
• NW40 center rings (included in the installation kit)

224 March 14, 2014, 715004387 Rev. B

 Connecting the Edwards oil-free roughing pump

• NW40 clamps (included in the installation kit)

• NW25/NW40 adaptor (included in the installation kit)
• 10-mm reducer fitting (included in the installation kit)
• 10-mm ID nylon tube (included in installation kit)
• 12.7-mm clear PVC exhaust tubing (included in the Waters Rotary
Pump Kit)
• PVC hose clamps (included in the Waters Rotary Pump Kit)
• 1-inch ID vacuum hose (included in the Waters Rotary Pump Kit)
Bear in mind these requirements when connecting the roughing pump:
• The pump must be horizontal, or within one degree of horizontal.
• The ambient temperature of area in which you place the pump must
range between 15 and 40 ºC.
• The pump must be oriented so that it permits easy access to the gas
ballast valve and oil-level sight glass.
For proper ventilation, the following minimum clearances must apply:

Back-side minimum clearance Right-side minimum clearance

is 15.24 cm (6 inches) is 15.24 cm (6 inches)

TP03165
Left-side minimum clearance Front-side minimum clearance
is 15.24 cm (6 inches) is 35.56 cm (14 inches)

March 14, 2014, 715004387 Rev. B 225

B External Connections

To connect the oil-free roughing pump:

Warning: To avoid personal contamination with biohazards

or toxic materials, and to avoid spreading contamination to
uncontaminated surfaces, wear clean, chemical-resistant,
powder-free gloves when working with the pump and its
connections.

Warning: To avoid skeletal or muscle injury, at least two

people must lift the pump.

1. Place the pump on the floor, within 1.5 m (5 feet) of the instrument.
2. Attach the NW25/NW40 adaptor to the roughing pump inlet flange
using an NW40 center ring, and then secure the connection with an
NW40 clamp, using the 7-mm nut driver to install the clamp.
3. Attach the NW25 tee to the NW25/NW40 adaptor using an NW25 center
ring, and then secure the connection with an NW25 clamp, using the
7-mm nut driver to install the clamp.
4. Using the NW25 center rings and clamp, and the 7-mm nut driver,
attach the flanged end of a length of 1-inch ID vacuum hose to the top
port on the NW25 tee, and the 10-mm reducer fitting and a length of
10-mm ID nylon tubing to the middle (perpendicular) port on the tee.
5. Using 2 hose clamps, connect the opposite end of the length of 1-inch
vacuum hose in step 4 to the 1-inch OD straight vacuum port on the
instrument’s rear panel.
6. Connect the opposite end of the 10-mm nylon tube to the 10-mm source
vent port on the instrument’s rear panel.

Notice: To prevent serious damage to the instrument, two

separate exhaust systems are required: one for nitrogen, the other
for the roughing pump. Vent the exhausts to atmosphere through
separate lines. Oil mist can seriously damage the instrument if the
nitrogen exhaust line connects with the roughing pump exhaust
line. Your warranty does not cover damage caused by routing
exhaust lines incorrectly.

7. Using 1 hose clamp, connect a length of 12.7-mm clear PVC exhaust

tubing to the roughing pump exhaust port NW25 nozzle fitting.

226 March 14, 2014, 715004387 Rev. B

 Connecting the Edwards oil-free roughing pump

Requirement: Use the sharp knife to cut the PVC exhaust tubing
squarely (that is, perpendicularly to its horizontal axis).
8. Route the open end of the exhaust tubing to a suitable exhaust vent.
9. Connect electric cables to the roughing pump (see page 227).

Connecting electric cables to the Edwards oil-free roughing pump

Roughing pump connections:

Roughing pump
d.c. connector

Roughing pump
connector

TP03165

To power source Roughing pump main

power connector

To connect cables:
1. Connect the relay cable from the roughing pump’s d.c. connector to the
pump connector on the mass spectrometer’s rear panel.
2. Connect the roughing pump power cord to the main power source.

March 14, 2014, 715004387 Rev. B 227

B External Connections

Connecting to the nitrogen gas supply

Required materials
• Chemical-resistant, powder-free gloves
• Sharp knife
• Wrench
• 6-mm PTFE tubing (included in the Waters Rough Pump Connect Kit)
• Nitrogen regulator

To connect the nitrogen gas supply:

1. Use the sharp knife to cut a 3.8-cm to 5.0-cm (1.5-inch to 2-inch) length
of 6-mm PTFE tubing.
Requirement: Cut the tubing squarely (that is, perpendicularly to its
horizontal axis).
2. Connect one end of the 6-mm tubing to one end of the nitrogen supply
in-line filter.
3. Connect the remaining length of the 6-mm PTFE tubing to the other end
of the filter.
4. Connect the free end of the short piece of 6-mm PTFE tubing to the
nitrogen inlet port on the rear of the instrument.

228 March 14, 2014, 715004387 Rev. B

 Connecting to the nitrogen gas supply

Gas and exhaust connections:

Source vacuum

Turbo vacuum
Collision cell
gas inlet
(Argon)

Source vent Nitrogen inlet

5. Attach the nitrogen regulator to the nitrogen supply.

6. Install the 6-mm stud into the regulator outlet.

7. Connect the free end of the long piece of 6-mm PTFE tubing to the 6-mm
stud.

March 14, 2014, 715004387 Rev. B 229

B External Connections

Connecting to the collision cell gas supply

Required materials
• Chemical-resistant, powder-free gloves
• Wrench
®
• 1/8-inch Swagelok nut and ferrule
• 1/8-inch stainless steel tube (supplied with the instrument)

To connect the collision cell gas supply:

1. Use the 1/8-inch Swagelok nut and ferrule to connect the 1/8-inch
stainless steel tube to the collision cell gas inlet on the rear of the
instrument (see the figure on page 229).
2. Use the wrench to tighten the 1/8-inch Swagelok nut.
3. Connect the free end of the tube to the collision gas supply.

Connecting the nitrogen exhaust line

Required materials
• Chemical-resistant, powder-free gloves
• Sharp knife
• 10-mm and 12-mm PTFE tubing (included in the Waters Rough Pump
Connect Kit)
®
• snoop (or equivalent) leak detector liquid

230 March 14, 2014, 715004387 Rev. B

 Connecting the nitrogen exhaust line

To connect the nitrogen exhaust line:

Warning: To avoid exposure to biohazards or toxic LC solvents

carried in the nitrogen exhaust, ensure that the nitrogen exhaust
is vented via the nitrogen exhaust trap bottle and laboratory
exhaust system. The laboratory exhaust system must provide a
minimum vacuum of 0.20 kPa (2 mbar, 0.03 psi) below
atmospheric pressure (negative pressure).

Warning: To avoid personal contamination with biologically

hazardous, or toxic materials, and to avoid spreading
contamination to uncontaminated surfaces, wear clean,
chemical-resistant, powder-free gloves when working with the
exhaust connections.

Warning: To avoid the buildup of hazardous gases, do not place the

nitrogen exhaust trap bottle in an enclosed cabinet.

Notice: To prevent serious damage to the instrument, two

separate exhaust systems are required: one for nitrogen, the other
for the roughing pump. Vent the exhausts to atmosphere through
separate exhaust lines. Oil mist can seriously damage the
instrument if the nitrogen exhaust line connects with the roughing
pump exhaust line. Your warranty does not cover damage caused
by routing exhaust lines incorrectly.

1. Locate the exhaust trap bottle in an accessible area below the

instrument (see the figure on page 232).
2. Cut a length of 12-mm tubing long enough to connect the instrument to
the exhaust trap bottle.
Requirement: Cut the tubing squarely (that is, perpendicularly to its
horizontal axis).
3. Connect one end of the tubing to the exhaust port on the rear panel and
the other end to one of two ports on the exhaust trap bottle.
4. Cut a length of 10-mm tubing long enough to connect the exhaust trap
bottle to the exhaust vent.
5. Insert one end of the tubing into the remaining port on the exhaust trap
bottle and route the other end to the exhaust vent.

March 14, 2014, 715004387 Rev. B 231

B External Connections

Warning: To prevent leaks in the source exhaust system,

confirm the integrity of the system by performing the
following leak test. Leaks can result in the release of
biohazardous or toxic materials.

Notice: To avoid damage to the instrument, use snoop (or its

equivalent) leak detector liquid only for the purpose
described in the following step. Do not use it on any other
part of the instrument.

6. Use snoop (or equivalent) leak detector liquid to ensure that there are no
leaks at the instrument exhaust and laboratory exhaust system line
connections.

Exhaust trap bottle:

From instrument
waste (12-mm)
To laboratory
exhaust (12-mm)

Valve control
cable (from
instrument)

232 March 14, 2014, 715004387 Rev. B

 Connecting the liquid waste line

Connecting the liquid waste line

Required material
Chemical-resistant, powder-free gloves

To connect the liquid waste line:

Warning: To prevent personal contamination with biohazards or

toxic materials, always wear chemical-resistant, powder-free
gloves while performing this procedure. The waste line and
connection can be contaminated.

1. Place a suitable waste container below the instrument.

Notice: To avoid distorting the drip tray or causing the drain cup
to leak, restrain the drain cup when attaching or removing the
waste line.

2. Slide a drain line over the barbed fitting of the drain (located at the
bottom of the instrument).

Drain cup

TP02684

Drain line Barbed fitting

March 14, 2014, 715004387 Rev. B 233

B External Connections

Warning: To prevent leakage of biohazards or toxic

materials, ensure that the,
• drain line does not crimp or bend, impeding flow to the
waste container.
• waste container is emptied before the lower end of the
drain tube is covered by waste solvent.

3. Route the waste line to the waste container. If necessary, shorten the
waste tube so that its end is above the surface of the waste solvent.

Positioning of drain tube:

Correct Incorrect
TP01807

234 March 14, 2014, 715004387 Rev. B

 Connecting the workstation

Connecting the workstation

Warning: 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.

Before connecting the workstation to the instrument, set up the workstation

according to its accompanying instructions. Locate the workstation within
5 meters (16 feet) of the instrument.
Requirement: Use shielded network cables with the instrument to reduce
susceptibility to radio and electrical frequency interference.

To connect the workstation:

1. Connect the monitor to the PC.
2. Connect one end of the shielded network cable to the appropriate port on
the rear panel of the instrument.
3. Connect the other end of the shielded network cable to the port labeled
Instrument LAN on the workstation rear panel.

To connect the instrument to the power source:

Requirement: Do not connect the instrument’s power supply cord until
you complete the installation procedures in the previous sections.
1. Select the correct power cord for your location.
2. Connect the female end of the power cord to the power port on the rear
panel of the instrument.

March 14, 2014, 715004387 Rev. B 235

B External Connections

Connecting Ethernet cables

Requirement: Use shielded Ethernet cables with the instrument to ensure
compliance with FCC, and other, limits.

To make Ethernet connections:

1. Connect one end of one shielded Ethernet cable to the network switch,
and then connect the other end to the Ethernet card on the
®
preconfigured ACQUITY workstation.
Tip: On preconfigured systems, the Ethernet card is identified as the
Instrument LAN card.
2. Connect one end of the other shielded Ethernet cable to the back of the
instrument, and then connect the other end to the network switch.

236 March 14, 2014, 715004387 Rev. B

 I/O signal connectors

I/O signal connectors

Warning: To avoid electric shock, separate all electrical connections to

the rear panel from hazardous voltages by double or reinforced
insulation. Circuits of this type are classified as safety extra low voltage
(SELV). Examples of circuits that are typically SELV include contact
closure inputs and outputs for autosamplers, and UV, RI, and
fluorescence detector signal outputs for LC/MS systems. The electrical
connections on the rear panel of this mass spectrometer are all SELV.
To avoid electric shock and damage to the instrument, do not apply more
than,
• ±30 V d.c. to the Analog (Out) connection.
• 30 V d.c. to the Stop Flow (Out), Inject Start (In), Switch 2 (Out),
Switch 3 (Out), and Switch 4 (Out) connections.

The instrument’s rear panel includes two removable connectors that hold the
screw terminals for I/O signals. These connectors are keyed so that they can
receive a signal cable inserted only one way.

I/O signal connectors:

Connector I Connector II

1 + Analog (Out) 1 + Inject Start (In)

2 − Analog (Out) 2 − Inject Start (In)
3 Ground 3 Ground
4 Not Used 4 + Event (In)
5 Not Used 5 − Event (In)
6 Stop Flow (Out) 6 + Switch 3 (Out)
7 Stop Flow (Out) 7 − Switch 3 (Out)
8 Ground 8 Ground
9 + Switch 2 (Out) 9 + Switch 4 (Out)
10 − Switch 2 (Out) 10 − Switch 4 (Out)

March 14, 2014, 715004387 Rev. B 237

B External Connections

Signal connections
Instrument analog-out/event-in connections:

Signal connections Description

Analog (Out) Used for analog chart output functionality. The
output voltage range is 0 to 1 V. The resolution of
the voltage output is 12 bits.
Stop Flow (Out) Used to stop the solvent flow if the nitrogen gas
supply fails. Maximum 30 V, 0.5 A, 10 W.
Inject Start (In) Signals the start of an injection. Maximum 30 V.
Event (In) Allows an external device to start data acquisition.
Maximum 30 V.
Switch 2 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.
Switch 3 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.
Switch 4 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.

Requirement: To meet the regulatory requirements of immunity from

external electrical disturbances, install connection covers over the signal
connectors.

To make signal connections:

1. Reference the signal connection location from the silk-screened label for
inject start or any other input/output connection you plan to use from
Connector I or II on the rear panel of each instrument.

238 March 14, 2014, 715004387 Rev. B

 I/O signal connectors

2. To make the signal connections, attach the positive and negative leads of
the signal cable to the connector.

Connector

Signal cable

TP02585

3. Slide the clamp (with the bend facing down) into the protective shield.
4. Insert the clamp and shield (with the bend facing down) into the
connection cover, and loosely tighten with one self-tapping screw.

Clamp

Connection cover

Shield
TP02586

March 14, 2014, 715004387 Rev. B 239

B External Connections

5. Insert the connector with the signal cable into the connection cover, and
position the clamp over the cable leads. Tighten the clamp into place
with the second self-tapping screw.

Cable leads

Clamp

6. Place the second connection cover over the first cover, and snap it into
place.

Signal connector

Connection cover

TP02588

240 March 14, 2014, 715004387 Rev. B

 Connecting to the power supply

Connecting to the power supply

The instrument requires a separate, grounded power source. The ground
connection in the electrical outlet must be common and connected near the
system.

To connect to the power source:

Recommendation: Use a line conditioner or an uninterruptible power supply
(UPS) for optimum long-term input voltage stability.

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 be replaced with one of adequate rating. For information regarding
what cord to use in other countries, contact your local Waters
distributor.

1. Connect the female end of the power cord to the receptacle on the rear
panel of the instrument.
2. Connect the male end of the instrument power cord to the 200 to 240 V
AC wall outlet prepared as described in the instrument Site Preparation
Guide.
3. Connect the power cord from the roughing pump relay box to the 200 to
240 V AC wall outlet prepared as described in the instrument Site
Preparation Guide.
Tip: The system software controls electrical power to the pump.

March 14, 2014, 715004387 Rev. B 241

B External Connections

242 March 14, 2014, 715004387 Rev. B

C Materials of Construction and
Compliant Solvents

Warning: To avoid injury caused by personal exposure to

biohazards or toxic materials, you must confirm the
integrity of the source exhaust system, and address any
safety issues raised by the contents of this Appendix.

Contents:

Topic Page
Preventing contamination ............................................................... 244
Items exposed to solvent.................................................................. 244
Solvents used to prepare mobile phases ......................................... 245

March 14, 2014, 715004387 Rev. B 243

C Materials of Construction and Compliant Solvents

Preventing contamination
For information on preventing contamination, refer to Controlling
Contamination in LC/MS Systems (part number 715001307). Visit
http://www.waters.com.

Items exposed to solvent

The items that appear in the following table can be exposed to solvent. You
must evaluate the safety issues if the solvents used in your application differ
from the solvents normally used with these items. See page 245 for details
about the most common ingredients used to prepare mobile phases.
Items exposed to solvent:

Item Material
Autotune reservoirs High-density polyethylene
Corona discharge pin mounting PEEK™
contact
Gas exhaust port Aluminum
Gas tubes Fluorinated ethylene propylene
Ion block Stainless steel
Ion block support PEEK
Isolation valve Gold-plated aluminum/bronze
O-rings ®
Viton or PTFE-encapsulated Viton
Probe adjuster bellows PTFE/Viton
Probe adjuster assembly Anodized aluminum, glass-filled
acetal, and stainless steel
Probe shaft PEEK
Push-in gas fittings Nickel/brass
Solvent waste/leak management Tygon tubing
Source enclosure Alochromed aluminum
Source enclosure view port Toughened plate glass

244 March 14, 2014, 715004387 Rev. B

 Solvents used to prepare mobile phases

Items exposed to solvent:

Item Material
Trap bottle Polypropylene
Trap bottle push-in fittings Nitrile butadiene rubber, stainless
steel, polybutylene terephthalate,
and polyoxymethylene

Solvents used to prepare mobile phases

These solvents are the most common ingredients used to prepare mobile
phases for reverse-phase LC/MS (API):
• Water
• Methanol
• Acetonitrile
• Formic acid (<0.1%)
• Acetic acid (<0.1%)
• Trifluoroacetic acid (<0.1%)
• Ammonium acetate (<10 mM)
• Ammonium formate (<10 mM)
These solvents are not expected to cause any problems with the materials
identified in the table on page 244.

March 14, 2014, 715004387 Rev. B 245

C Materials of Construction and Compliant Solvents

246 March 14, 2014, 715004387 Rev. B

D Plumbing the IntelliStart Fluidics
System
This appendix provides reference information for replacing the tubing in
the IntelliStart™ Fluidics system.

Warning: To avoid electric shock, do not use stainless steel

tubing or stainless steel “finger tight” screws to connect the
selector valve to the source probes; use the PEEK tubing and
natural (beige) colored PEEK “finger tight” screws specified
on page 250.

Warning: To avoid personal contamination, always wear

chemical-resistant, powder-free gloves while working on the
system.

Contents:

Topic Page
Preventing contamination ............................................................... 248
The selector valve............................................................................. 248
Plumbing schematic......................................................................... 249
Tubing and connection specifications ............................................. 250

March 14, 2014, 715004387 Rev. B 247

D Plumbing the IntelliStart Fluidics System

Preventing contamination
For information on preventing contamination, refer to Controlling
Contamination in LC/MS Systems (part number 715001307). You can find
this document on http://www.waters.com; click Services and Support >
Support.

The selector valve

The selector valve is located on the right-hand side of the instrument, behind
the visor. The letters etched on the front of the valve represent the
components to which the associated port is connected. Etched letters with a
light background indicate inputs, while letters with a dark, etched
background indicate outputs. The following table outlines the component to
which each port connects, and whether the port is a fluid input or output.

Selector valve connections:

Port Component Input/Output

P Infusion pump Both
A Sample reservoir A Input
B Sample reservoir B Input
R Rinse/wash bottle Input
W Waste bottle Output
LC LC column Input
S ®
Xevo TQD ion source Output

248 March 14, 2014, 715004387 Rev. B

 Plumbing schematic

Plumbing schematic
Selector valve

W
LC LC R Waste
column
S P
B
A

Xevo
Pump Wash
TQD probe

Reservoir A Reservoir B

Requirement: Ensure that the end of the tubing is fully submerged in the
solvent in the wash reservoir.

March 14, 2014, 715004387 Rev. B 249

D Plumbing the IntelliStart Fluidics System

Tubing and connection specifications

Notice: To avoid leaks, when plumbing the IntelliStart Fluidics system,

use only the tubes, nuts, and ferrules shown in the following tables, to
ensure over-pressure protection. The use of parts not recommended here
can result in leaks that the built-in leak sensor does not always detect.

When replacing tubing and connectors, refer to the tables below for the correct
specifications.
Replacement tubing specifications:

ID
Port Color Length (m)
(inches)
R, A, and B 0.020 Orange 0.65
W 0.005 Red 0.2
S 0.004 Black 0.4
LC 0.004 Black As required

Replacement nut and ferrule specifications:

Port Nut code Ferrule code

P P245 P200
LC F196 F192
S, W, R, A and B F130 -

Important: The tubing for the sample reservoirs (ports A and B) is not
user-serviceable. To replace the tubing, contact Waters to arrange an engineer
visit.

250 March 14, 2014, 715004387 Rev. B