Waters Xevo TQ-XS Mass Overview And Maintenance Manual

Waters Xevo TQ-XS Mass
Spectrometry System

Overview and Maintenance Guide

715004990
Revision A

Copyright © Waters Corporation 2016

All rights reserved

General information

Copyright notice

© 2016 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® is a registered trademark of Waters Corporation.

ACQUITY UPLC® is a registered trademark of Waters Corporation.

Alliance® is a registered trademark of Waters Corporation.

Connections INSIGHT® is a registered trademark of Waters Corporation.

DART® is a registered trademark of ionSense Inc.

ESCi® is a registered trademark of Waters Corporation.

EdwardsTM is a trademark of Edwards Limited.

GELoader® is a registered trademark of Eppendorf-Netheler-Hinz GmbH.

iKeyTM is a trademark of Waters Corporation.

ionKeyTM is a trademark of Waters Corporation.

IntelliStartTM is a trademark of Waters Corporation.

LDTDTM is a trademark of Phytronix Technologies Inc.

Leybold® is a registered trademark of Oerlikon Leybold Vacuum GmbH.

LockSprayTM is a trademark of Waters Corporation.

MassLynx® is a registered trademark of Waters Corporation.

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Nano LCTM is a trademark of Waters Corporation.

nanoACQUITY® is a registered trademark of Waters Corporation.

NanoFlowTM is a trademark of Waters Corporation.

nanoTile® is a registered trademark of Waters Corporation.

Oerlikon® is a registered trademark of OC Oerlikon Corporation AG.

OpenLynxTM is a trademark of Waters Corporation.

PEEKTM is a trademark of Victrex PLC.

PEEKsilTM is a trademark of SGE Analytical Science Pty Ltd.

RADARTM is a trademark of Waters Corporation.

ScanWaveTM is a trademark of Waters Corporation.

StepWaveTM is a trademark of Waters Corporation.

Swagelok® is a registered trademark of Swagelok Company.

SymbiosisTM is a trademark of Spark Holland Inc.

T-WaveTM is a trademark of Waters Corporation.

THE SCIENCE OF WHAT'S POSSIBLE® is a registered trademark of Waters Corporation.

TRIZAIC® is a registered trademark of Waters Corporation.

TargetLynxTM is a trademark of Waters Corporation.

UNIFI® is a registered trademark of Waters Corporation.

UniSprayTM is a trademark of Waters Corporation.

UPLC® is a registered trademark of Waters Corporation.

UltraPerformance LC® is a registered trademark of Waters Corporation.

Viton® is a registered trademark of DuPont Performance Elastomers LLC.

Waters® is a registered trademark of Waters Corporation.

Xevo® is a registered trademark of Waters Corporation.

ZSprayTM is a trademark of Waters Corporation.

All other trademarks or registered trademarks are the sole property of their respective owners.

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

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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

[e-mail].

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

Telephone and fax From the USA or Canada, phone [phone], or fax [phone].

worldwide.
Visit www.waters.com

For other locations worldwide, phone and fax numbers appear in the
Waters Web site.

Conventional mail Waters Corporation

Global Support Services
34 Maple Street
Milford, MA 01757
USA

System manufacturing information

Manufacturer:

Waters Corporation

34 Maple Street

Milford, MA 01757

USA

Manufacturing site:

Waters Technologies Ireland Ltd.

Wexford Business Park

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Drinagh, Wexford, Ireland

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 with. Always follow Good Laboratory Practice
(GLP), and consult your organization’s standard operating procedures as well as your local
requirements for safety.

Considerations specific to the device

Power cord replacement hazard

Warning: To avoid electric shock, use the SVT-type power cord in the United States

and HAR-type (or better) cord in Europe. The main power cord must be replaced only
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 avoid exposure to toxic substances and biohazards from O-ring leaks in the

source exhaust system, observe these precautions:

• Replace the source O-rings at intervals not exceeding one year.

• Prevent chemical degradation of the source O-rings, which can withstand exposure only to
certain solvents, by determining whether any solvents you use are chemically compatible with
the composition of the O-rings.

Bottle placement prohibition

Warning: To avoid injury from electrical shock or fire, and damage to the equipment, do not

place vessels containing liquid atop the workstation or ancillary equipment or otherwise expose
those units to dripping or splashing liquids.

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Prohibited: Do not place vessels containing liquid—such as solvent bottles—atop the

workstation or ancillary equipment or otherwise expose those units to dripping or
splashing liquids.

Spilled solvents hazard

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 the bottles in the bottle tray, which serves as secondary containment in the event
of spills.

Flammable solvents hazard

Warning: To prevent the ignition of flammable solvent vapors in the enclosed space of

a mass spectrometer’s ion source, ensure that these conditions are met:

• Nitrogen flows continuously through the source.

• A gas-fail device is installed, to interrupt the flow of LC solvent should the nitrogen
supply fail.

• The nitrogen supply pressure does not fall below 400 kPa (4 bar, 58 psi) during an
analysis requiring the use of flammable solvents.

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.

Glass breakage hazard

Warning: To avoid injuries from broken glass, falling objects, or exposure to toxic substances,

never place containers on top of the instrument or on its front covers.

High temperature hazard

Warning: To avoid burn injuries, avoid touching the source ion block assembly when

operating or servicing the instrument.

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Mass spectrometer high temperature hazard

Source ion block assembly

Hazards associated with removing an instrument from service

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

Warning: To avoid puncture injuries, handle sample needles, syringes, fused silica

lines, and borosilicate tips with extreme care.

Warning: To avoid eye injury from broken fused silica lines, use eye protection when

performing this procedure.

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

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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.

Electrical power safety notice

Do not position the instrument so that it is difficult to disconnect the power cord.

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.

Equipment misuse notice

If equipment is used in a manner not specified by its manufacturer, protections against personal
injury inherent in the equipment’s design can be rendered ineffective.

Safety advisories

Consult the "Safety advisories" appendix in this publication for a comprehensive list of warning
advisories and notices.

Operating this device

When operating this device, follow standard quality-control (QC) procedures and the guidelines
presented in this section.

Applicable symbols

Symbol Definition

Manufacturer

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Symbol Definition

REF

Date of manufacture

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

Consult instructions for use

Alternating current

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.

Serial number

Part number catalog number

Audience and purpose

This guide is for operators of varying levels of experience. It gives an overview of the device and
explains how to prepare it for operation, change its modes of operation, and maintain it.

Intended use of the device

Waters designed the Xevo TQ-XS for use as a research tool to accurately, reproducibly, and
robustly quantify target compounds present at the lowest possible levels in highly complex
sample matrices. It is not for use in diagnostic procedures.

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When fitted with Waters options (APCI, APGC, APPI, ASAP, ESCi, NanoFlow ESI, TRIZAIC,
UniSpray, UPLC, ionKey), or optional third-party sources (DART, DESI, or LDTD), the Xevo TQ­XS does not comply with the European Union In Vitro Diagnostic Device Directive 98/79/EC.

Calibrating

To calibrate LC systems, adopt acceptable calibration methods using at least five standards to
generate a standard curve. The concentration range for standards must 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 an
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.

EMC considerations

FCC radiation emissions notice

Changes or modifications not expressly approved by the party responsible for compliance, could
void the user's 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.

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.

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ISM classification: ISM group 1 class A

This classification has been assigned in accordance with IEC CISPR 11 Industrial Scientific and
Medical (ISM) instruments requirements.

Group 1 products apply to intentionally generated and/or used conductively coupled radio­frequency 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.

EMC grounding requirements

Notice: To avoid difficulties in ensuring electromagnetic compatibility, if the

instrument's pump control cable is attached to the vacuum hose, ensure that the cable
is grounded to the mass spectrometer.

EC authorized representative

Address Waters Corporation

Stamford Avenue
Altrincham Road
Wilmslow SK9 4AX UK

Telephone [phone]

Fax [phone]

Contact Quality manager

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Table of contents

General information .......................................................................................................ii

Copyright notice ..................................................................................................................................... ii

Trademarks............................................................................................................................................ ii

Customer comments..............................................................................................................................iii

Contacting Waters ................................................................................................................................ iv

System manufacturing information ....................................................................................................... iv

Safety considerations............................................................................................................................. v

Considerations specific to the device .............................................................................................. v

Electrical power safety notice........................................................................................................viii

Safety hazard symbol notice .........................................................................................................viii

Equipment misuse notice ..............................................................................................................viii

Safety advisories ...........................................................................................................................viii

Operating this device ...........................................................................................................................viii

Applicable symbols........................................................................................................................viii

Audience and purpose.................................................................................................................... ix

Intended use of the device ............................................................................................................. ix

Calibrating .......................................................................................................................................x

Quality control.................................................................................................................................. x

EMC considerations............................................................................................................................... x

FCC radiation emissions notice....................................................................................................... x

Canada spectrum management emissions notice........................................................................... x

ISM classification: ISM group 1 class A.......................................................................................... xi

EMC grounding requirements......................................................................................................... xi

EC authorized representative ............................................................................................................... xi

1 Waters Xevo TQ-XS Overview .................................................................................19

1.1 IntelliStart technology....................................................................................................................20

1.2 ACQUITY UPLC/MS Xevo TQ-XS systems..................................................................................21

1.2.1 ACQUITY UPLC system......................................................................................................21

1.2.2 Waters ACQUITY Xevo TQ-XS UPLC/MS system.............................................................. 21

1.2.3 ACQUITY UPLC M-Class system........................................................................................22

1.2.4 Non-ACQUITY devices for use with the Xevo TQ-XS .........................................................22

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1.2.5 Software and data system ...................................................................................................23

1.3 Ionization techniques and source probes...................................................................................... 23

1.3.1 Electrospray ionization ........................................................................................................24

1.3.2 ESCi.....................................................................................................................................24

1.3.3 APCI ....................................................................................................................................24

1.3.4 Dual-mode APPI/APCI source............................................................................................. 24

1.3.5 UniSpray..............................................................................................................................25

1.3.6 Low-flow ESI probe..............................................................................................................25

1.3.7 NanoFlow ESI source..........................................................................................................25

1.3.8 Atmospheric solids analysis probe (ASAP) .........................................................................25

1.3.9 APGC...................................................................................................................................26

1.3.10 TRIZAIC UPLC source ......................................................................................................26

1.3.11 ionKey source....................................................................................................................26

1.4 IntelliStart fluidics system..............................................................................................................26

1.4.1 Overview..............................................................................................................................26

1.4.2 System components ............................................................................................................28

1.4.3 System operation................................................................................................................. 28

1.5 Ion optics.......................................................................................................................................28

1.6 MS operating modes ..................................................................................................................... 29

1.7 MS/MS operating modes............................................................................................................... 30

1.7.1 Product (daughter) ion mode...............................................................................................31

1.7.2 Precursor (parent) ion mode................................................................................................ 31

1.7.3 MRM mode ..........................................................................................................................32

1.7.4 Constant neutral loss mode.................................................................................................33

1.7.5 Constant neutral gain mode.................................................................................................33

1.7.6 ScanWave daughter scan mode..........................................................................................33

1.8 Leak sensors.................................................................................................................................34

1.9 Vacuum system............................................................................................................................. 34

1.10 Rear panel...................................................................................................................................35

2 Preparing the mass spectrometer for operation ................................................... 37

2.1 Preparing to start the mass spectrometer ..................................................................................... 37

2.2 Starting the mass spectrometer ....................................................................................................38

2.3 Verifying the instrument’s state of readiness ................................................................................39

2.4 Monitoring the mass spectrometer LEDs ...................................................................................... 39

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2.4.1 Power LED...........................................................................................................................39

2.4.2 Operate LED........................................................................................................................ 40

2.5 Tuning and calibration information ................................................................................................ 40

2.6 Running the mass spectrometer at high flow rates ....................................................................... 40

2.7 Preparing the IntelliStart Fluidics system ...................................................................................... 41

2.7.1 Installing the reservoir bottles..............................................................................................41

2.7.2 Installing the low-volume vials .............................................................................................42

2.7.3 Adjusting the solvent delivery tube positions.......................................................................42

2.8 Purging the fluidics........................................................................................................................43

2.9 Rebooting the mass spectrometer ................................................................................................43

2.10 Leaving the mass spectrometer ready for operation...................................................................44

2.11 Emergency shutdown of the mass spectrometer ........................................................................ 45

3 Changing the mode of operation ............................................................................46

3.1 Changing the Mode of Operation .................................................................................................. 46

3.2 ESI, ESCi, and APCI modes ......................................................................................................... 46

3.2.1 ESI mode.............................................................................................................................46

3.2.2 ESCi mode...........................................................................................................................47

3.2.3 APCI mode ..........................................................................................................................47

3.2.4 Configuring for ESI/ESCi/APCI modes................................................................................47

3.2.5  Installing the probe adaptor ................................................................................................50

3.2.6 Installing the probe assembly ..............................................................................................53

3.2.7 Removing the probe adaptor ...............................................................................................60

3.2.8 Installing and removing the corona pin................................................................................61

3.3 Combined APPI/APCI source .......................................................................................................65

3.3.1 APPI operation.....................................................................................................................65

3.3.2 APCI operation ....................................................................................................................66

3.3.3 Dual-mode operation ...........................................................................................................67

3.3.4 The combined APPI/APCI source components...................................................................68

3.3.5 Installing the combined APPI/APCI source..........................................................................69

3.3.6 Removing the combined APPI/APCI source enclosure.......................................................70

3.4 UniSpray source............................................................................................................................ 71

3.4.1 Installing the UniSpray source.............................................................................................73

3.4.2 Removing the UniSpray source...........................................................................................76

3.5 NanoFlow ESI source ...................................................................................................................77

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3.5.1 Installing the NanoFlow source............................................................................................77

3.5.2 Fitting a borosilicate glass capillary (nanovial) ....................................................................80

3.5.3 Positioning the borosilicate glass capillary tip......................................................................83

3.5.4 Restarting a stalled borosilicate glass capillary electrospray...............................................83

3.6 ionKey source ...............................................................................................................................83

3.6.1 Installing the ionKey source................................................................................................. 84

3.6.2 Installing ionKey source software .......................................................................................88

3.6.3 Installing the camera in the ionKey source..........................................................................88

3.6.4 Removing an ionKey source................................................................................................ 88

4 Maintenance procedures ......................................................................................... 91

4.1 Maintenance schedule ..................................................................................................................91

4.2 Spare parts....................................................................................................................................93

4.3 Troubleshooting with Connections INSIGHT ................................................................................93

4.4 Safety and handling ......................................................................................................................94

4.5 Preparing the instrument for working on the source .....................................................................95

4.5.1 Using MassLynx software to prepare the instrument for operations on or inside its

source............................................................................................................................................95

4.6 Removing and refitting the source enclosure................................................................................96

4.6.1 Removing the source enclosure from the instrument ..........................................................96

4.6.2 Fitting the source enclosure to the instrument..................................................................... 98

4.7 Operating the source isolation valve ............................................................................................. 98

4.7.1 Closing the source isolation valve .......................................................................................99

4.7.2 Opening the source isolation valve.................................................................................... 100

4.8 Removing O-rings and seals.......................................................................................................100

4.9 Cleaning the instrument case...................................................................................................... 101

4.10 Emptying the nitrogen exhaust trap bottle................................................................................. 101

4.11 Maintaining the roughing pump.................................................................................................103

4.12 Cleaning the source components.............................................................................................. 103

4.13 Cleaning the sampling cone assembly...................................................................................... 103

4.13.1 Removing the sampling cone assembly from the source ................................................104

4.13.2 Disassembling the sampling cone assembly...................................................................105

4.13.3 Cleaning the sample cone and cone gas nozzle .............................................................108

4.13.4 Assembling the sampling cone assembly........................................................................ 109

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4.13.5 Fitting the sampling cone assembly to the source........................................................... 110

4.14 Cleaning the ion block assembly............................................................................................... 111

4.14.1 Removing the ion block assembly from the source assembly.........................................111

4.14.2 Disassembling the source ion block assembly ................................................................114

4.14.3 Cleaning the ion block components................................................................................. 118

4.14.4 Assembling the source ion block assembly.....................................................................119

4.14.5 Fitting the ion block assembly to the source assembly....................................................120

4.15 Cleaning the StepWave ion guide assembly............................................................................. 121

4.15.1 Handling the StepWave ion guide assembly ...................................................................121

4.15.2 Removing the ion block support from the source assembly ............................................121

4.15.3 Removing the StepWave assembly from the source assembly.......................................123

4.15.4 Disassembling the StepWave ion guide assembly..........................................................127

4.15.5 Cleaning the StepWave ion guide assembly ...................................................................130

4.15.6 Assembling the StepWave ion guide assembly............................................................... 132

4.15.7 Fitting the StepWave assembly to the source assembly .................................................134

4.15.8 Fitting the ion block support to the source.......................................................................137

4.16 Replacing the probe assembly..................................................................................................137

4.16.1 Removing the probe assembly ........................................................................................137

4.17 Replacing the ESI probe tip and gasket....................................................................................139

4.17.1 Removing the ESI probe tip and gasket ..........................................................................139

4.17.2 Fitting the ESI probe tip and gasket.................................................................................141

4.18 Cleaning the APCI probe tip...................................................................................................... 142

4.19 Replacing the APCI probe heater .............................................................................................143

4.19.1 Removing the APCI probe heater.................................................................................... 143

4.19.2 Fitting the new APCI probe heater...................................................................................144

4.20 Cleaning or replacing the corona pin ........................................................................................146

4.21 Replacing the ion block source heater ...................................................................................... 146

4.22 Replacing the source assembly seals.......................................................................................150

4.22.1 Removing the probe adjuster assembly probe and source enclosure seals ...................151

4.22.2 Fitting the new source enclosure and probe adjuster assembly probe seals .................. 153

4.23 Replacing the air filter inside the front door............................................................................... 154

4.24 APPI/APCI source - changing the UV lamp bulb ......................................................................156

4.25 APPI/APCI source—cleaning the lamp window ........................................................................ 158

4.26 APPI/APCI source - replacing the APPI lamp drive seals.........................................................158

4.26.1 Removing the APPI lamp drive assembly seals ..............................................................159

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4.26.2 Fitting the new APPI lamp drive assembly O-rings..........................................................163

4.27 Replacing the UniSpray probe assembly .................................................................................. 165

4.27.1 Removing the UniSpray probe assembly ........................................................................165

4.27.2 Fitting the UniSpray probe assembly............................................................................... 166

4.28 Maintaining the UniSpray impactor pin .....................................................................................168

4.28.1 Removing and installing the UniSpray impactor pin ........................................................168

4.28.2 Cleaning or replacing the UniSpray impactor pin ............................................................169

4.29 Replacing the fluidic lines of the ionKey source........................................................................170

4.29.1 Removing a fluidic line..................................................................................................... 171

4.29.2 Installing a fluidic line....................................................................................................... 175

4.30 Cleaning the ionKey source and connectors............................................................................. 176

4.30.1 To remove buildup from electronic connectors................................................................ 177

4.30.2 To clean the outside surfaces of the ionKey source........................................................178

A Safety advisories ...................................................................................................179

A.1 Warning symbols ........................................................................................................................179

A.1.1 Specific warnings ..............................................................................................................180

A.2 Notices........................................................................................................................................182

A.3 Bottles Prohibited symbol ...........................................................................................................182

A.4 Required protection ....................................................................................................................182

A.5 Warnings that apply to all Waters instruments and devices .......................................................183

A.6 Warnings that address the replacing of fuses............................................................................. 187

A.7 Electrical symbols ....................................................................................................................... 188

A.8 Handling symbols .......................................................................................................................189

B External connections............................................................................................. 191

B.1 External wiring and vacuum connections ...................................................................................191

B.2 Connecting the EBARA oil-free roughing pump .........................................................................192

B.3 Making the electrical connections to the Ebara oil-free roughing pump .....................................197

B.4 Connecting to the nitrogen gas supply .......................................................................................198

B.5  Connecting to the collision cell gas supply ................................................................................199

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B.6  Connecting the nitrogen exhaust line ........................................................................................199

B.7 Connecting liquid waste lines .....................................................................................................201

B.8 Connecting the workstation (systems with no ACQUITY LC).....................................................204

B.8.1 Connecting to the workstation...........................................................................................204

B.9 Connecting Ethernet cables (systems with ACQUITY LC) ......................................................... 204

B.10 Input/output signal connectors..................................................................................................205

B.11 Connecting to the electricity source..........................................................................................207

C Materials of Construction and Compatible Solvents..........................................208

C.1 Preventing contamination ........................................................................................................... 208

C.2 Items exposed to solvent............................................................................................................208

C.3 Solvents used to prepare mobile phases ...................................................................................209

D IntelliStart Fluidics System Plumbing.................................................................. 211

D.1 Preventing contamination ........................................................................................................... 211

D.2 Plumbing schematic ...................................................................................................................211

D.3 ionKey and TRIZAIC source plumbing .......................................................................................212

D.4 Tubing specifications .................................................................................................................. 213

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1 Waters Xevo TQ-XS Overview

The Xevo TQ-XS is a tandem quadrupole, atmospheric pressure ionization (API) mass
spectrometer. It is designed for routine HPLC/MS/MS and UPLC/MS/MS analyses in quantitative
and qualitative applications, and can operate at fast acquisition speeds compatible with
UltraPerformance LC.

You can use theXevo TQ-XS with the following high-performance ZSpray dual-orthogonal API
sources:

• Standard multi-mode electrospray ionization/atmospheric pressure chemical ionization/
combined electrospray ionization and atmospheric pressure chemical ionization (ESI/APCI/
ESCi)

Requirement: Dedicated APCI operation requires an additional probe.

• Optional UniSpray source

• Optional dual-mode atmospheric pressure photoionization (APPI)/APCI

• Optional low-flow ESI

• Optional NanoFlow ESI

• Optional atmospheric solids analysis probe (ASAP)

• Optional atmospheric pressure gas chromatography (APGC)

• Optional TRIZAIC UPLC

• Optional ionKey source

You can also use the Xevo TQ-XS with the following optional third-party sources:

• Direct analysis in real time (DART)

• Desorption electrospary ionization (DESI)

• Laser diode thermal desorption (LDTD)

For additional details, refer to the appropriate manufacturer’s documentation.

Available source options can vary, depending on the software you use to operate the Xevo TQ­XS. Refer to the MassLynx or UNIFI online Help for more information about supported sources.

For mass spectrometer specifications, see the Waters Xevo TQ-XS Site Preparation Guide
(715005172).

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Figure 1–1: Waters Xevo TQ-XS

Source enclosure

1.1 IntelliStart technology

IntelliStart technology monitors instrument performance and indicates 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 open­access applications.

The IntelliStart fluidics system1 is built into the mass spectrometer. It delivers sample directly to
the MS probe from the LC column or from three integral reservoirs. The integral reservoirs can
also deliver sample through direct or combined infusion, enabling you to optimize instrument
performance at analytical flow rates.

See IntelliStart fluidics system and the mass spectrometer’s online Help for further details on
IntelliStart technology.

1

In Waters documents, the term “fluidics” refers to the IntelliStart Fluidics system, which is the instrument’s onboard system that
delivers sample and solvent to the probe of the mass spectrometer. It can also denote plumbing components and fluid pathways
within and between system modules.

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1.2 ACQUITY UPLC/MS Xevo TQ-XS systems

The Waters Xevo TQ-XS is compatible with the ACQUITY UPLC systems. If you are not using an
ACQUITY UPLC system, refer to the documentation relevant to your LC system.

1.2.1 ACQUITY UPLC system

The ACQUITY UPLC system includes a binary or quaternary solvent manager, sample manager,
column heater or column manager, optional sample organizer, one or more detectors, a
specialized ACQUITY UPLC column, and software to control the system.

For additional information, see the ACQUITY UPLC System Operator's Guide or Controlling
Contamination in UltraPerformance LC/MS and HPLC/MS Systems (part number 715001307).
You can find these documents on www.waters.com; click Services & Support > Support.

1.2.2

Waters ACQUITY Xevo TQ-XS UPLC/MS system

Figure 1–2: Waters ACQUITY Xevo TQ-XS UPLC/MS System

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Probe adaptor

Source enclosure

Source enclosure release

Xevo TQ-XS

Access door to the fluidics

Sample manager

Binary solvent manager or Quaternary solvent manager

Sample organizer (optional on the ACQUITY UPLC system)

Column heater

Solvent tray

Access door to the fluidics valve

Removable panel for ACQUITY arm

Probe high voltage connector

Source interface sliding door

1.2.3 ACQUITY UPLC M-Class system

The ACQUITY UPLC M-Class system is designed for nano-scale and micro-scale separations.

M-Class system components are optimized for use with sub-2µm particle liquid chromatography
and use reduced fluid volumes. The supported flow rate for a gradient elution ranges from 200
nL/min to 100 µL/min at 15,000 psi.

For further information, see the ACQUITY UPLC M-Class System Guide or Controlling
Contamination in UltraPerformance LC/MS and HPLC/MS Systems (part number 715001307).
You can find these documents on www.waters.com; click Services & Support > Support.

1.2.4

Non-ACQUITY devices for use with the Xevo TQ-XS

The following non-ACQUITY LC devices are validated for use with the Xevo TQ-XS:

• Waters Alliance 2695 separations module

• Waters Alliance 2795 separations module

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• Waters 2998 PDA detector

• Waters 2487 UV detector

• Waters 1525µ binary gradient pump + 2777 autosampler

1.2.5 Software and data system

You can use MassLynx software v4.2 to control the mass spectrometer. The software enables
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

• Acquiring data

• Monitoring the run

• Processing data

• Reviewing data

1.2.5.1

1.3

• Printing data

MassLynx software

MassLynx software acquires, analyzes, manages, and distributes mass spectrometry, ultraviolet
(UV), evaporative light scattering (ELS), and analog data. OpenLynx and TargetLynx XS
application managers are included with MassLynx software.

See the MassLynx software 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 Control application.

The Instrument Control software, which functions independently of MassLynx software, does not
recognize or control data systems.

See the online Help for the Instrument Console system for additional details.

Ionization techniques and source probes

Note: Available source options can vary depending on the software used to operate the Xevo

TQ-XS. Refer to the instrument software's online Help for more information about supported
sources.

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1.3.1 Electrospray ionization

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.

To operate the source in ESI mode, you fit the source enclosure with an ESI probe adaptor and
ESI probe assembly.

The standard ESI probe assembly accommodates flow rates of up to 2 mL/min, making it suitable
for LC applications in the range of 100 µL/min to 2 mL/min. To reduce peak broadening for lower­flow-rate LC applications, such as 1-mm UPLC columns, use the optional, small-bore capillary,
which can accommodate a maximum flow rate of 200 µL/min.

See also: ESI, ESCi, and APCI modes for further details.

1.3.2

1.3.3

1.3.4

ESCi

ESCi mode is supplied as standard equipment on the mass spectrometer. In ESCi, the standard
ESI probe adaptor is used in conjunction with a corona pin, to allow alternating acquisition of ESI
and APCI ionization data, which facilitates high throughput and wider compound coverage.

See ESI, ESCi, and APCI modes for further details.

APCI

An optional dedicated high-performance APCI interface is available. 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 APCI
probe adaptor.

See ESI, ESCi, and APCI modes for further details.

Dual-mode APPI/APCI source

The optional, combined APPI/APCI source comprises an APCI probe adaptor 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.

See Combined APPI/APPI source for further details.

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1.3.5 UniSpray

The UniSpray source enables the detection of a wide range of compounds in a single analysis. In
contrast to Electrospray ionization, UniSpray uses a grounded capillary, and the resulting spray is
directed at an impactor pin held at a voltage, creating smaller charged droplets, amenable to easy
desolvation.

See UniSpray source for further details.

1.3.6

1.3.7

Low-flow ESI probe

The optional low-flow ESI probe is fitted with a narrow bore capillary suitable for use with flow
rates from 5 µL/min to 100 µL/min. Its probe tip is optimized for this capillary.

The low-flow ESI probe replaces the standard ESI probe in the instrument’s source housing.

See the Low-flow ESI Probe Operator's Guide for further details.

NanoFlow ESI source

NanoFlow is the name given to several techniques that use low flow rate ESI. The NanoFlow
source allows ESI in the flow rate range of 5 to 1,000 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.

1.3.8

• Borosilicate glass capillaries (nanovials).
Metal-coated, glass capillaries allow the lowest flow rates. They are usable for one sample,
and then must 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.
See NanoFlow ESI source for further details.

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

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replaces the ESI or APCI 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.

1.3.9 APGC

The Waters APGC couples an Agilent GC with the Xevo TQ-XS. Doing so enables you to perform
LC and GC analyses in the same system, without compromising performance. The APGC
provides complementary information to the LC/MS instrument, enabling analysis of compounds of
low molecular weight and low-to-intermediate polarity.

See the Atmospheric Pressure GC Operator's Guide Supplement for further details.

1.3.10

1.3.11

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.

ionKey source

The ionKey source integrates UPLC separation into the source of the mass spectrometer. The
source accepts an iKey Separation Device, which contains the fluidic connections, electronics,
ESI interface, heater, e-cord, and chemistry. Inserting the iKey simultaneously engages the
electronic and fluidic connections. This technology eliminates the need to manually connect
electronic cables and tubing, and simplifies the user experience.

See the ACQUITY UPLC M-Class System Guide (part number 715003588) and the ionKey/MS
System Guide (part number 715004028) for further details.

See also: ionKey source.

1.4

IntelliStart fluidics system

1.4.1 Overview

The IntelliStart fluidics system is a solvent delivery system built into the mass spectrometer. It
delivers sample directly to the MS probe in one of these ways:

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• From the LC column.

• From three integral reservoirs. (The reservoirs can also deliver sample, by 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.

For further information on the IntelliStart fluidics system, see IntelliStart Fluidics Plumbing and the
diagram located on the inside of the fluidics access door (see Waters ACQUITY Xevo TQ-XS

UPLC/MS system).

Figure 1–3: IntelliStart fluidics system:

Reservoir C

Reservoir B

Reservoir A

Pump

Wash bottle, located in solvent tray

To waste system

LC

Column

Diverter valve

Probe

7-port selector valve

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1.4.2 System components

The onboard system incorporates a 7-port selector valve, a multi-position diverter valve, a pump,
and three sample reservoirs.

The sample reservoirs are mounted on the instrument’s front panel. When you select a solvent
from the instrument console, an LED illuminates the appropriate reservoir. You can
simultaneously illuminate all three reservoirs or extinguish the LEDs for light-sensitive samples.

Recommendation: Use reservoir A for the calibrant solution, reservoir B for tuning

compounds, and reservoir C for analyte/optimization solution.

1.4.3

System operation

The software automatically controls solvent and sample delivery during auto-tuning, auto­calibration, and method development, via the instrument console.

See the mass spectrometer’s online Help for additional details on IntelliStart software and
operation of the instrument’s solvent delivery system.

1.5 Ion optics

The mass spectrometer’s ion optics operate as follows:

1. Samples from the LC or instrument’s solvent delivery system are introduced at atmospheric
pressure into the ionization source, where they are ionized.

2. The ions pass through the sample cone into the vacuum system.

3. The resulting ion beam passes through the source sampling orifice, undergoing a certain
amount of expansion.

4. The ion beam then passes into the entrance of the StepWave transfer optics. The entrance
is large enough to efficiently capture ions in the expanded beam. The StepWave transfer
optics comprise two stages. The first stage (conjoined ion guide) focuses the ion beam and
directs it to the second stage (T-Wave ion guide). The off-axis design ensures that any
neutral materials entering the source sampling orifice are actively extracted from the
system.

5. The ions then pass to the first quadrupole, where they can be filtered according to their
mass-to-charge ratio (m/z).

6. The mass-separated ions pass into the T-Wave/ScanWave collision cell, where they
undergo collision-induced dissociation (CID) or pass to the second quadrupole. Any
fragment ions can then be mass-analyzed by the second quadrupole.

7. The transmitted ions are detected by the photomultiplier detection system.

8. The signal is amplified, digitized, and sent to the mass spectrometry software:

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Quadrupole 1 (MS1)

T-Wave/ScanWave collision cell

Quadrupole 2 (MS2)

Conversion dynode

Detector assembly

Photomultiplier tube

Source sampling orifice

Isolation valve

Z-Spray ion source

Sample inlet

Sample cone

Conjoined ion guide

StepWave

T-Wave ion guide

1.6 MS operating modes

The following table shows the MS operating modes.

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Table 1–1: MS operating modes:

Operating mode MS1 Collision cell MS2

MS Pass all masses Resolving (scanning)

SIR Pass all masses Resolving (static)

MS1 Resolving (scanning) Pass all masses

In MS mode, the instrument can acquire data at scan speeds as high as 20,000 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 MS/MS

operating modes for further details) . 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 versus time).

1.7 MS/MS operating modes

The following table shows the MS/MS operating modes.

Table 1–2: MS/MS operating modes:

Operating mode MS1 Collision cell MS2

Product (daughter)
ion spectrum

Precursor (parent)
ion spectrum

MRM Static (at precursor

Constant neutral
loss spectrum

Constant neutral
gain spectrum

ScanWave
daughter scan

Static (at precursor
mass)

Scanning Static (at product

mass)

Scanning
(synchronized with
MS2)

Scanning
(synchronized with
MS2)

Static (at precursor
mass)

Fragment precursor ions
and pass all masses

Scanning

Scanning

mass)

Static (at product
mass)

Scanning
(synchronized with
MS1)

Scanning
(synchronized with
MS1)

(synchronized with
collision cell)

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RADAR is an additional mode with which you simultaneously collect data from the MRM and full
scan MS modes. RADAR mode can also acquire all detectable ions in both positive and negative
full scan MS.

1.7.1 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.

Figure 1–4: Product ion mode:

MS1 - Static (at precursor mass)

Collision cell - Fragment precursor ions and pass all masses

MS2 - Scanning

1.7.1.1 Typical applications

You typically use product ion mode 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).

1.7.2

Precursor (parent) ion mode

Figure 1–5: Precursor ion mode:

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MS1 - Scanning

Collision cell - Fragment precursor ions and pass all masses

MS2 - Static (at product mass)

1.7.2.1 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.

1.7.3

MRM mode

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.

Figure 1–6: MRM mode:

MS1 - Static (at precursor mass)

Collision cell - Fragment precursor ions and pass all masses

MS2 - Static (at product mass)

1.7.3.1 Typical application

You typically use MRM mode to quantify known analytes in complex samples:

• drug metabolite and pharmacokinetic studies

• environmental studies; for example, pesticide and herbicide analysis

• forensic or toxicology studies; for example, screening for target drugs in sports testing

MRM mode does not produce a spectrum, because only one transition is monitored at a time. As
in SIR mode, a chromatogram is produced.

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1.7.4 Constant neutral loss mode

Constant neutral loss mode detects the loss of a specific neutral fragment or functional group
from an unspecified precursor or precursors.

The scans of MS1 and MS2 are synchronized. When MS1 transmits a specific precursor ion,
MS2 determines 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 lost a
fragment of a certain mass.

Figure 1–7: Constant neutral loss mode:

MS1 - Scanning (synchronized with MS2)

Collision cell - Fragment precursor ions and pass all masses

MS2 - Scanning (synchronized with MS1)

1.7.4.1 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.

1.7.5

Constant neutral gain mode

Similar to constant neutral loss mode, constant neutral gain mode detects the gain of a specific
neutral fragment or functional group from an unspecified precursor or precursors. The mode is
infrequently used because the mass selected by MS2 is seldom higher than that of MS1.

See also: Constant neutral loss mode.

1.7.6

ScanWave daughter scan mode

This operating mode is very similar to the conventional product ion mode in that you can specify
an ion of interest for fragmentation in the collision cell, yielding structural information. In this
ScanWave mode, the cell accumulates fragment ions and then releases them, according to their

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mass, in synchrony with the second quadrupole mass analyzer. This mode results in a significant
increase in the signal intensity of full scan spectra.

Figure 1–8: ScanWave daughter scan mode:

MS1 - Scanning

Collision cell - ScanWave enabled, fragments precursor ions, accumulates fragment ions
and passes all masses

MS2 - Scanning (synchronized with collision cell)

1.7.6.1 Typical applications

You typically use product ion mode for the following applications:

1.8

1.9

• 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).

Leak sensors

Leak sensors in the instrument’s drip trays continuously monitor for liquid 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 software displays an error message alerting you that
a leak has developed. Consult the Waters ACQUITY UPLC Leak Sensor Maintenance
Instructions (part number 71500082506) for complete details.

Vacuum system

An external roughing (rotary vane) pump and three internal turbomolecular pumps create the
source vacuum. The turbomolecular pumps evacuate the analyzer and ion transfer region.

Vacuum leaks and electrical or vacuum pump failures cause vacuum loss. To protect the
instrument in the event of vacuum loss, the vacuum interlock switches off the Operate voltages.

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The system monitors the turbomolecular pump speeds and continuously measures vacuum

Auxiliary

10MB
/100MB

Activity

ExternalConnections 2

10 1

ExternalConnections 1

10 1

LAN

EPCCom Port

VideoOutput

ServiceBus

123

4

567

8910

+

-

EventIn 1

ExternalConnections1

Notused

CE

Interlock

OUT

+

-

EventIn 2

Notused

­IN IN

Com

N/C

N/
O

Com

N/C

N/O

12345678910

+

-

Analogue

Out

ExternalConnections2

OUT

GasFail

Interlock

Notused

­OUTOUT

+

­EventOu

t1

+

­EventOut2

OUT

pressure with built-in Pirani and Penning gauges. The gauges also serve as switches, stopping
operation when vacuum loss is detected.

A vacuum isolation valve isolates the source sample cone from the mass analyzer, allowing you
to perform routine maintenance without venting the system.

1.10

Rear panel

The following figure shows the rear panel locations of the connectors used to operate the mass
spectrometer with external devices. For further details, see External connections.

Figure 1–9: Mass spectrometer rear panel:

Shielded Ethernet

Video connection (for use with the optional NanoFlow ESI or ionKey source)

Event inputs and outputs

Power connection

Roughing pump connections

Roughing pump grounding connection

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Source vent

Nitrogen inlet

Pilot valve port

Turbo vacuum

Source vacuum

Collision cell gas inlet

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2 Preparing the mass spectrometer for

operation

This chapter describes how to start and shut down the mass spectrometer.

2.1 Preparing to start the mass spectrometer

This instrument 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 the Xevo TQ-XS).

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

solvents.

See also: For more details, refer to the following sources:

• Appendix Materials of Construction and Compatible Solvents of this guide, for mass
spectrometer solvent information.

• Appendix C of the ACQUITY UPLC System Operator's Guide for solvent compatibility with
ACQUITY devices.

To prepare the mass spectrometer:

1. On the rear panel, ensure that the nitrogen supply is connected to the instrument’s nitrogen
inlet connection (see the figure Connecting the nitrogen gas supply).

Requirements:

• 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).

• A gas-fail device must be installed, to interrupt the flow of LC solvent should the
nitrogen supply fail.

2. Ensure that the wash solvent bottle is placed in the solvent tray on top of the instrument
and that the end of the tubing from the fluidics valve is fully submerged in the solvent.

Note: For additional information on the fluidics connections, see the diagram on the inside

of the fluidics valve access door, and Plumbing schematic.

3. Ensure that the collision gas supply is connected to the instrument’s collision cell gas inlet.

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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).

2.2 Starting the mass spectrometer

Starting the mass spectrometer comprises powering-on the workstation, logging in, powering-on
the mass spectrometer and all other instruments, and then starting the software.

Requirements:

• Ensure that you have prepared the mass spectrometer. See Preparing to start the mass

spectrometer.

• Power-on and log in to the workstation, to ensure that it assigns the IP addresses of the
system instruments.

See also: The mass spectrometer’s online Help for details on the software.

To start the mass spectrometer:

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

2. Press the power switch on the top, left-hand side of the ACQUITY instruments and then
the mass spectrometer.

Result: Each system instrument runs a series of startup tests.

3. Wait three minutes for the embedded PC to initialize, as indicated by an audible alert.

Tip: The power and operate LEDs change as follows:

• During initialization, the binary solvent manager LED and sample manager LED flash
green.

• After the instruments are successfully powered-on, all power LEDs show steady green.
The binary solvent manager flow LED, the sample manager run LED, and the mass
spectrometer Operate LED remain off.

4. Start the MassLynx software, and monitor the Instrument Console software for messages
and LED indications.

5. Pump down (evacuate) the mass spectrometer by following these steps:

a. In the lower, left-hand corner of the MassLynx main window, click IntelliStart.

Result: The mass spectrometer console appears. The mass spectrometer is in

Standby mode.

b. To start the roughing pumps, click Control > Pump.

Tip: The Operate LED remains off.

c. Wait a minimum of three hours for the instrument to be fully pumped-down

(evacuated).

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Tips:

• In the Instrument Console, the System Ready indicator shows green when the
instrument is fully pumped-down (evacuated).

• Expect the Analyzer Penning gauge readback to show less than 1e-5 mbar
vacuum.

Warning: To prevent the ignition of flammable solvent vapors in the

enclosed space of a mass spectrometer’s ion source, ensure that these
conditions are met:

• Nitrogen flows continuously through the source.

• A gas-fail device is installed, to interrupt the flow of LC solvent should
the nitrogen supply fail.

• The nitrogen supply pressure does not fall below 400 kPa (4 bar, 58
psi) during an analysis requiring the use of flammable solvents.

6. Start the nitrogen gas flowing through the source by clicking API .

7. Click Operate .

2.3

2.4

2.4.1

Result: When the mass spectrometer is in good operating condition, IntelliStart software

displays Ready in the Instrument Console.

Verifying the instrument’s state of readiness

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

Monitoring the mass spectrometer LEDs

LED on the mass spectrometer indicate its operational status.

Power LED

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

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2.4.2 Operate LED

The Operate LED, located on the right-hand side of the power LED, indicates the operating
condition.

See the mass spectrometer’s online Help topic “Monitoring the mass spectrometer LEDs” for
details on the Operate LED indications.

2.5 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 . For further instruction, see the mass spectrometer’s
online Help.

2.6 Running the mass spectrometer at high flow rates

The ACQUITY UPLC system runs at high flow rates. To optimize desolvation and sensitivity, run
the ACQUITY Xevo TQ-XS system at appropriate gas flows and desolvation temperatures. When
you specify a flow rate, IntelliStart software automatically specifies the settings shown in the
following table.

Table 2–1: Flow rate versus temperature and gas flow:

Flow rate (mL/min) Source temperature

(°C)

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.

Table 2–2: Flow rate versus APCI probe temperature and gas flow:

Flow rate (mL/min) APCI probe temperature (°C) Desolvation gas flow (L/h)

0.000 to 0.020 400 800

0.021 to 0.500 500 1000

>0.500 600 1000

Desolvation
temperature (°C)

Desolvation gas flow
(L/h)

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2.7 Preparing the IntelliStart Fluidics system

For additional information, see Connecting liquid waste lines.

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 the bottles in the bottle tray, which serves as secondary containment in the event
of spills.

2.7.1 Installing the reservoir bottles

Use standard reservoir bottles (30-mL) for instrument setup and calibration. Use the Low-volume
Adaptor Kit (included) to infuse smaller volumes. The low-volume vials have a volume of 1.5 mL.

Required materials

Chemical-resistant, powder-free gloves

To install the reservoir bottles:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

1. Remove the reservoir bottle caps.

2. Screw the reservoir bottles onto the mass spectrometer, as shown below.

Figure 2–1:

Reservoir bottle

Solvent delivery tube

3. For each reservoir bottle, ensure that the ends of the solvent delivery tubes are positioned
so that they are close to, but do not touch, the bottom of the bottle (see Adjusting the

solvent delivery tube positions).

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2.7.2 Installing the low-volume vials

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

To install low-volume vials:

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

2. Screw the low-volume adaptors into the manifold and finger-tighten them.

Figure 2–2:

2.7.3

Low-volume adaptor

Low-volume vial

Solvent delivery tube

Warning: To avoid laceration injuries caused by the shattering of fragile, low-

volume glass vials, take care when screwing them in, and never use force.

3. Screw the low-volume vials into the adaptors.

4. For each low-volume vial, ensure that the ends of the solvent delivery tubes are positioned
so that they are close to, but do not touch, the bottom of the vial (see Adjusting the solvent

delivery tube positions).

Adjusting the solvent delivery tube positions

For correct operation of the IntelliStart Fluidics system, you must adjust each solvent delivery
tube so that its end is close to, but does not touch, the bottom of the reservoir bottle or low
volume vial.

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To adjust the position of a solvent delivery tube:

1. Open the access door to the fluidics pump (see Waters ACQUITY Xevo TQ-XS UPLC/MS

system).

2. Loosen the finger-tight fitting for the solvent delivery tube you are adjusting.

Finger-tight fitting

Solvent delivery tube

2.8

2.9

3. Move the solvent delivery tube so that its end is close to, but does not touch, the bottom of
the reservoir bottle or low volume vial.

4. Tighten the finger-tight fitting.

5. Close the access door.

Purging the fluidics

Whenever you replace a solution bottle, purge the fluidics 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 system can require more than one purge cycle to

minimize carryover.

Rebooting the mass spectrometer

Pressing the reset button shuts down the electronics momentarily and causes the mass
spectrometer to reboot.

Reboot the mass spectrometer when either of these conditions applies:

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• The software fails to establish communication or loses communication with the mass
spectrometer.

• You perform a software upgrade.

To reboot the mass spectrometer:

1. Ensure that the mass spectrometer software is closed.

2. Open the mass spectrometer’s front, left-hand door.

3. Insert a short length (7.5 cm) of PEEK tubing, or similar object, into the reset button
aperture to operate the reset button.

Figure 2–3:

2.10

Reset button aperture

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

5. Close the mass spectrometer’s door.

6. Wait until the reboot sequence completes before starting the mass spectrometer software.

Tip: An audible alert sounds when the reboot sequence completes.

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).

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Notice: For ionKey operation, to protect the iKey when you leave the mass

spectrometer in Operate mode with no flow, set the capillary voltage to zero.

2.11 Emergency shutdown of the mass spectrometer

Warning: To avoid electric shock, observe the following procedure to isolate the

instrument from the main power supply. The instrument's power switch does not isolate
it from the main power supply.

Notice: To avoid losing data, use the following procedure only in an emergency. To

reboot the mass spectrometer, follow the procedure in Rebooting the mass

spectrometer.

To shut down the mass spectrometer in an emergency:

1. Press the power button on the front of the mass spectrometer.

2. Disconnect the power cable from the rear panel.

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3 Changing the mode of operation

3.1 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)

• Low flow ESI

• UniSpray

• NanoFlow ESI

3.2

3.2.1

• ionKey source

For details about other Waters and third-party source options, refer to the documentation supplied
with the source.

ESI, ESCi, and APCI modes

ESI, ESCi, and APCI modes are all configured using a standard source enclosure.

ESI mode

To operate in ESI mode, you must fit the ESI probe adaptor to the source enclosure, and install a
probe assembly.

The ESI probe adaptor fitted with a standard ESI probe assembly accommodates eluent flow
rates as fast as 2 mL/min.

For further details, see ESI.

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3.2.2 ESCi mode

To operate in ESCi mode, you must fit an ESI probe adaptor and corona pin to the source
enclosure.

The system, with the ESI probe adaptor installed and corona discharge pin fitted, can alternate
between ESI and APCI ionization modes, facilitating data acquisition in ESI and APCI modes in
parallel.

3.2.3

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 APCI
probe adaptor. 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.

Figure 3–1: APCI mode:

APCI probe

Corona pin

Sample cone

3.2.4

Hot gas from the APCI 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 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.

Configuring for ESI/ESCi/APCI modes

To operate in ESI, ESCi or APCI mode, you must fit the correct probe adaptor and install a probe
assembly.

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Figure 3–2: Probe adaptor types

APCI probe adaptor

APCI label

APCI probe heater

ESI probe tip

ESI label

ESI probe adaptor

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Figure 3–3: Probe assembly

Probe inlet PEEK fitting

Identification label for part number

Capillary

Probe adaptor PEEK fitting

For ESCi and APCI modes, you must also install a corona pin.

Table 3–1: Configuration for ESI/ESCi/APCI modes

Mode Probe adaptor Install corona pin

ESI ESI No

ESCi ESI Yes

APCI APCI Yes

For more information on using each mode, see the Xevo TQ-XS system online Help.

The following sections explain how to complete the following tasks:

• Installing the probe adaptor

• Installing the probe assembly

• Removing the probe adaptor

• Installing and removing the corona pin

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3.2.5 Installing the probe adaptor

Figure 3–4: Probe adaptor parts

Probe adaptor cap removed from probe adaptor

Probe adaptor cap tether

Locking ring

Probe adaptor identification label

Probe adaptor cap release buttons

Required materials

• Chemical-resistant, powder-free gloves

To install the probe adaptor:

Warning: To avoid personal contamination with biohazards or compounds that are toxic, wear

clean, chemical-resistant, powder-free gloves when performing this procedure.

Warning: To avoid puncture wounds, handle sharp parts and materials with care.

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1. To prepare for installing a probe assembly, press together the probe-adaptor-cap release
buttons, in the direction shown by the arrows in the following figure, and lift the probe
adaptor cap off the probe adaptor.

Figure 3–5: Probe adaptor cap release

2. For ESI probe adaptors, remove the protective cap, if fitted, from the probe tip.

Figure 3–6: ESI probe protective cap

Protective cap

3. Carefully slide the probe adaptor into the hole in the probe adjuster assembly, ensuring
that the probe location dowel aligns with the location hole in the probe adjuster assembly.

Figure 3–7: Probe location dowel

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Probe location dowel

Figure 3–8: Locating the ESI probe adaptor

Location hole for probe location dowel

Probe adjuster assembly

Figure 3–9: Locating the APCI probe adaptor

Location hole for probe location dowel

Probe adjuster assembly

4. Rotate the probe adaptor locking ring clockwise to secure the probe adaptor in place.

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Figure 3–10: Probe adaptor, mounted on the source enclosure:

Probe adaptor cap tether

Probe adaptor cap

3.2.6

Source enclosure

Probe adjuster assembly

High voltage connector

ESI probe adaptor cable (ESI probe adaptor only)

Probe adaptor locking ring

5. For ESI probe adaptors, connect the ESI probe adaptor’s cable to the high voltage
connector.

6. Install the probe assembly, see Installing the new probe assembly.

Installing the probe assembly

Requirements:

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• Ensure that you use a probe assembly appropriate for your application. For example, using an
ESI probe assembly with an APCI probe adaptor compromises instrument performance. You
can use the part number on the identification label to verify the probe assembly type.

• Ensure that the probe adaptor is installed on the source, with the probe adaptor cap removed.
See Installing the probe adaptor.

• Select the shortest probe assembly that can connect the diverter valve to the probe. Doing so
minimizes delays and dispersion.

Recommendation: To connect the probe assembly directly to the fluidics valve, use the 500-

mm ESI or APCI probe assembly.

Notice: Do not adjust the length of the probe assembly. Cutting the PEEKsil tubing

renders the probe assembly unusable.

Figure 3–11: Probe assembly

Probe inlet fitting

Identification label showing part number

Capillary

Probe adaptor fitting

Required materials

• Chemical-resistant, powder-free gloves

To install the probe assembly:

Warning: To avoid personal contamination with biohazards or compounds that are toxic, wear

clean, chemical-resistant, powder-free gloves when performing this procedure.

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Warning: To avoid electric shock, do not insert any item into the probe cap aperture

when the probe cap is fitted to the instrument.

Notice: To avoid damaging the probe assembly, take care when inserting the capillary

into the probe adaptor. Do not use force.

Warning: To avoid harmless, static-like 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.

1. Carefully insert the probe assembly capillary into the probe adaptor.

Tip: To aid insertion, turn the capillary gently as you insert it, feeding the entire capillary in

to the probe adaptor.

Figure 3–12: Inserting the probe assembly

Probe assembly capillary

Probe adaptor

2. Screw the probe adaptor fitting into the probe adaptor, finger-tight only, until you hear a
click.

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Figure 3–13: Probe assembly fitted to the probe adaptor

Probe adaptor fitting

Tip: The probe adaptor fitting on the UniSpray probe assembly is not compatible with the

probe adaptor. If you cannot fit the probe adaptor cap, ensure that you are installing the
correct probe assembly.

3. Tilt the probe adaptor cap, so that the ball-bearing is located in the recess at the bottom of
the aperture, and insert the probe assembly tubing through the aperture.

Figure 3–14: Probe adaptor cap

Probe cap aperture from the underside

Probe cap aperture from the top

Tip: The probe assembly tubing can pass through the aperture only when the ball-bearing

is located in the recess at the bottom and does not block the aperture.

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Figure 3–15:

Probe adaptor cap

Probe adaptor cap tether

Probe adaptor

Probe assembly tubing

4. Slide the probe adaptor cap along the probe assembly, over the probe adaptor PEEK
fitting.

5. Push the probe adaptor cap on to the probe adaptor until it clicks.

Tips:

• Do not squeeze the probe adaptor cap release buttons when fitting the probe adaptor
cap.

• Ensure that the probe adaptor cap is correctly seated, and that both release buttons
engage with the probe adaptor, producing a click.

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Figure 3–16: Seating the probe adaptor cap

Probe adaptor cap seated incorrectly; edge does not align with the edge of the probe
adaptor

Probe adaptor cap seated correctly; edge aligns with the edge of the probe adaptor

6. If you are not immediately connecting the probe assembly to the fluidics, insert the probe
inlet PEEK fitting in to the PEEK fitting holder.

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Figure 3–17: PEEK fitting holder

Probe inlet PEEK fitting

PEEK fitting holder

Probe assembly tubing

Warning: To avoid electric shock or solvent ignition, when connecting ESI or

UPC2 source probes directly to non-Waters equipment, ensure that the liquid
outlet connection is grounded.

7. To connect the probe inlet PEEK fitting to the IntelliStart Fluidics system:

a. Open the access door to the IntelliStart Fluidics system (see Waters ACQUITY Xevo

TQ-S UPLC/MS system).

b. Screw the probe inlet PEEK fitting into port 2 (the top port) of the diverter valve,

finger-tight only, until you hear a click.

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Figure 3–18: Tubing connection between the diverter valve and the ESI probe

Tip: The other plumbing connections are omitted for clarity.

Probe adaptor cap

3.2.7

PEEK fitting holder

Leak tray

Probe adaptor

Probe inlet PEEK fitting connected to diverter valve

Tubing

c. Close the access door to the IntelliStart Fluidics system.

Tip: If fluid collects in the leak tray, inspect the connection at the diverter valve.

Removing the probe adaptor

Remove the probe adaptor before performing any of the following actions:

• Switching between ESI and APCI modes (see Installing the probe adaptor).

• Installing the Low-flow ESI probe (see the Low-flow ESI Probe Operator's Guide).

• Replacing the ESI probe tip or gasket (see Replacing the ESI probe tip or gasket).

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You can remove the probe adaptor with or without the probe assembly installed. To remove the
probe assembly, see Removing the existing probe assembly.

Required materials

Chemical-resistant, powder-free gloves

To remove the ESI probe adaptor:

Warning: To avoid personal contamination with biohazards or compounds that are toxic, wear

clean, chemical-resistant, powder-free gloves when performing this procedure.

Warning: To avoid harmless, static-like 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.

Warning: To avoid burn injuries, take great care while working with the probe and

source; these components can be hot.

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

3.2.8

Warning: To avoid electric shock or solvent ignition, when connecting ESI or

UPC2 source probes directly to non-Waters equipment, ensure that the liquid
outlet connection is grounded.

2. If the probe assembly is fitted, open the access door to the IntelliStart Fluidics system (see

Waters ACQUITY Xevo TQ-XS UPLC/MS system), and disconnect the fluidics tubing from

the diverter valve.

3. For ESI probes, disconnect the probe adaptor cable from the high voltage connector.

4. Unscrew the probe adaptor locking ring.

Warning: To avoid puncture wounds, handle sharp parts and materials with

care.

5. Carefully remove the probe adaptor from the probe adjustor assembly.

6. For ESI probe adaptors, if available, fit the protective cap to the probe tip.

Installing and removing the corona pin

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

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3.2.8.1 Installing the corona pin in the source

Required materials

Chemical-resistant, powder-free gloves

To install the corona pin in the source:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

Warning: To avoid harmless, static-like 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.

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

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

enclosure open.

Warning: To avoid puncture wounds, handle sharp parts and materials with

care.

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

3. Remove the blanking plug from the corona pin mounting contact.

Tip: Store the blanking plug in a safe location.

Figure 3–19: Corona pin mounting contact:

Corona pin mounting contact blanking plug

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Warning: To avoid puncture wounds, handle sharp parts and materials with

care.

4. Fit the corona pin to the corona pin mounting contact, ensuring that the corona pin is
securely mounted and that its tip aligns with the sample cone orifice.

Figure 3–20: Corona pin:

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 the
corona pin.

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Figure 3–21: Source enclosure

Source window

Vernier probe adjuster

3.2.8.2 Removing the corona pin from the source

Required materials

Chemical-resistant, powder-free gloves

To remove the corona pin from the source:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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

on the source before commencing this procedure.

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1. Prepare the instrument for working on the source (see Prepare the instrument for working

on the source).

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

procedure.

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) outwards, and
swing open the enclosure.

3. Remove the corona pin from its mounting contact (see the figure in Installing the corona

pin in the source).

Tip: Store the corona pin in a safe location.

4. Fit the blanking plug to the corona pin mounting contact (see the figure in Installing the

corona pin in the source).

5. Close the source enclosure.

3.3 Combined APPI/APCI source

The combined APPI/APCI source uses an optional, replacement source enclosure. You can
operate the source in APPI mode, APCI mode, or dual-mode APPI/APCI. Dual-mode APPI/APCI
performs rapid switching between ionization modes.

3.3.1

APPI operation

In APPI mode, the source is fitted with an APCI probe adaptor, and the APPI lamp drive
assembly is advanced into the source.

Figure 3–22: APPI mode:

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Sample molecules

APPI lamp drive assembly

Repeller electrode

UV lamp

Photons from the UV lamp

Sample cone

Sample ions

APCI probe

The APCI probe introduces vaporized sample into the source where photons generated by an
ultra-violet (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.

3.3.2

APCI operation

APCI 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. If unused, the
APPI lamp drive assembly is retracted from the source.

Figure 3–23: APCI mode:

Retracted APPI lamp drive assembly

Corona pin

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Sample cone

APCI probe

The APCI 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.

3.3.3

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.

Figure 3–24: Dual operation in APCI mode:

Repeller electrode inactive

Corona pin with current applied

Photons from the UV lamp

Sample cone

APCI probe

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.

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Figure 3–25: Dual operation in APPI mode:

Repeller electrode with voltage applied

Corona pin inactive

Photons from the UV lamp

Sample cone

APCI probe

3.3.4 The combined APPI/APCI source components

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

Figure 3–26: The combined APPI/APCI source enclosure:

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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.

The UV lamp, which you ignite via a control in the MassLynx software 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.

Figure 3–27: APPI lamp drive assembly inside the source enclosure:

UV lamp and repeller electrode

Desolvation heater nozzle

Source enclosure

APPI lamp drive assembly

3.3.5 Installing the combined APPI/APCI source

Required materials

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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

before commencing this procedure.

To install the combined APPI/APCI source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

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

and source; these components can be hot.

2. Remove the probe adaptor from the currently installed source (see Removing the probe

adaptor).

3. Remove the existing source enclosure (see Removing the source enclosure from the

instrument).

4. Install the combined APPI/APCI source enclosure (see Fitting the source enclosure to the

instrument).

5. Install the specially shaped corona pin (see Installing the corona pin in the source).

6. Slide open the instrument’s source interface door (see the figure on Waters ACQUITY

Xevo TQ-S UPLC/MS system).

3.3.6

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

Tip: The front panel connectors and cables are color-coded. Ensure that the color of the

connector and the cable match.

8. Connect the source enclosure 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.

9. Close the instrument’s source interface door.

10. Install the APCI probe adaptor to the source (see Installing the probe adaptor).

11. Install the APCI probe assembly (see Installing the probe assembly).

Tip: An automatic pressure test is performed each time the source enclosure is closed

and the probe cap is fitted, and when the instrument starts.

Removing the combined APPI/APCI source enclosure

Required materials

Chemical-resistant, powder-free gloves

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Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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, before performing maintenance operations that

involve handling components inside the mass spectrometer's ion source, allow the
source interior to cool.

To remove the combined APPI/APCI source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

2. Remove the APCI probe adaptor (see Removing the probe adaptor).

3. Disconnect the source enclosure 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 Removing the source enclosure from the instrument).

6. Remove the corona pin (see Removing the corona pin from the source).

3.4

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

UniSpray source

The UniSpray source enables the detection of a wide range of compounds in a single analysis.

The following sections explain how to install and remove the UniSpray source.

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Figure 3–28: UniSpray source - front and rear view

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Probe inlet shaft

Vertical probe adjuster

Horizontal probe adjuster

Impactor pin

Capillary adjuster

Source enclosure front panel

See also: For information about maintaining the source components:

• Replacing the UniSpray probe assembly

• Maintaining the UniSpray impactor pin

3.4.1

Installing the UniSpray source

Required materials

• Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

To install the UniSpray source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

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

mode before commencing this procedure.

Warning: To avoid burn injuries, exercise care when handling the components

of the source enclosure heated to high temperatures. Wait until the hot
components have sufficiently cooled before you handle them.

2. Remove the existing source enclosure (see Removing the source enclosure from the

instrument).

3. Ensure that the probe assembly is connected to the UniSpray source before you fit the
source to the mass spectrometer.

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Tip: If you must fit the probe assembly, do so by inserting the probe assembly into the

probe inlet shaft atop the source, and screwing the probe fitting into the probe inlet. See

Fitting the UniSpray probe assembly.

4. Using two hands, fit the UniSpray source enclosure to the two supporting studs on the
adaptor housing.

Figure 3–29: Fitting the source

Supporting studs

Source enclosure

Cable storage positions

5. Swing the source enclosure to the closed position, ensuring that it locks into place.

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Figure 3–30: UniSpray source connections

Probe adjuster cable (yellow)

High-voltage connector

6. Slide open the instrument's source interface door.

Figure 3–31: UniSpray Source connections to mass spectrometer

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Instrument source interface door

High-voltage cable socket

Probe adjuster cable socket (yellow)

7. Connect the high-voltage cable to the high-voltage cable socket on the mass spectrometer.

8. Connect the probe adjuster cable to the probe adjuster cable socket on the mass
spectrometer.

9. Close the instrument's source interface door.

10. Screw the probe assembly's PEEK fitting into the LC flow or syringe pump.

3.4.2

Removing the UniSpray source

You can remove the UniSpray source, and replace it with another compatible interface.

Required materials

• Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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

on the source before commencing this procedure.

To remove the UniSpray source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

Warning: To avoid burn injuries, exercise care when handling the components

of the source enclosure heated to high temperatures. Wait until the hot
components have sufficiently cooled before you handle them.

2. Disconnect the PEEK fitting connecting the probe assembly to the LC.

3. Swing open the UniSpray source enclosure unit from the source mounting on the mass
spectrometer.

4. Disconnect the probe adjuster cable.

5. Disconnect the high-voltage cable.

6. Carefully remove the UniSpray source module, and store it safely.

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3.5 NanoFlow ESI source

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

Figure 3–32: NanoFlow source, stage and microscope camera:

3.5.1

Microscope camera

Sprayer enclosure

X, Y, Z stage

A sprayer is mounted on an X, Y, Z stage (three-axis manipulator), which slides on a pair of guide
rails that allow its withdrawal from the source enclosure for maintenance and changes.

A light within the source provides illumination for the spray, which you can observe using the
video 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 materials

Chemical-resistant, powder-free gloves

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Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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, before performing maintenance operations that

involve handling components inside the mass spectrometer's ion source, allow the
source interior to cool.

To install the NanoFlow source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

Warning: To avoid burn injuries, exercise care when handling the components

of the source enclosure heated to high temperatures. Wait until the hot
components have sufficiently cooled before you handle them.

2. Remove the existing source enclosure (see Removing the source enclosure from the

instrument).

Notice: To prevent damage to the instrument, always retract the stage before

installing the source enclosure or closing the door.

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

Figure 3–33:

Retaining screw

Stop screw

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

5. Close the source enclosure door.

6. 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 instructions on how to fit each sprayer, see the corresponding reference:

• Universal NanoFlow Sprayer Installation and Maintenance Guide (part number

71500110107)

• Fitting a borosilicate glass capillary (nanovial)

• Capillary Electrophoresis and Capillary Electrochromatography Sprayer Operator's
Guide (part number 6666522)

7. Open the instrument’s source interface door (see Waters ACQUITY Xevo TQ-XS

UPLC/MS system).

8. Connect the probe cable to the instrument’s PROBE connection.

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

Note: The NanoFlow stage contains a high-voltage interlock, so that unless the sprayer is

pushed fully forward in the source, the capillary voltage (the voltage applied to the sprayer
assembly) and the sampling cone voltage are disabled.

Figure 3–34:

High-voltage cable

10. Close the instrument’s source interface door.

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3.5.2 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 tubing cutter

To fit a borosilicate glass capillary (nanovial):

Warning: To avoid lacerations, puncture injuries, and possible contamination with biohazardous

and toxic samples, do not touch the sharp end of the capillary.

Warning: To avoid eye injury from broken fused silica lines, use eye protection when

performing this procedure.

Notice: To avoid damaging capillaries, take great care when handling them; they are

extremely fragile. Always hold the blunt end, never the sharp end.

Warning: To avoid electric shock, ensure that the NanoFlow stage is fully retracted

from the source before beginning this procedure.

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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.

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

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Figure 3–35:

Capillary

Union

6. Remove the existing capillary from the sprayer.

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

Figure 3–36:

Capillary

Foam

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.

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 five mm of conductive elastomer over the blunt
end of the capillary.

10. Fit the capillary into the holder (probe).

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11. Finger-tighten the nut so that five mm of glass capillary protrudes from its end.

Tip: Measure the protrusion from the end of the nut to the shoulder of the glass capillary.

Figure 3–37: Sprayer Assembly:

PTFE tubing

Ferrule

Union

Knurled nut

Blue conductive elastomer

Glass capillary

5-mm protrusion

12. Screw the sprayer back into the assembly.

13. Replace the sprayer cover.

14. On the MassLynx MS Tune window, ensure that the Capillary parameter on the ES+/­Source tab is set to 0 kV.

Notice: To avoid damage to the capillary tip, adjust the sprayer tip position

before you push the sprayer inside the NanoFlow source enclosure. Ensure that
the capillary tip does not collide with the cone or the side of the source.

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

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3.5.3 Positioning the borosilicate glass capillary tip

x

2x

3x

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.

Figure 3–38: Capillary tip position:

Cone aperture diameter

For tuning instructions, see the MassLynx, Xevo TQ-XS online help, “Tuning manually for
NanoFlow operation”.

3.5.4

3.6

Restarting a stalled borosilicate glass capillary electrospray

Should the spray stop, you can restart it. To do so, in the 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.

ionKey source

The ionKey source integrates UPLC separation into the source of the mass spectrometer. For a
complete description, see ionKey source.

The following sections explain how to install or remove an ionKey source.

For additional information, see the ACQUITY UPLC M-Class System Guide (part number

715003588) and the ionKey/MS System Guide (part number 715004028).

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3.6.1 Installing the ionKey source

The ionKey source enclosure comprises the iKey docking port, the iKey locking handle, the
sprayer-enclosure, and a microscope camera.

Figure 3–39: ionKey source:

Microscope camera

Handle for locking and unlocking the iKey separation device

Front cover

Docking port for the iKey separation device

Required materials:

• Chemical-resistant, powder-free gloves

• Flat-blade screwdriver

• 1/4-inch open-end wrench

To install the ionKey source:

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

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Warning: To avoid burn injuries, exercise care when handling the components

of the source enclosure heated to high temperatures. Wait until the hot
components have sufficiently cooled before you handle them.

2. Remove the existing source enclosure (see Removing the source enclosure from the

instrument).

3. Using two hands, fit the ionKey source enclosure to the two supporting studs on the source
adaptor housing.

4. Swing the source enclosure to the closed position, ensuring that it locks into place.

Notice: To avoid damaging the µSample manager or mass spectrometer,

• ensure the µSample manager’s power is off before connecting the data/power
cable;

• ensure that the mass spectrometer is in Standby mode before beginning any
installation or maintenance.

Figure 3–40: ionKey source connections:

Fluid waste line

Optional post-column addition line

Fluid infusion line

Fluid inlet line

Data/power cable to PSPI connector on µSample manager

High-voltage cable

Options cable

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5. Connect the data/power cable to the PSPI connector on the rear of the µSample manager,
and use a screwdriver to firmly tighten the connector screws.

Figure 3–41: Source connections to mass spectrometer:

Data/power cable to PSPI µSample manager

High-voltage cable

Options cable

6. Connect the high-voltage cable (white) to the high-voltage supply outlet on the mass
spectrometer.

7. Connect the options cable (blue) to the options port on the mass spectrometer.

8. Identify the three fluid lines by the part numbers printed on their shrink-wrap tubing.

Table 3–2: ionKey tubing assemblies:

Part Number Order Number Description

430004188 700010399 Inlet tube

430004190 700010400 Infusion tube

430004212 700010401 Waste tube

430004476 700010470 Optional, post-column addition tube

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Figure 3–42: Fluid line aperture:

Aperture closed

Aperture open (spring-loaded)

Fluid line aperture

Figure 3–43: µSample manager injection valve:

Fluid inlet line connected to injection valve port 6

9. Connect the fluid inlet line to port 6 on the injection valve of the µSample manager.

10. Connect the fluid infusion line to port 2 on the fluidics divert valve.

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3.6.2 Installing ionKey source software

If you are installing an ionKey source on your Xevo TQ-XS for the first time, you must install the
appropriate MassLynx software SCN and the ACQUITY UPLC M-Class driver pack. For further
details, see the following documents:

• ACQUITY UPLC M-Class System Guide (part number 715003588) for detailed installation
procedures, and information on using the ACQUITY Inlet Switch Utility.

• MassLynx software v4.2 and related SCN release notes for detailed information about
installing MassLynx software and SCNs.

3.6.3

Installing the camera in the ionKey source

To install the camera in the ionKey source:

1. Connect the camera cable from the video output connector on the mass spectrometer’s
rear panel to the video-to-USB converter box.

Notice: To avoid damaging the video converter, make sure the workstation is

powered-off before connecting the converter to the workstation in the next step.

2. Connect the video-to-USB converter box to a USB port on the mass spectrometer’s
workstation.

3. On the Tune page, click Camera Viewer .

4. In Device settings dialog box, specify the parameter settings according to the following
table, and then click OK.

Tip: After you install the camera software, when you select the ionKey camera viewer for

the first time, the device settings dialog box opens. To subsequently open the device
settings dialog box, in the camera viewer, click View > Camera Options.

Table 3–3: Device settings for the camera:

Parameter Setting

Video norm PAL_B

Video format Y800 (768 x 576)

Frame rate (FPS) 25

Input channel 00 Video: Composite

3.6.4 Removing an ionKey source

You can remove the ionKey source, and replace it with a conventional interface.

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Alternative: If you are using the ionKey source with an ACQUITY UPLC M-Class system

mounted on an M-Class cart fitted with an ionKey or universal source holder, you can secure the
source enclosure to the holder. Doing so keeps the enclosure close to the Xevo TQ-XS, for when
it is next needed. Securing the source enclosure also assists with managing the ionKey source’s
fluid lines and helps prevent contamination of the fluid lines.

See the ACQUITY M-Class documentation for additional information about installing the ionKey
source holder on the M-Class cart, and securing the source enclosure to the holder.

See Installing and Using the Universal Source Holder (part number 715004884) for additional
information about installing and using the universal source holder on the M-Class cart, and
securing the source enclosure to the holder.

See also: The ionKey/MS System Guide (part number 715004028).

Required materials

• Chemical-resistant, powder-free gloves

• 1/4-inch open-end wrench

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

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

on the source before commencing this procedure.

To remove the ionKey source:

1. Prepare the instrument for working on its source (see Preparing the instrument for working

on the source).

Warning: To avoid burn injuries, exercise care when handling the column or

other components heated to high temperatures. Wait until the hot components
have sufficiently cooled before you handle them.

2. Remove the iKey from the docking port (see the ionKey/MS System Guide, part number

715004028).

3. Close the MassLynx software.

4. Power-off the µSample manager.

5. Disconnect the PSPI cable.

6. Using the ¼-inch open-end wrench, loosen and disconnect the fluid waste line and fluid
inlet lines from the µSample manager.

7. Disconnect the optional post-column addition line from the flow control module of the
auxiliary solvent manager.

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8. Swing open the ionKey source enclosure unit from the source mounting on the mass
spectrometer.

9. Disconnect the high-voltage cable (white) from the high-voltage supply outlet on the mass
spectrometer.

10. Disconnect the reference probe power cable (green) from the reference probe power inlet
on the mass spectrometer.

11. Disconnect the options cable (blue) from the options port on the mass spectrometer.

12. Disconnect the fluid infusion line from the onboard IntelliStart Fluidics system on the mass
spectrometer.

13. Carefully remove the ionKey source module, and store safely.

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4 Maintenance procedures

This section provides the maintenance guidelines and procedures necessary to maintain the
mass spectrometer's performance.

Keep to a maintenance schedule, and perform maintenance as required and described in this
section.

4.1 Maintenance schedule

The following table lists periodic maintenance schedules that ensure optimum instrument
performance.

Table 4–1: Maintenance schedule:

Procedure Frequency For information...

Clean the instrument case. As required. See Cleaning the instrument

case.

Empty the nitrogen exhaust
trap bottle.

Clean the source
components.

Replace the ESI probe tip. When sensitivity decreases to

Replace the probe
assembly.

Clean the APCI probe tip.
(Options using the APCI
probe adaptor only.)

Check daily, empty as required. See Emptying the nitrogen

When source components are
visibly fouled, the background or
high-peak contaminants are
unacceptably high, or sensitivity
decreases to unacceptable levels.

unacceptable levels, or if blocked
or damaged.

When sensitivity decreases to
unacceptable levels or signal is
unstable due to inconsistent
sample flow.

When sensitivity decreases to
unacceptable levels or when
significant chemical interference
is present.

exhaust trap bottle.

See Cleaning the source

components.

See Replacing the ESI probe

tip and gasket.

See Replacing the probe

assembly.

See Cleaning the APCI probe

tip.

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Table 4–1: Maintenance schedule: (continued)

Procedure Frequency For information...

Clean or replace the corona
pin (APCI and ESCi
modes).

Replace the APCI probe
heater. (Options using the
APCI probe adaptor only.)

Replace the probe
assembly (UniSpray mode).

Clean or replace the
impactor pin (UniSpray
mode).

Replace the ion block
heater cartridge.

Replace the source
assembly seals.

When the corona pin is corroded
or black, or the sensitivity

See Cleaning or replacing the

corona pin.

decreases to unacceptable levels.

If the heater fails to heat when the
instrument is switched to Operate.

When sensitivity decreases to
unacceptable levels or signal is

See Replacing the APCI

probe heater.

See Replacing the UniSpray

probe assembly.

unstable due to inconsistent
sample flow.

When the impactor pin is
corroded or black, or the

See Maintaining the UniSpray

impactor pin.

sensitivity decreases to
unacceptable levels.

If the heater fails to heat when the
instrument is pumped down

See Replacing the ion block

source heater.

(evacuated).

Annually. See Replacing the source

assembly seals.

Replace the roughing pump. Every 3 years. Contact Waters.

Replace the air filters. Annually. See Replacing the air filter

inside the front door.

Clean the APPI/APCI
source UV lamp window.

When the window becomes
visibly dirty, or when the

See APPI/APCI source—

cleaning the lamp window.

sensitivity decreases to
unacceptable levels.

Change the APPI/APCI
source UV lamp bulb.

Replace the APPI lamp
drive assembly O-rings.

When the bulb fails. See APPI/APCI source --

changing the UV lamp bulb.

Annually. See APPI/APCI source—

replacing the APPI lamp drive

seals.

Replace an ionKey source
fluid line.

Clean the ionKey source
surface, fluid connectors, or

As required or during periodic
maintenance.

As required or during periodic
maintenance.

See Replacing the fluidic lines

of the ionKey source.

See Cleaning the ionKey

source and connectors.

electronic connectors.

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4.2 Spare parts

Waters recommends that you replace only the parts mentioned in this document. For spare parts
details, see the Waters Quality Parts Locator on the Waters Web site’s Services & Support page
(http://www.waters.com/waters/en_US/Spare-Parts/nav.htm?cid=511444).

4.3

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 User's Guide (part number 715003036)

• Your sales representative

• Your local Waters subsidiary

• Waters Customer Support

To submit a Connections INSIGHT request:

1. Select Troubleshoot > Submit Connections INSIGHT Request.

2. In the Connections INSIGHT Request dialog box, type your name, telephone number, e­mail address, and a description of the problem.

3. Click Submit, and allow approximately five minutes to save the service profile.

Recommendation: A .ZIP file containing your Connections INSIGHT profile is

forwarded to Waters customer support for review. Saving a service profile or plot file from
the Instrument Console can require as much as 150 MB of file space.

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4.4 Safety and handling

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

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when

working with hazardous materials. Consult the Material Safety Data Sheets regarding
the solvents you use. Additionally, consult the safety representative for your
organization regarding its protocols for handling such materials.

Warning: To avoid electric shock, observe these precautions:

• Do not remove the mass spectrometer’s protective panels. The components they
cover are not user-serviceable.

• When the instrument is in Operate mode, avoid touching the areas marked with the
high voltage warning symbol. To touch external areas marked with the symbol, first
put the instrument in Standby mode.

Warning: To avoid burn injuries, take great care while working with the probe and

source; these components can be hot.

Warning: To avoid puncture wounds, take great care working with the source

enclosure open if one or both of these conditions apply:

• An ESI probe is fitted (the probe’s tip is sharp).

• A corona pin is fitted (the pin’s tip is sharp).

Warning: To avoid injury, ensure that these criteria are met when performing

maintenance operations 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.

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Notice: To avoid damaging the iKey:

• Handle it with care. The component parts are fragile.

• For recommendations regarding the maximum pressure to subject the device to, see
the iKey Separation Device Care and Use Manual (part number 720004897EN).

• Do not apply electrospray potential to the emitter without flow.

• Do not drop it.

• Do not immerse it in liquid.

• Do not freeze or overheat it. Keep the iKey within the allowed temperature ranges
during operation and in storage.

• Use the iKey sheath to protect the device when it is not in use.

• Do not bend or pull the capillary connection tubing at the ionKey source module
coupling.

• Avoid excess voltage, which can erode the emitter over time.

• Do not touch the electrospray emitter, for it can bend.

• Decompress the iKey before you remove it from the source.

See Safety advisories for safety advisory information.

4.5

4.5.1

Preparing the instrument for working on the source

For safety reasons, you must follow this procedure before working on the source (for example,
when changing the probe, installing or removing the corona pin, or operating the source isolation
valve), and when maintaining the source.

Follow the procedure for the software that controls your mass spectrometer:

Using MassLynx software to prepare the instrument for operations on or inside its source

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.

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Note: If column flow is required, divert the LC flow to waste:

1. 1. In the Instrument Console system tree, expand Xevo TQ-XS Detector, Interactive
Fluidics.

2. Click Control .

3. Select Waste as the flow state.

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

not illuminated.

3. Wait three 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.

4.6 Removing and refitting the source enclosure

Before performing certain maintenance procedures, or fitting the optional sources to the
instrument, you must remove the source enclosure that is currently fitted to the instrument.

Note: The following procedures apply to both the standard and optional source enclosures.

4.6.1

Removing the source enclosure from the instrument

Required materials

Chemical-resistant, powder-free gloves

To remove the source enclosure:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

1. Prepare the instrument for working on the source (see Prepare the instrument for working

on the source).

Warning: To avoid burn injuries, exercise care when handling the components

of the source enclosure heated to high temperatures. Wait until the hot
components have sufficiently cooled before you handle them.

2. Remove the probe adaptor from the source (Removing the probe adaptor).

3. Slide open the instrument’s source interface door (see Waters ACQUITY Xevo TQ-S

UPLC/MS system).

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4. Disconnect the probe adjuster and options cables from the instrument’s connectors.

Warning: To avoid puncture wounds, handle sharp parts and materials with

care.

Notice: To avoid damaging the sample inlet, when removing a NanoLockSpray

source enclosure, you must slide the sprayer platform out of the source enclosure
before you open the enclosure.

5. Pull the source enclosure release (located at the bottom, right-hand side) outwards, and

swing open the enclosure.

6. Using both hands, grasp the source enclosure, and lift it vertically off the two supporting

studs on the source adaptor housing.

Figure 4–1:

Supporting stud

Source enclosure

Cable storage positions

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

source enclosure.

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4.6.2 Fitting the source enclosure to the instrument

Required materials

Chemical-resistant, powder-free gloves

To fit the source enclosure to the instrument:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

Warning: To avoid puncture injuries, handle sample needles, syringes, fused silica

lines, and borosilicate tips with extreme care.

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

adaptor housing.

Notice: To avoid damaging the sample inlet, when removing a NanoLockSpray

source enclosure, you must slide the sprayer platform out of the source enclosure
before you open the enclosure.

4.7

2. Close the source enclosure.

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

Tip: The cables and connectors are color coded; the blue-sleeved cable connects to the

blue connector and the yellow-sleeved cable to the yellow connector.

4. Slide closed the instrument’s source interface door.

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 materials

Chemical-resistant, powder-free gloves

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4.7.1 Closing the source isolation valve

To close the source isolation valve before starting a maintenance procedure:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

1. Prepare the instrument for working on the source (see Preparing the instrument for working

on the source).

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

enclosure open.

Warning: To avoid puncture wounds, take great care working with the source

enclosure open if one or both of these conditions apply:

• An ESI probe is fitted (the probe’s tip is sharp).

• A corona pin is fitted (the pin’s tip is sharp).

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

swing open the enclosure.

3. Close the source isolation valve by turning its handle counterclockwise, to the vertical

position.

Figure 4–2:

Isolation valve handle in closed position

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4.7.2 Opening the source isolation valve

To open the source isolation valve after completing a maintenance procedure:

Warning: To avoid personal contamination with biohazards, toxic materials, and corrosive

materials, wear chemical-resistant gloves when performing this procedure.

Warning: To avoid puncture wounds, take great care working with the source

enclosure open if one or both of these conditions apply:

• An ESI probe is fitted (the probe’s tip is sharp).

• A corona pin is fitted (the pin’s tip is sharp).

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

Figure 4–3:

4.8

Isolation valve handle in open position

2. Close the source enclosure.

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 is provided with the instrument.

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