Waters Xevo TQ-S micro Overview And Maintenance Manual

Waters Xevo TQ-S micro

Overview and Maintenance Guide

715004599/ Revision B

Copyright © Waters Corporation 2014 – 2016

All rights reserved

ii January 11, 2016, 715004599 Rev. B

General Information

Copyright notice

© 2014 – 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 no tice and should not be
construed as a commitment by Waters Corporation. Waters Corporation assumes no
responsibility for any errors that may appear in this document. This document is believed
to be complete and accurate at the time of publication. In no event shall Waters
Corporation be liable for incidental or consequential damages in connection with, or
arising from, its use. For the most recent revision of this document, consult the Waters
Web site (waters.com).

Trademarks

ACQUITY, ACQUITY UltraPerformance LC, ACQUITY UPLC, Alliance, Connections
INSIGHT , ESCi, MassLynx, “THE SCIENCE OF WHAT’S POSSIBLE”, UPLC, Waters,
Waters Quality Parts, and Xevo are registered trademarks of Waters Corporation, and
iKey, IntelliStart, ionKey, ionKey/MS, IonSABRE, NanoFlow, RADAR, T-Wave, and
ZSpray are trademarks of Waters Corporation.

DART is a registered trademark of JEOL USA Inc.
GELoader is a registered trademark of New Brunswick Scientific, Co., Inc.
LDTD is a trademark of Phytronix Technologies Inc.
PEEK is a trademark of Victrex Corporation.
Phillips and Pozidriv are registered trademarks of Phillips Screw Company, Inc.
snoop and Swagelok are registered trademarks of Swagelok Company.
Spark Holland and Symbiosis are trademarks of Spark-Holland BV.
Viton is a registered trademark of DuPont.
Other registered trademarks or trademarks are the sole property of their owners.

January 11, 2016, 715004599 Rev. B iii

Customer comments

Waters’ Technical Communications organization invites you to report any errors that you
encounter in this document or to suggest ideas for otherwise improving it. Help us better
understand what you expect from our documentation so that we can continuously improve
its accuracy and usability.

We seriously consider every customer comment we receive. You can reach us at
[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

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

Waters locations worldwide. Visit www.waters.com.

fax [phone].
For other locations worldwide, phone and fax

numbers appear in the Waters Web site.

Conventional mail Waters Corporation

34 Maple Street
Milford, MA 01757
USA

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, and consult your organization’s standard operating procedures.

iv January 11, 2016, 715004599 Rev. B

Safety hazard symbol notice

Documentation needs to be consulted in all cases where the symbol is used to find
out the nature of the potential hazard and any actions which have to be taken.

Considerations specific to the Xevo TQ-S micro

Power cord replacement hazard

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

States and HAR-type (or better) in Europe. The main power cord must only be
replaced with one of adequate rating. For information regarding what cord to use in
other countries, contact your local Waters distributor.

Solvent leakage hazard

The source exhaust system is designed to be robust and leak-tight. Waters recommends
you perform a hazard analysis, assuming a maximum leak into the laboratory atmosphere
of 10% LC eluate.

Warning:

• To confirm the integrity of the source exhaust system, renew the source
O-rings at intervals not exceeding one year.

• To avoid chemical degradation of the source O-rings, which can
withstand exposure only to certain solvents (see page 258), determine
whether any solvents you use that are not listed are chemically
compatible with the composition of the O-rings.

January 11, 2016, 715004599 Rev. B v

Spilled solvent s hazard

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

not place reservoir bottles on top of the instrument or on its front ledge.

Flammable solvents hazard

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

of a mass spectrometer’s ion source, ensure that nitrogen flows continuously
through the source. The nitrogen supply pressure must not fall below 400 kPa
(4 bar, 58 psi) during an analysis requ iring the use of flammable solvents. Also a
gas-fail device must be installed, to interrupt the flow of LC solvent should the
nitrogen supply fail.

When using flammable solvents, ensu re that a stream of nitrogen continuously flushes the
instrument’s source, and the nitrogen supply pressure remains above 400 kPa (4 bar,
58 psi). You must also install a gas-fail device that interrupts the solvent flowing from the
LC system in the event the supply of nitrogen fails.

Overload hazard

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

TQ-S micro does not exceed 15kg.

vi January 11, 2016, 715004599 Rev. B

Glass-breakage hazard

Source enclosure assemblySource enclosure assembly

Warning: To avoid injuries from broken glass, falling objects, or

exposure to toxic or biohazardous substances, never place containers
on top of the instrument or on its front covers.

High temperature hazard

Warning: To avoid burn injuries, ensure the source heater is turned off and the ion

block is cool before performing maintenance on these components. The source ion
block, located behind the source enclosure assembly, can become hot.

Xevo TQ-S micro high temperature hazard:

January 11, 2016, 715004599 Rev. B vii

Hazards associated with removing an instrument from service

Warning: To avoid personal contamination with biohazards, toxic

materials, or corrosive materials, wear chemical-resistant gloves
during all phases of instrument decontamination.

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

lines, and borosilicate tips with extreme care.

When you remove the instrument from use to repair or dispose of it, you must
decontaminate all of its vacuum areas. These are the areas in which you can expect to
encounter the highest levels of contamination:

• Source interior

• Waste tubing

• Exhaust system

• Rotary pump oil (where applicable)

The need to decontaminate other vacuum areas of the instrument depends on the kinds of
samples the instrument analyzed and their levels of concentration. Do not dispose of the
instrument or return it to Waters for repair until the authority responsible for approving its
removal from the premises specifies the extent of decontamination required and the level
of residual contamination permissible. That authority must also prescribe the method of
decontamination to be used and the appropriate protection for personnel undertaking the
decontamination process.

You must handle items such as syringes, fused silica lines, and borosilicate tips used to
carry sample into the source area in accordance with laboratory procedures for
contaminated vessels and sharps. To avoid contamination by carcinogens, toxic
substances, or biohazards, you must wear chemical-resistant gloves when handling or
disposing of used oil.

Bottle placement prohibition

Prohibited: To avoid injury from electric shock or fire, and to prevent damage to

the workstation and ancillary equipment, do not place objects filled with
liquid—such as solvent bottles—on these items, or expose them to dripping or
splashing liquids.

viii January 11, 2016, 715004599 Rev. B

FCC radiation emissions notice

Changes or modifications not expressly approved by the party responsible for compliance,
could void the users authority to operate the equipment. This device complies with Part 15
of the FCC Rules. Operation is subject to the following two conditions: (1) this device
may not cause harmful interference, and (2) this device must accept any interference
received, including interference that may cause undesired operation.

Electrical power safety notice

Do not position the instrument so that it is difficult to operate the disconnecting device.

Equipment misuse notice

If the equipment is used in a manner not specified by the manufacturer, the protection
provided by the equipment may be impaired.

Safety advisories

Consult Appendix A for a comprehensive list of warning advisories and notices.

January 11, 2016, 715004599 Rev. B ix

Operating this instrument

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

Applicable symbols

Symbol Definition

Manufacturer

Date of manufacture

Part number catalog number

5()

Serial number

Supply ratings

Authorized representative of the European Community

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

Australia EMC Compliant

or

Confirms that a manufactured product complies with all
applicable United States and Canadian safety requirements

x January 11, 2016, 715004599 Rev. B

Symbol Definition

Consult instructions for use

Electrical and electronic equipment with this symbol may
contain hazardous substances and should not be disposed
of as general waste.

For compliance with the Waste Electrical and Electronic
Equipment Directive (WEEE) 2012/19/EU, contact W aters
Corporation for the correct disposal and recycling
instructions.

January 11, 2016, 715004599 Rev. B xi

Audience and purpose

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

Intended use of the Xevo TQ-S micro

Waters designed the Xev o TQ-S mic r o for use as a research tool to accurately,
reproducibly, and robustly quantify target compounds present at the lowest possible levels
in highly complex sample matrices. The Xevo TQ-S micro is not intended for use in
diagnostic applications.

Calibrating

To calibrate LC systems, follow accepta ble calibration methods using at least five
standards to generate a standard curve. The concentration range for standards should
include the entire range of QC samples, typical specimens, and atypical specimens.

When calibrating mass spectrometers, consult the instrument’s online Help system for
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.

When analyzing samples from a complex matrix such as soil, tissue, serum/plasma, whole
blood, and other sources, note that the matrix components can adversely affect LC/MS
results, enhancing or suppressing ionization. To minimize these matrix effects, adopt the
following measures:

• Prior to the instrumental analysis, use appropriate sample pretreatment such as
protein precipitation, liquid/liquid extraction (LLE), or solid phase extraction (SPE)
to remove matrix interferences.

• Whenever possible, verify method accuracy and precision using matrix-matched
calibrators and QC samples.

xii January 11, 2016, 715004599 Rev. B

• Use one or more internal standard compounds, preferably isotopically labeled
analytes.

EMC considerations

Canada spectrum management emissions notice

This class A digital product apparatus complies with Canadian ICES-001.
Cet appareil numérique de la classe A est conforme à la norme NMB-001.

ISM Classification: ISM Group 1 Class A

This classification has been assigned in accordance with CISPR 11 Industrial Scientific
and Medical, (ISM) instrument requirements. Group 1 products apply to intentionally
generated and/or used conductively coupled radio-frequency energy that is necessary for
the internal functioning of the equipment. Class A products are suitable for use in all
establishments other than residential locations and those directly connected to a low
voltage power supply network supplying a building for domestic purposes.

There may be potential difficulties in ensuring electromagnetic compatibility in other
environments due to conducted as well as radiated disturbances.

Do not use the equipment in close proximity to sources of strong electromagnetic radiation
(for example, unshielded intentional RF sources), as these may interfere with the
equipment’s proper operation.

This equipment complies with the emission and immunity requirements described in the
relevant parts of IEC/EN 61326: Electrical equipment for measurement, control and

laboratory use — EMC requirements.

January 11, 2016, 715004599 Rev. B xiii

EC authorized representative

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

Telephone: [phone]
Fax: [phone]
Contact: Quality manager

xiv January 11, 2016, 715004599 Rev. B

Table of Contents

Copyright notice ..................................................................................................................... iii

Trademarks ............................................................................................................................. iii

Customer comments ................................................ .............................................................. iv

Contacting Wa ters ................................................................................................................. iv

Safety considerations ............................................................................................................. iv

Safety hazard symbol notice............................................................................................... v

Considerations specific to the Xevo TQ-S micro............................................................... v

FCC radiation emissions notice......................................................................................... ix

Electrical power safety notice............................................................................................ ix

Equipment misuse notice................................................................................................... ix

Safety advisories................................................................................................................ ix

Operating this instrument ...................................................................................................... x

Applicable symbols ............................................................................................................ x

Audience and purpose....................................................................................................... xii

Intended use of the Xevo TQ-S micro.............................................................................. xii

Calibrating ........................................................................................................................ xii

Quality control.................................................................................................................. xii

EMC considerations ............................................................................................................. xiii

Canada spectrum management emissions notice............................................................. xiii

ISM Classification: ISM Group 1 Class A...................................................................... xiii

EC authorized representative ............................................................................................. xiv

1 Specifications and Operating Modes ....................................................................... 23

Uses and compatibility ......................................................................................................... 24

ACQUITY Xevo TQ-S micro UPLC/MS systems........................................................... 26

Software and data system ................................................................................................. 29

Ionization techniques and source probes ........................................................................... 31

Electrospray ionization (ESI) ........................................................................................... 31

January 11, 2016, 715004599 Rev. B xv

Combined ESI and APCI (ESCi)...................................................................................... 31

Atmospheric pressure chemical ionization (APCI).......................................................... 31

Dual-mode APPI/APCI source......................................................................................... 31

NanoFlow source.............................................................................................................. 32

Atmospheric solids analysis probe (ASAP) ..................................................................... 33

Atmospheric pressure gas chromatography (APGC) ....................................................... 33

ionKey source................................................................................................................... 33

IntelliStart Fluidics system .............................................................................. ..... ............... 34

Functionality..................................................................................................................... 34

System operation .............................................................................................................. 35

Ion optics ............................................................................................................................... 36

MS operating modes ............................................................................................................ 36

MS/MS operating modes ..................................................................................................... 38

Product (daughter) ion mode............................................................................................ 39

Precursor (parent) ion mode ............................................................................................. 40

Multiple reaction monitoring mode.................................................................................. 40

Constant neutral loss mode............................................................................................... 42

Sample inlet ............................................ .... ..... ..................................................................... 43

Leak sensors ...................................................................... .... ............................................... 43

Vacuum system ..................................................................................................................... 43

Rear panel connections ........................................................................................................ 44

2 Preparing for Operation ........................................................................................... 45

Starting the mass spectrometer ........................................................................................... 46

Verifying the instrument’s state of readiness.................................................................... 49

Monitoring the instrument LEDs...................................................................................... 49

Tuning and calibration information.................................................................................. 49

Running the instrument at different flow rates................................................................. 50

Preparing the IntelliStart Fluidics system ......................................................................... 51

Installing the reservoir bottles .......................................................................................... 51

Purging the infusion pump................................................................................................ 53

xvi January 11, 2016, 715004599 Rev. B

Rebooting the instrument .................................................................................................... 53

Leaving the mass spectrometer ready for operation ........................................................ 54

Emergency shutdown of the mass spectrometer............................................................... 54

3 Changing the Mode of Operation ............................................................................ 55

ESI mode ............................................................................................................................... 56

Installing the ESI probe.................................................................................................... 56

Removing the ESI probe................................................................................................... 59

ESCi mode ............................................................................................................................ 60

Optimizing the ESI probe for ESCi operation.................................................................. 60

APCI mode ........................................................................................................................... 60

Installing the IonSABRE II probe .................................................................................... 61

Removing the IonSABRE II probe................................................................................... 64

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

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

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

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

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

Installing the combined APPI/APCI source..................................................................... 70

Removing the IonSABRE II probe and APPI/APCI source enclosure ............................ 71

NanoFlow source .................................................................................................................. 72

Installing the NanoFlow source........................................................................................ 73

Fitting a borosilicate glass capillary (nanovial)................................................................ 76

Positioning the borosilicate glass capillary tip................................................................. 79

ionKey source ....................................................................................................................... 80

Installing the ionKey source............................................................................................. 80

Installing ionKey source software.................................................................................... 85

Installing the camera in the ionKey source....................................................................... 86

Removing the ionKey source............................................................................................ 86

January 11, 2016, 715004599 Rev. B xvii

4 Maintenance Procedures .......................................................................................... 89

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

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

Troubleshooting with Connections INSIGHT ................................................................... 94

Safety and handling ............................................................................................................. 95

Preparing the instrument for operations on or inside its source ..................................... 97

Removing and refitting the source enclosure .................................................................... 98

Removing the source enclosure from the instrument....................................................... 98

Fitting the source enclosure to the instrument................................................................ 100

Installing and removing the corona pin ............................................ .... ..... ...................... 101

Installing the corona pin in the source............................................................................ 101

Removing the corona pin from the source...................................................................... 103

Operating the source isolation valve ................................................................................ 104

Removing O-rings and seals .............................................................................................. 107

Cleaning the instrument case ............................................................................................ 108

Emptying the exhaust trap bottle ..................................................................................... 108

Gas ballasting the roughing pump .................................................................................... 110

Checking the roughing pump oil level ............................................................................... 112

Adding oil to the roughing pump ....................................................................................... 113

Cleaning the source components ......................................... ..... .... ..................................... 114

Cleaning the sampling cone assembly ............................................................................... 115

Removing the sampling cone assembly from the source................................................. 115

Disassembling the sampling cone assembly.................................................................... 117

Cleaning the sample cone and cone gas nozzle.............................................................. 120

Assembling the sampling cone assembly....................................................................... 122

Fitting the sampling cone assembly to the source.......................................................... 123

Cleaning the ion block assembly ....................................................................................... 125

Removing the ion block assembly from the source assembly........................................ 125

xviii January 11, 2016, 715004599 Rev. B

Disassembling the source ion block assembly................................................................ 127

Cleaning the ion block components................................................................................ 132

Assembling the source ion block assembly.................................................................... 133

Fitting the ion block assembly to the source assembly................................................... 135

Cleaning the ion guide assembly ....................................................................................... 135

Removing the pumping block assembly and ion guide assembly from the instrument . 136
Removing the ion guide assembly and differential aperture from the pumping block

assembly................................................................................................................... 137

Removing the differential aperture support and the differential aperture from the ion guide

assembly................................................................................................................... 138

Cleaning the differential aperture................................................................................... 140

Cleaning the ion guide assembly.................................................................................... 141

Fitting the differential aperture and the differential aperture support onto the ion guide

assembly................................................................................................................... 143

Fitting the ion guide assembly and differential aperture onto the pumping block assembly.

144

Fitting the pumping block assembly and ion guide assembly onto the instrument........ 145

Replacing the ESI probe tip and gasket ........................................................................... 146

Replacing the probe tip and gasket................................................................................. 146

Replacing the ESI probe capillary.................................................................................. 150

Cleaning the IonSABRE II probe tip ............................................................................... 166

Replacing the IonSABRE II probe sample capillary ...................................................... 167

Removing the existing capillary..................................................................................... 167

Installing the new capillary............................................................................................. 169

Cleaning or replacing the corona pin ............................................................................... 172

Replacing the IonSABRE II probe heater ....................................................................... 174

Removing the IonSABRE II probe heater...................................................................... 174

Fitting the new IonSABRE II probe heater .................................................................... 176

Replacing the ion block source heater .............................................................................. 177

Replacing the source assembly seals ................................................................................. 180

Removing the probe adjuster assembly probe and source enclosure seals..................... 181

Fitting the new source enclosure and probe adjuster assembly seals............................. 183

January 11, 2016, 715004599 Rev. B xix

Replacing the air filter ....................................................................................................... 184

Replacing the roughing pump oil ..................................................................................... 187

Replacing the roughing pump’s oil demister element .................................................... 190

APPI/APCI source—changing the UV lamp bulb .......................................................... 195

APPI/APCI source—cleaning the lamp window ............................................................. 196

APPI/APCI source—replacing the APPI lamp drive seals ............................................ 198

Removing the APPI lamp drive assembly seals............................................................. 198

Fitting the new APPI lamp drive assembly O-rings..................................... ..... .... ......... 204

Replacing the fluidic lines of the ionKey source .............................................................. 206

Removing a fluidic line .............................................................. ..... ............................... 207

Installing a fluidic line.................................................................................................... 210

Cleaning the ionKey source and connectors ..................................................................... 211

Replacing the instrument’s fuses ...................................................................................... 214

A Safety Advisories .................................................................................................... 215

Warning symbols ................................................................................................................ 216

Specific warnings............................................................................................................ 217

Notices ................................................................................................................................. 220

Prohibition symbol ............................................................................................................. 220

Warnings that apply to all Waters instruments and devices .......................................... 221

Warnings that address the replacing of fuses .................................................................. 226

Electrical and handling symbols ....................................................................................... 227

Electrical symbols........................................................................................................... 227

Handling symbols........................................................................................................... 228

B External Connections ............................................................................................. 231

External wiring and vacuum connections ........................................................................ 232

Connecting the oil-filled roughing pump ......................................................................... 233

Connecting electric cables to the oil-filled roughing pump............................................ 237

xx Janua ry 11, 2016, 715004599 Rev. B

Connecting the Edwards oil-free roughing pump ........................................................... 238

Connecting electric cables to the Edwards oil-free roughing pump............................... 241

Connecting to the nitrogen gas supply ............................................................................. 242

Connecting to the collision cell gas supply ....................................................................... 243

Connecting the nitrogen exhaust line ............................................................................... 244

Connecting the liquid waste line ....................................................................................... 246

Connecting the workstation .............................................................................................. 249

Connecting Ethernet cables .............................................................................................. 250

I/O signal connectors ......................................................................................................... 251

Signal connections.......................................................................................................... 252

Connecting to the power supply ....................................................................................... 255

C Materials of Construction and Compliant Solvents ........................................... 257

Preventing contamination ................................................................................................. 258

Items exposed to solvent .................................................................................................... 258

Solvents used to prepare mobile phases ........................................................................... 259

D Plumbing the IntelliStart Fluidics System ........................................................... 261

Preventing contamination ................................................................................................. 262

The selector valve ............................................................................................................... 262

Plumbing schematic ........................................................................................................... 263

Tubing and connection specifications ............................................................................... 264

January 11, 2016, 715004599 Rev. B xxi

xxii January 11, 2016, 715004599 Rev. B

1 Specifications and Operating

Modes

This chapter describes the instrument, including its controls and connections for gas
and plumbing.

Contents:
Topic Page

Uses and compatibility ................................................................................. 24

Ionization techniques and source probes...................................................... 31

IntelliStart Fluidics system........................................................................... 34

Ion optics ...................................................................................................... 36

MS operating modes..................................................................................... 36

MS/MS operating modes.............................................................................. 38

Sample inlet.................................................................................................. 43

Leak sensors ................................................................................................. 43

Vacuum system............................................................................................. 43

Rear panel connections................................................................................. 44

January 11, 2016, 715004599 Rev. B 23

1 Specifications and Operating Modes

Uses and compatibility

The Waters® Xevo® TQ-S micro is a triple quadrupole, atmospheric pressure ionization
(API) mass spectrometer. Designed for routine HPLC/MS/MS and UPLC

analyses in quantitative and qualitative applications, it can operate at fast acquisition
speeds compatible with UltraPerformance LC

You can use the TQ-S micro with the following high-performance Waters ZSpray™
sources:

• Standard multimode electrospray ionization/atmospheric pressure chemical
ionization/combined electrospray ionization and atmospheric pressure chemical

ionization (ESI/APCI/ESCi

Requirement: Dedicated APCI operation requires an additional probe

(IonSABRE™ II).

• Optional dual-mode APPI/APCI source

• Optional NanoFlow™ ESI source

• Optional ionKey

®

source

®

) source.

®

applications.

®

/MS/MS

• Optional APGC source

• Optional ASAP probe

For information on installing and removing the optional APGC, and ASAP probe, refer to
the operator’s guide supplements supplied with them.

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

• DART

®

• DESI

• LDTD™

For further details, refer to the appropriate manufacturer’s documentatio n.

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

Xevo TQ-S micro. Refer to the MassLynx

®

online Help for more information about

supported sources.
For mass spectrometer specifications, see the Waters Xevo TQ-S micro Site Preparation

Guide.

24 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Xevo TQ-S micro shown with visor down, and visor up:

TP03407

Visor up

Uses and compatibility

IntelliStart technology

IntelliStart™ technology monitors LC/MS/MS performance and reports when the
instrument is ready for use.

The software automatically tunes and mass calibrates the instrument, displays
performance readbacks, and enables simplified setup of the system for use in routine
analytical and open access applications. (See page 29.)

January 11, 2016, 715004599 Rev. B 25

1 Specifications and Operating Modes

The IntelliStart Fluidics1 system is built into the instrument. It delivers sample directly to
the MS probe from the LC column or from two integral reservoirs. The integral reservoirs
can also deliver sample through direct or combined infusion so that you can optimize
instrument performance at analytical flow rates. See the instrument’s online Help for
further details of IntelliStart.

ACQUITY Xevo TQ-S micro UPLC/MS systems

The Waters Xevo TQ-S micro is compatible with the following ACQUITY UPLC®
systems:

• ACQUITY UPLC

• ACQUITY UPLC H-Class

• ACQUITY UPLC I-Class

• ACQUITY UPLC M-Class (with NanoFlow or ionKey source)

If you are not using one of these systems, refer to the documentation relevant to your LC
system.

The ACQUITY
ACQUITY UPLC H-Class, or ACQUITY UPLC I-Class and the Waters Xevo TQ-S
micro fitted with the ESI/APCI/ESCi source.

The ACQUITY
M-Class system and the W aters Xevo TQ-S micro fitted with either a Nanoflow source, or
an ionKey source.

®

Xevo TQ-S micro UPLC/MS system includes an ACQUITY UPLC,

®

Xevo TQ-S micro UPLC/MS system can include an ACQUITY UPLC

If you are not using your instrument as part of an ACQUITY UPLC system, refer to the
documentation for your LC system.

Note: ACQUITY system options can vary depending on the software used to operate the

Xevo TQ-S micro.

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

26 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Uses and compatibility

ACQUITY system core components

Core system components for each ACQUITY system are listed below:

System Core components

ACQUITY UPLC • Binary solvent manager

• Sample manager

• Column heater

•UPLC detectors

• Solvent tray

• ACQUITY UPLC column

• Software to control the system

ACQUITY UPLC H-Class • Quaternary solvent manager

• Sample manager with flow-through needle

• Column heater-active

•UPLC detectors

• Solvent tray

• ACQUITY UPLC column

• Software to control the system

ACQUITY UPLC I-Class • Binary solvent manager

• Sample manager

• Column heater-active

•UPLC detectors

• Solvent tray

• ACQUITY UPLC column

• Software to control the system

January 11, 2016, 715004599 Rev. B 27

1 Specifications and Operating Modes

System Core components

ACQUITY UPLC M-Class • µBinary solvent manager

For further instruction, see the ACQUITY UPLC System Operator’s Guide, ACQUITY

UPLC H-Class System Guide, ACQUITY UPLC I-Class System Guide, and Controlling
Contamination in UPLC/MS and HPLC/MS Systems (part number 715001307). You can

find the documents on http://www.waters.com; click Services and Support > Support
Library.

• µSample manager - FL

• Trap Valve Manager (including active column
heater)

• TuV and PDA UPLC detectors

• Solvent tray

• ACQUITY UPLC columns of internal diameters
ranging from 75 µm to 1 mm. The column
hardware and the matched outlet tubing can
withstand pressure of as much as 15,000 psi.

• Software to control the system

28 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Xevo TQ-S micro with ACQUITY UPLC system:

Sample organizer (optional)

Solvent tray

Column heater

Xevo TQ-S micro

Sample manager

Binary solvent
manager

Uses and compatibility

Software and data system

MassLynx v4.1 software can control the mass spectrometer. See page 30 for more
information about those applications.

MassLynx 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

• Running samples

• Monitoring the run

• Acquiring data

• Processing data

• Reviewing data

• Printing data

spectrometer

January 11, 2016, 715004599 Rev. B 29

1 Specifications and Operating Modes

MassLynx v4.1

MassLynx software acquires, analyzes, manages, and distributes mass spectrometry,
ultraviolet (UV), evaporative light scattering, and analog data. OpenLynx

TM

TargetLynx
See the MassLynx v4.1 user documentation and online Help for information about using

MassLynx software.
You configure settings, monitor performance, run diagnostic tests, and maintain the

system and its modules via the MassLynx Instrument Console application.
The Instrument Console software, which functions independently of MassLynx software,

does not recognize or control data systems.
See the online Help for the Instrument Console system for details.

application managers are included as standard software with MassLynx.

TM

and

30 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Ionization techniques and source probes

Ionization techniques and source probes

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

Xevo TQ-S micro. Refer to the MassLynx online Help for more information about
supported sources.

Electrospray ionization (ESI)

In electrospray ionization (ESI), a strong electrical charge is applied to the eluent as it
emerges from a nebulizer. The droplets that compose the resultant aerosol undergo a
reduction in size (solvent evaporation). As solvent continues to evaporate, the charge
density increases until the droplet surfaces eject ions (ion evaporation). The ions can be
singly or multiply charged.

The standard ESI probe accommodates eluent flow rates as high as 2 mL/min, making it
suitable for LC applications in the range 100 µL/min to 2 mL/min.

See page 56 for further details.

Combined ESI and APCI (ESCi)

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

See page 60 for further details.

Atmospheric pressure chemical ionization (APCI)

A dedicated high-performance APCI interface is offered as an option. APCI produces
singly charged protonated or deprotonated molecules for a broad range of nonvolatile
analytes.

The APCI interface consists of the ESI/APCI/ESCi enclosure fitted with a corona pin and
an IonSABRE II probe.

See page 60 for further details.

Dual-mode APPI/APCI source

The optional, combined atmospheric pressure photoionization/atmospheric pressure
chemical ionization (APPI/APCI) source comprises an IonSABRE II probe and the APPI

January 11, 2016, 715004599 Rev. B 31

1 Specifications and Operating Modes

lamp drive assembly. The APPI lamp drive assembly comprises a UV lamp and a repeller
electrode. In addition, a specially shaped, dual, APPI/APCI corona pin can be used. You
can operate the source in APPI, APCI, or dual mode, which switches rapidly between
APPI and APCI ionization modes.

NanoFlow source

“NanoFlow” is the name given to several techniques that use low flow rate electrospray
ionization. The NanoFlow source allows electrospray ionization in the flow rate range 5 to
1000 nL/min. For a given sample concentration, the ion currents observed approximate
those seen in normal flow rate electrospray. However, for similar experiments,
NanoFlow’s significant reduction in sample consumption accompanies significant
increases in sensitivity.

The following options are available for the spraying capillary:

• Universal nebulizer sprayer (Nano-LC).
This option is for flow injection or for coupling to nano-UPLC. It uses a pump to

regulate the flow rate downward to 100 nL/min. If a syringe pump is used, a
gas-tight syringe is necessary to effect correct flow rates without leakage. A volume
of 250 µL is recommended.

• Borosilicate glass capillaries (nanovials).
Metal-coated, glass capillaries allow the lowest flow rates. Usable for one sample,

they must then be discarded.

• Capillary Electrophoresis (CE) or Capillary Electrochromatography (CEC) sprayer .
This option uses a make-up liquid at the capillary tip that provides a stable
electrospray. The ma ke-up flow rate is less than 1 µL/min.

32 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Ionization techniques and source probes

Atmospheric solids analysis probe (ASAP)

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

See the Atmospheric Solids Analysis Probe Operator’s Guide Supplement for further
details.

Atmospheric pressure gas chromatography (APGC)

The Waters APGC couples an Agilent GC with the Xevo TQ-S micro, making it possible
to perform LC and GC analyses in the same system, without compromising performance.
The APGC provides complementary information to the LCMS instrument, enabling
analysis of compounds of low molecular weight and/or low-to-intermediate polarity.

See the Atmosheric Pressure GC Operator’s Guide Supplement for further details.

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.

January 11, 2016, 715004599 Rev. B 33

1 Specifications and Operating Modes

P

W

R

B

A

S

LC

LC
Column

Xevo
TQ-S micro
probe

Pump

Reservoirs

B

Wash

Waste

Selector valve

A

IntelliStart Fluidics system

Functionality

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

• From the LC column.

• From two integral reservoirs. Use standard reservoir bottles (15-mL) for instrument
setup and calibration. Use 1.5-mL, low-volume vials (sold separately) to infuse
smaller volumes (see page 51).

The reservoirs can also deliver sample through direct or combined infusion to
enable optimization at analytical flow rates.

• From a wash reservoir that contains solvent for automated flushing of the
instrument’s solvent delivery system.

The onboard system incorporates a selector valve, an infusion pump, and two sample
reservoirs mounted on the bottom, right-hand side of the instrument.

Recommendation: Use reservoir A for the calibrant solution and tuning compounds,

and reservoir B for analyte/optimization solution.

IntelliStart Fluidics system:

34 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

System operation

The software automatically controls solvent and sample delivery during auto-tuning,
auto-calibration, and method development. The selector valve systematically makes
connections between the fluidics components to carry out the operations processed by the
software.

You can set IntelliStart fluidics configuration requirements in the system console. You can
edit the parameters, frequency, and extent of the automation. See the mass spectrometer’s
online Help for further details on IntelliStart software and operation of the solvent delivery
system.

For information on plumbing the IntelliStart Fluidics system, see Appendix D.

IntelliStart Fluidics system

January 11, 2016, 715004599 Rev. B 35

1 Specifications and Operating Modes

T-W ave collision
cell

mini stepwave Detector

Conversion dynodeSample inlet Ion guide 2

Quadrupole MS2 qua drupole

Ion optics

The mass spectrometer’s ion optics operate as follows:

1. Samples from the LC or Intellistart fluidics system are introduced at atmospheric
pressure into the ionization source.

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

3. The ions pass through the transfer optics (the ion guide) to the segmented
quadrupole, where the are filtered according to their mass-to-charge ratios.

4. The mass-separated ions pass into the T-Wave™ collision cell where they either
undergo collision-induced dissociation (CID).

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

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

Ion optics overview:

MS operating modes

The following table shows the MS operating modes.

36 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

MS operating modes

MS operating modes:

Operating mode MS1 Collision cell MS2

MS Pass all masses Resolving

(scanning)

SIR Pass all masses Resolving

(static)

In MS mode, the instrument can acquire data at scan speeds as high as 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 page 38). In SIR and MRM modes, the quadrupole is not scanned, therefore
no spectrum (intensity versus mass) is produced. The data obtained from SIR or MRM
analyses derive from the chromatogram plot (specified mass intensity (SIR), or specified
transition (MRM) versus time).

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1 Specifications and Operating Modes

MS/MS operating modes

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

MS/MS operating modes:

Operating mode MS1 Collision cell MS2

Product (daughter)
ion spectrum

Precursor (parent)
ion spectrum

MRM Static (at precursor

PICS (Product Ion
Confirmation Scan)

RADAR™ RADAR mode allows you to create experiments containing both

Constant neutral
loss spectrum

Static (at precursor
mass)

Scanning Static (at product

mass)
Static (at precursor

mass)

MS and MS/MS functions.
Scanning

(synchronized with
MS2)

Fragment precursor
ions and pass all
masses

Scanning

mass)
Static (at product

mass)
Switching between

static (at product
mass) and scanning

Scanning
(synchronized with
MS1)

38 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Product (daughter) ion mode

MS1
Static (at precursor mass)

MS2
Scanning

Collision cell
Fragmenting
precursor ions and
passing all masses

MS1
Scanning

MS2
Static (at product mass)

Collision cell
Fragmenting
precursor ions and
passing all masses

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

Product ion mode:

Typical applications

Product ion mode is typically used for the following applications:

MS/MS operating modes

• 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)

Precursor (parent) ion mode

Precursor ion mode:

January 11, 2016, 715004599 Rev. B 39

1 Specifications and Operating Modes

MS1
Static (at precursor mass)

MS2
Static (at product mass)

Collision cell
Fragmenting
precursor ions and
passing all masses

Typical application

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

Multiple reaction monitoring mode

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

Multiple reaction monitoring mode:

PICS mode

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

RADAR

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

40 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

MS/MS operating modes

Typical application

You typically use RADAR mode during method development prior to performing MRM
or PICS to quantify known analytes in complex samples:

• Drug metabolite and pharmacokinetic studies

• Environmental, for example, pesticide and herbicide analysis

• Forensic or toxicology, for example, screening for target drugs in sports

MRM analysis with no associated RADAR or PICS operation does not produce a
spectrum because only one transition is monitored at a time. As in SIR mode, a
chromatogram is produced.

January 11, 2016, 715004599 Rev. B 41

1 Specifications and Operating Modes

MS1
Scanning
(synchronized with MS2)

Collision cell
Fragmenting
precursor ions and
passing all masses

MS2
Scanning
(synchronized with MS1)

Constant neutral loss mode

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

The scans of MS1 and MS2 are synchronized. When MS1 transmits a specific precursor
ion, MS2 “looks” to see whether that precursor loses a fragment of a certain mass. If it
does, the loss registers at the detector.

In constant neutral loss mode, the spectrum shows the masses of all precursors that
actually lost a fragment of a certain mass.

Constant neutral loss mode:

Typical application

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

42 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Sample inlet

Either of two methods delivers solvent and sample to the installed probe:

• An LC system, which delivers the eluent from an LC analysis.

• IntelliStart Fluidics system, which uses onboard solutions to automate instrument
optimization. You can deliver solutions by direct or combined infusion.

Leak sensors

Leak sensors in the Xevo TQ-S micro and the drip trays of the ACQUITY UPLC system
continuously monitor system components for leaks. A leak sensor stops system flow when
its optical sensor detects about 1.5 mL of accumulated, leaked liquid in its surrounding
reservoir. At the same time, the ACQUITY UPLC Console displays an error message
alerting you that a leak has developed.

See Waters ACQUITY UPLC Leak Sensor Maintenance Instructions for complete details.

Vacuum system

Sample inlet

An external roughing pump and an internal split-flow turbomolecular pump combine to
create the source vacuum. The turbomolecular pump evacuates the analyzer an d ion
transfer region.

Vacuum leaks and electrical or vacuum pump failures cause vacuum loss, the damage
from which is prevented by protective interlocks. The system monitors turbomolecular
pump speed and continuously measures vacuum pressure with a built-in Pirani gauge. The
gauge also serves as a switch, stopping operation when it senses vacuum loss.

A vacuum isolation valve isolates the source from the analyzer region, allowing routine
source maintenance without venting.

January 11, 2016, 715004599 Rev. B 43

1 Specifications and Operating Modes

Power

Turbo vacuum

Source vent

Nitrogen inlet

Collision cell
gas inlet
(Argon)

Source vacuum

Roughing pump
control

Shielded
Ethernet

Event inputs
and outputs

Waste bottle
electrical connection

nano camera
connection

Rear panel connections

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

Instrument rear panel:

44 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

2 Prep aring for Operation

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

Contents:
Topic Page

Starting the mass spectrometer..................................................................... 46

Preparing the IntelliStart Fluidics system..................................................... 51

Rebooting the instrument.............................................................................. 53

Leaving the mass spectrometer ready for operation..................................... 54

January 11, 2016, 715004599 Rev. B 45

2 Preparing for Operation

Starting the mass spectrometer

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

solvents only. For more details, refer to the following sources:

•See page 257 for solvent information.

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

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

Requirement: You must power-on and log in to the workstation first to ensure that it

obtains the IP addresses of the system instruments.
See the mass spectrometer’s online help for details on MassLynx and IntelliS tart software.

To start the mass spectrometer:

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

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

1. On the rear panel, ensure the nitrogen supply is connected to the instrument’s
nitrogen inlet connection (see the figure on page 44).

Requirement: The nitrogen must be dry and oil-free, with a purity of at least 95%

or, for APGC use, at least 99.999%. Regulate the supply at 600 to 690 kPa (6.0 to

6.9 bar, 90 to 100 psi).
For more information on connections, see the figure on page 44.

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

Requirement: The collision gas is argon; it must be dry and of high purity

(99.997%). Regulate the supply at 50 kPa (0.5 bar, 7 psi).

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

4. Press the power switch on the top, right-hand side of the mass spectrometer and the
switches on the top, left-hand sides of the ACQUITY instruments.

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

46 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Starting the mass spectrometer

5. Allow 3 minutes for the embedded PC (located inside the mass spectrometer) to
initialize and to sound an alert indicating that the PC is ready.

Tip: The power and status LEDs change as follows:

• Each system instrument’s power LED shows green.

• During initialization, the binary or quaternary solvent manager’s and sample

manager’s status LED flashes green.

• After the instruments successfully power-on, all power LEDs show steady

green. The binary solvent manager’s flow LED, the sample manager’s run
LED, and the mass spectrometer’s Operate LED remain off.

6. Start the MassLynx software, and monito r the Instrument Console software for
messages and LED indications.

January 11, 2016, 715004599 Rev. B 47

2 Preparing for Operation

7. To evacua te (pump down) the mass spectrometer, follow the procedure below for
MassLynx software.

MassLynx software:

a. Click IntelliStart in the MassLynx main window’s lower left-hand corner.

Result: The mass spectrometer’s console appears. The mass spectrometer is

in Standby mode.

b. Click Control > Pump, to start the roughing pump.

Tip: After a 20-second delay, during which the turbopump is starting, the

roughing pump starts. IntelliStart displays “Instrument in standby”, and the
Operate LED remains off.

c. Wait a minimum of 2 hours for the instrument to be fully pumped down

(evacuated).

Tip: In the Instrument Console, the System Ready indicator shows green when

the instrument is fully pumped down (evacuated).

d. Click Resolve or Operate .

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

IntelliStart software displays “Ready” in the Instrument Console.

Tip: If clicking Resolve fails to put the instrument into Operate mode,

IntelliStart software displays corrective actions in the Instrument Console.

48 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Verifying the instrument’s state of readiness

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

Monitoring the instrument LEDs

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

Power LED

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

Operate LED

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

See the instrument’s online Help for details of the Operate LED indications.

Starting the mass spectrometer

Tuning and calibration information

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

January 11, 2016, 715004599 Rev. B 49

2 Preparing for Operation

Running the instrument at different flow rates

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

Flow rate versus temperature and gas flow:

Flow rate
(mL/min)

0.000 to 0.020 150 200 800

0.021 to 0.100 150 300 800

0.101 to 0.500 150 500 1000
>0.500 150 600 1000

If you are using an APCI interface, IntelliStart software automatically sets the parameters
according to the following table.

Flow rate versus IonSABRE II probe temperature and gas flow:

Flow rate
(mL/min)

0.000 to 0.020 400 800

0.021 to 0.500 500 1000
>0.500 6001000

Source temp (°C)

IonSABRE II
probe
temperature (°C)

Desolvation
temp (°C)

Desolvation gas
flow (L/h)

Desolvation gas
flow (L/h)

50 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Preparing the IntelliStart Fluidics system

Preparing the IntelliStart Fluidics system

For additional information, see page 246 and Appendix D.

Notice: To avoid damaging the mass spectrometer by accidentally spilling solvent

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

Installing the reservoir bottles

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

Required material

Chemical-resistant, powder-free gloves

January 11, 2016, 715004599 Rev. B 51

2 Preparing for Operation

TP03410

Warning: To avoid personal contamination with biohazards or toxic

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

To install the reservoir bottles:

1. Remove the reservoir bottle caps.

2. Screw the reservoir bottles onto the instrument, as shown below.

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

To install low-volume vials:

Warning: To avoid personal contamination with biohazards or toxic

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

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

2. Screw the low-volume adaptor into the manifold and tighten it.

3. Screw the low-volume vial into the adaptor.

4. For each low-volume vial, ensure that the end of the solvent delivery tube is
positioned so that it is close to, but does not touch, the bottom of the vial.

52 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Purging the infusion pump

TP03415

Reset button aperture

Whenever you replace a solution bottle, purge the infusion pump with the solution that
you are going to use next. See the mass spectrometer’s online Help for details.

Requirement: Ensure that the end of the tubing is fully submerged in the solvent in the

wash reservoir.

Tip: Depending on the solutions used, the instrument’s solvent delivery system can

require more than one purge cycle to minimize carryover.

Rebooting the instrument

The reset button causes the mass spectrometer to reboot.
Reboot the instrument when either of these conditions applies:

• Immediately following a software upgrade.

• The mass spectrometer software fails to initialize.

To reboot the instrument:

Rebooting the instrument

1. Ensure that the mass spectrometer software is closed.

2. Insert a short length (7.5 cm) of PEEK™ tubing, or similar object, into the reset
button aperture at the top, right-hand side of the instrument’s front panel.

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

4. Wait until the reboot sequence ends before starting the mass spectrometer software.

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2 Preparing for Operation

Tip: An audible alert sounds when the reboot sequence is complete.

Leaving the mass spectrometer ready for operation

Leave the mass spectrometer in Operate mode except in the following cases:

• When performing routine maintenance

• When changing the source

• When leaving the mass spectrometer unused for a long period

In these instances, put the mass spectrometer in Standby mode. See the online Help for
details.

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

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

Emergency shutdown of the mass spectrometer

To shut down the instrument in an emergency:

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

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

Notice: To avoid losing data, reboot the instrument as described on page 53. Data

can be lost when you perform an emergency shutdown.

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

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

54 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

3 Changing the Mode of Operation

This chapter describes how to prepare the mass spectrometer for the following
modes of operation:

• ESI (electrospray ionization)

• ESCi (combined electrospray and atmospheric pressure chemical ionization)

• APCI (atmospheric pressure chemical ionization)

• Combined Atmospheric Pressure Photoionization (APPI/APCI)

•NanoFlow
For details about other Waters and third-party source options, refer to the

documentation supplied with the source.

Note: A vailable sour ce options can vary depending on the software used to operate

the Xevo TQ-S micro. Refer to the MassLynx online Help for more information
about supported sources.

Contents:
Topic Page

ESI mode ...................................................................................................... 56

ESCi mode.................................................................................... .... ..... ....... 60

APCI mode ................................................................................................... 60

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

NanoFlow source.......................................................................................... 72

ionKey source............................................................................................... 80

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3 Changing the Mode of Operation

ESI mode

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

Installing the ESI probe

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

To install the ESI probe:

1. Prepare the instrument for installing the probe according to the procedure on

page 97, “Preparing the instrument for operations on or inside its source”.

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

probe tip is sharp.

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

56 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

TP03129

Location hole of the probe
adjuster assembly

Probe location dowel

Probe label

Probe locking ring

ESI mode

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

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

Requirement: Fully tighten the probe locking ring. Doing so ensures a successful

result on the automatic pressure test, which runs when the probe is correctly seated,
and the source enclosure door is closed.

5. Connect the ESI probe’s cable to the high-voltage connector.

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3 Changing the Mode of Operation

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

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

6. Using PEEK tubing equal to 0.004-inch ID, connect port S of the selector valve to
the ESI probe.

Recommendation: To reduce peak broadening, use 0.004-inch ID tubing for

sample flow rates ≤1.2 mL/min; use 0.005-inch ID tubing for sample flow rates
>1.2 mL/min.

Requirements:

• If you are replacing the tubing between the selector valve and the probe,

minimize the length to reduce peak broadening.

• When cutting the tubing to length, cut it squarely (that is, perpendicular to its

horizontal axis).

58 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Removing the ESI probe

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

To remove the ESI probe:

1. Prepare the instrument for removing the probe according to the procedure on

page 97, “Preparing the instrument for operations on or inside its source”.

ESI mode

2. Disconnect the tubing from the ESI probe.

3. Disconnect the ESI probe cable from the high-voltage connector.

4. Unscrew the probe locking ring.

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

probe tip is sharp.

5. Carefully remove the ESI probe from the probe adjuster assembly.

6. If available, fit the protective sleeve to the ESI probe tip.

January 11, 2016, 715004599 Rev. B 59

3 Changing the Mode of Operation

Sample cone

Corona pin

ESI probe

ESCi mode

T o run ESCi applications, you must fit an ESI probe and corona pin to the ESI/APCI/ESCi
source enclosure.

See “Installing the ESI probe” on page 56, “Installing the corona pin in the source” on

page 101, and “IntelliStart Fluidics System” on page 34.

ESCi mode:

Optimizing the ESI probe for ESCi operation

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

APCI mode

APCI mode, an option for the mass spectrometer, produces singly charged protonated or
deprotonated molecules for a broad range of nonvolatile analytes.

The APCI interface consists of the ESI/APCI/ESCi enclosure fitted with a corona pin and
an IonSABRE II probe. Mobile phase from the LC column enters the probe, where it is
pneumatically converted to an aerosol, rapidly heated, and vaporized or gasified at the
probe tip.

60 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

APCI mode

IonSABRE II probe

Sample cone

Corona pin

APCI mode:

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

Installing the IonSABRE II probe

Required materials

• Chemical-resistant, powder-free gloves

• Sharp knife or PEEK tubing cutter

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

January 11, 2016, 715004599 Rev. B 61

3 Changing the Mode of Operation

TP03129

Location hole of the probe
adjuster assembly

Probe location dowel

Probe label
Probe locking ring

To install the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 97).

2. With the probe label facing toward you, carefully slide the IonSABRE II probe into
the hole in the probe adjuster assembly, ensuring that the probe location dowel
aligns with the probe adjuster assembly location hole.

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

Requirement: Fully tighten the probe locking ring. Doing so ensures a successful

result on the automatic pressure test, which runs when the probe is correctly seated,
and the source enclosure door is closed.

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

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

4. Using tubing equal to 0.004-inch ID, connect port S of the selector valve to the
IonSABRE II probe.

Recommendation: To reduce peak broadening, use 0.004-inch ID tubing for

sample flow rates ≤1.2 mL/min; use 0.005-inch ID tubing for sample flow rates
>1.2 mL/min.

Requirements:

62 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

• If you are replacing the tubing between the selector valve and the probe,

minimize the length to reduce peak broadening.

• When cutting the tubing to length, cut it squarely (that is, perpendicular to its

horizontal axis).

5. Install the corona pin (see page 101).

APCI mode

January 11, 2016, 715004599 Rev. B 63

3 Changing the Mode of Operation

Removing the IonSABRE II probe

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

To remove the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 97).

2. Remove the corona pin (see page 101).

3. Disconnect the selector valve tubing from the IonSABRE II probe.

4. Unscrew the probe locking ring.

5. Carefully remove the probe from the probe adjuster assembly.

64 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Combined APPI/APCI source

IonSABRE II probe

Sample molecules

APPI lamp drive assembly

Repeller electrodeUV lamp

Sample ions

Sample cone

Photons from
the UV lamp

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

APPI operation

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

APPI mode:

Combined APPI/APCI source

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

A repeller electrode (mounted on the APPI lamp drive assembly) deflects and focuses the
sample ions toward the sample cone.

January 11, 2016, 715004599 Rev. B 65

3 Changing the Mode of Operation

IonSABRE II probe

Retracted APPI lamp drive
assembly

Sample cone

APCI corona pin

APCI operation

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

APCI mode:

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

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Dual-mode operation

Sample cone

IonSABRE II probe

Photons from the UV lamp

Repeller electrode inactive

Corona pin with current applied

Sample cone

IonSABRE II probe

Photons from the UV lamp

Repeller electrode with
voltage applied

Corona pin inactive

Dual-mode operation enables rapid switching between APPI and APCI ionization modes
and allows high-throughput operations (for example, for sample screening).

You replace the standard corona pin with a specially shaped APPI/APCI corona pin, so
that the APPI lamp holder can be advanced into the source for dual operation.

When the source is configured for dual operation in APCI mode, current is applied to the
corona pin, but the repeller electrode is inactive.

Dual operation in APCI mode:

Combined APPI/APCI source

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

Dual operation in APPI mode:

January 11, 2016, 715004599 Rev. B 67

3 Changing the Mode of Operation

APPI lamp drive assembly

The combined APPI/APCI source components

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

The combined APPI/APCI source enclosure:

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

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

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Combined APPI/APCI source

TP03201

APPI lamp drive
assembly

Source enclosure

UV lamp and
repeller electrode

IonSABRE II probe

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

APPI lamp drive assembly inside the source enclosure:

January 11, 2016, 715004599 Rev. B 69

3 Changing the Mode of Operation

Installing the combined APPI/APCI source

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

To install the combined APPI/APCI source:

1. Prepare the instrument for working on the source (see page 97).

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

probe and source; these components can be hot.

2. Remove the probe from the currently installed source.

• If you are removing an ESI probe, see page 59.

• If you are removing an IonSABRE II probe, see page 64.

3. Remove the existing source enclosure (see page 98).

4. Install the combined APPI/APCI source enclosure (see page 100).

5. Install the corona pin (see page 101).

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

70 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Combined APPI/APCI source

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

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

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

8. Install the IonSABRE II probe to the source, and ensure that it is working correctly
(see page 61).

Tip: An automatic pressure test runs each time you close the source enclosure and

when the instrument starts.

Removing the IonSABRE II probe and APPI/APCI source enclosure

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

the instrument according to the procedure on page 97, “Preparing the

instrument for operations on or inside its source”.

To remove the combined APPI/APCI source

1. Prepare the instrument for working on the source (see page 97).

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

probe and source; these components can be hot.

2. Remove the IonSABRE II probe (see page 64).

3. Disconnect the HT cable from the instrument’s front panel.

4. Disconnect the APPI drive cable from the instrument’s front panel.

5. Remove the source enclosure (see page 98).

6. Remove the corona pin (see page 103).

January 11, 2016, 715004599 Rev. B 71

:

3 Changing the Mode of Operation

X, Y, Z stage

Microscope Camera

Sprayer enclosure

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

NanoFlow source

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

NanoFlow source, stage and microscope camera:

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

A light within the source provides illumination for the spray, which you can observe using
the microscope camera mounted on the corner of the source housing.

72 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

The low flow rates involved with operating the NanoFlow source prohibit its use with the
instrument’s solvent delivery system.

Installing the NanoFlow source

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazards or toxic

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

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

working on the source before commencing this procedure.

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

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

NanoFlow source

To install the NanoFlow source:

1. Prepare the instrument for working on the source (see page 97).

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

probe and source; these components can be hot.

2. Remove the probe from the currently installed source.

• If you are removing an ESI probe, see page 59.

• If you are removing an IonSABRE II probe, see page 64.

3. Remove the existing source enclosure (see page 98).

January 11, 2016, 715004599 Rev. B 73

3 Changing the Mode of Operation

Stop screw

Retaining screw

Notice: To prevent the sprayer from colliding with the cone and breaking,

always retract the stage before installing the source enclosure or closing the
door.

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

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

6. Close the source enclosure door.

7. Connect a 1/16-inch PTFE tube between the mass-flow controller output (mounted
beneath the stage on the front of the NanoFlow source) and your sprayer.

Tip: For details regarding how to fit each sprayer, see the corresponding reference:

• Waters Universal NanoFlow Sprayer Installation and Maintenance Guide

(part number 71500110107)

• “Fitting a borosilicate glass capillary (nanovial)” on page 76

• Capillary Electrophoresis/Capillary Electrochromatography Sprayer User's

Guide (part number 6666522)

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

74 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

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

High-voltage cable

NanoFlow source

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

(the voltage applied to the sprayer assembly) and the sampling cone voltage remain
disabled until the sprayer is pushed fully forward in the source.

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

January 11, 2016, 715004599 Rev. B 75

3 Changing the Mode of Operation

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

• Fused silica cutter

Warning: To avoid lacerations, puncture injuries, and possible

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

Notice: To avoid damaging capillaries, take great care when handling

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

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

fully retracted from the source before beginning this procedure.

®

tip

To fit a borosilicate glass capillary (nanovial):

1. Loosen the stage retaining screw.

2. Pull the stop screw to release the stage.

3. Slide the stage out of the NanoFlow source enclosure and remove the magnetic
cover.

4. Unscrew the retaining screw, and lift the sprayer from the stage.

76 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

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

Capillary
Union

Foam

Capillary

6. Remove the existing capillary from the sprayer.

NanoFlow source

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

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.

January 11, 2016, 715004599 Rev. B 77

3 Changing the Mode of Operation

5mm

PTFE tubing

Ferrule

Union
Knurled nut

Blue conductive elastomer

Glass capillary

Recommendation: When using a GELoader tip, break the glass capillary in half,

scoring it with a fused silica cutter so that the GELoader can reach the capillary’s
tip.

9. Thread the knurled nut and approximately 5 mm of conductive elastomer over the
blunt end of the capillary.

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

11. Finger-tighten the nut so that 5 mm of glass capillary protrude from its end.

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

capillary.

Sprayer assembly:

12. Screw the sprayer back into the assembly.

13. Replace the sprayer cover.

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

78 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Notice: To prevent the capillary tip from colliding with the cone or the side

d

2d

3d

Cone aperture diameter

of the source, adjust the sprayer tip position before you push the sprayer
inside the NanoFlow source enclosure.

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

Positioning the borosilicate glass capillary tip

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

Capillary tip position:

NanoFlow source

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

January 11, 2016, 715004599 Rev. B 79

3 Changing the Mode of Operation

Microscope
camera

Handle for locking
and unlocking the
iKey separation
device

Front cover

Docking port
for the iKey
separation
device

ionKey source

The ionKey source integrates UPLC separation into the source of the mass spectrometer.
For a complete description, see “ionKey source” on page 33.

The following sections explain how to install or remove an ionKey source.
For further information, see the ACQUITY UPLC M-Class System Guide (part number

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

Installing the ionKey source

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

ionKey source:

80 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Required materials

• Chemical-resistant, powder-free gloves

• Screwdriver

• ¼-inch wrench

Warning: To avoid personal contamination with biohazards or toxic

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

Warning: To avoid electric shock, prepare the instrument for work performed on

its source before beginning this procedure.

To install the ionKey source:

1. Prepare the instrument for working on its source (see page 97).

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

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

2. Remove the probe from the currently installed source:

• If you are removing an ESI probe, see page 59.

• If you are removing an IonSABRE II probe, see page 64.

ionKey source

3. Remove the existing source enclosure (see page 98).

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

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

Notice: To avoid damaging the ionKey source or µSample manager,

• 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.

January 11, 2016, 715004599 Rev. B 81

3 Changing the Mode of Operation

Data/power cable
to PSPI
connector on
µSample
manager

High voltage cable

Options cable

Fluid infusion line

Fluid inlet line

Optional post-column addition (PCA) line

Fluid waste line

ionKey source connections:

82 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

6. 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.

ionKey source

Data/power
cable to PSPI
connector on
µSample
manager

High voltage
cable

Options
cable

Source connections to mass spectrometer:

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

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

January 11, 2016, 715004599 Rev. B 83

3 Changing the Mode of Operation

Fluid line aperture

Aperture open
(spring-loaded)

Aperture closed

9. Identify each fluid line by the part numbers printed on their shrink-wrap tubing.

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

Fluid line aperture:

84 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

ionKey source

TP03519

Fluid inlet line connected
to injection valve port 6

µSample manager injection valve:

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

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

12. Connect the optional post-column addition line to outlet B on the flow control
module of the auxiliary solvent manager.

13. Connect the waste line to a suitable waste container.

Installing ionKey source software

If you are installing an ionKey source on your Xevo TQ-S micro 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 Driver Pack Installation and Configuration Guide (part
number 715004448) for detailed installation procedures, and information on using
the ACQUITY Inlet Switch Utility.

• MassLynx software v4.1 and related SCN release notes for detailed information
about installing MassLynx software and SCNs.

January 11, 2016, 715004599 Rev. B 85

3 Changing the Mode of Operation

Installing the camera in the ionKey source

To install the camera software for 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. T o subsequently open
the device settings dialog box, in the camera viewer, click View > Camera Options.

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

Removing the ionKey source

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

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

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

86 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

ionKey source

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

See M-Class Cart Universal Source Holder (part number 715004884) for further
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.

Required materials

• Chemical-resistant, powder-free gloves

• ¼-inch wrench

Warning: To avoid personal contamination with biohazards or toxic

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

Warning: To avoid electric shock, prepare the instrument for work performed on

its source before beginning this procedure.

To remove the ionKey source:

1. Prepare the instrument for working on its source (see page 97).

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

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

2. Remove the iKey from the docking port (see the ionKey/MS System Guide, part
number 715004028).

3. Shut down the MassLynx software.

4. Power-off the µSample manager.

5. Disconnect the PSPI cable.

6. Using the ¼-inch wrench, loosen and disconnect the fluid waste line (if required)
and fluid inlet lines from the µSample manager.

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

8. Disconnect the fluid-infusion line from the onboard IntelliStart Fluidics on the mass
spectrometer.

January 11, 2016, 715004599 Rev. B 87

3 Changing the Mode of Operation

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

10. Disconnect the high v oltage cable (white) from the high voltage supply outlet on the
mass spectrometer.

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

12. Carefully lift off the ionKey source module and store safely.

88 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

4 Maintenance Procedures

This chapter provides the maintenance guidelines and procedures necessary to
maintain the instrument’s performance.

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

Contents:
Topic Page

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

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

Troubleshooting with Connections INSIGHT.............................................. 94

Safety and handling ...................................................................................... 95

Preparing the instrument for operations on or inside its source................... 97

Removing and refitting the source enclosure............................................... 98

Installing and removing the corona pin........................................................ 101

Operating the source isolation valve ............................................................ 104

Removing O-rings and seals......................................................................... 107

Cleaning the instrument case........................................................................ 108

Emptying the exhaust trap bottle.................................................................. 108

Gas ballasting the roughing pump................................................................ 110

Checking the roughing pump oil level ......................................................... 112

Adding oil to the roughing pump ................................................................. 113

Cleaning the source components.................................................................. 114

Cleaning the sampling cone assembly.......................................................... 115

Cleaning the ion guide assembly.................................................................. 135

Cleaning the ion block assembly.................................................................. 125

Cleaning the ion guide assembly.................................................................. 135

Replacing the ESI probe tip and gasket........................................................ 146

Replacing the ESI probe capillary................................................................ 150

January 11, 2016, 715004599 Rev. B 89

4 Maintenance Procedures

Contents:
Topic Page

Cleaning the IonSABRE II probe tip............................................................ 166

Replacing the IonSABRE II probe sample capillary.................................... 167

Cleaning or replacing the corona pin............................................................ 172

Replacing the IonSABRE II probe heater .................................................... 174

Replacing the ion block source heater.......................................................... 177

Replacing the source assembly seals............................................................ 180

Replacing the air filter.................................................................................. 184

Replacing the roughing pump oil ................................................................. 187

Replacing the roughing pump’s oil demister el ement.................................. 190

APPI/APCI source—changing the UV lamp bulb ....................................... 195

APPI/APCI source—cleaning the lamp window.......................................... 196

APPI/APCI source—replacing the APPI lamp drive seals .......................... 198

Replacing the fluidic lines of the ionKey source.......................................... 206

Cleaning the ionKey source and connectors................................................. 211

Replacing the instrument’s fuses.................................................................. 214

90 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Maintenance schedule

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

The maintenance frequencies shown apply to instruments that normally receive moderate
use.

Maintenance schedule:

Procedure Frequency For information...

Clean the instrument case. As required. See page 108.
Empty the exhaust trap bottle in

the instrument exhaust line.
Replace the oil-free (scroll)

pump’s seals.

Gas ballast the roughing pump. ESI – weekly. See page 110.

Maintenance schedule

Check daily, empty as
required.

Annually. See Edwards

See page 108.

document XDS35i

Instruction Manual
A730-01-880.

Inspect and adjust the roughing
pump oil level.

Clean the source components. When they are visibly

Clean or replace the ESI probe tip. When sensitivity

Replace the ESI probe capillary. When sensitivity

Weekly. See page 112.

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

decreases to unacceptable
levels.

decreases to unacceptable
levels or sample flow is
inconsistent.

January 11, 2016, 715004599 Rev. B 91

See page 114.

See page 184.

See page 150.

4 Maintenance Procedures

Maintenance schedule:

Procedure Frequency For information...

Clean the IonSABRE II probe tip.
(Options using the IonSABRE II
probe only.)

When sensitivity
decreases to unacceptable
levels or when significant

See page 166.

chemical interference is
present.

Replace the IonSABRE II probe
capillary. (Options using the
IonSABRE II probe only.)

When sensitivity
decreases to unacceptable
levels or sample flow is

See page 167.

inconsistent.

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

When the corona pin is
corroded or black, the

See page 172.

corona current cannot be
stabilized, or the
sensitivity decreases to
unacceptable levels.

Replace the IonSABRE II probe
heater. (Options using the
IonSABRE II probe only.)

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

See page 174.

(evacuated).

Replace the ion block heater
cartridge.

If the heater fails to heat
when the instrument is

See page 177.

pumped down

(evacuated).
Replace the source assembly seals. Annually. See page 180.
Replace the instrument’s air filters. Annually. See page 184.
Change the roughing pump oil. Annually. See page 187.
Replace ionKey source fluid lines. As required or during

Clean the ionKey source surface,
fluid connectors, or electronic
connectors.

92 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

periodic maintenance.

As required or during

periodic maintenance.

See page 206

See page 211.

Spare parts

Maintenance schedule:

Procedure Frequency For information...

Replace the roughing pump’s
demister element.

Clean the APPI/APCI source UV
lamp window.

Change the APPI/APCI source UV
lamp bulb.

Replace the APPI lamp drive
assembly O-rings.

Spare parts

Replace only spare parts, which are the parts mentioned in this document. For details
about spare parts, use the W aters Quality Parts

& Support page.

Annually.

See page 190.

Tip: Applications that

contaminate the roughing

pump oil reduce this

period, which must be

determined from

experience.

When the window

See page 196.
becomes visibly dirty or
when the sensitivity
decreases to unacceptable
levels.

When the bulb fails. See page 195.

Annually. See page 198.

®

Locator on the W aters Web site’s Services

January 11, 2016, 715004599 Rev. B 93

4 Maintenance Procedures

Troubleshooting with Connections INSIGHT

Connections INSIGHT® is an “intelligent” device management (IDM) Web service that
enables W aters to provide proactive service and support for the ACQUITY UPLC system.
To use Connections INSIGHT, you must install its service agent software on your
workstation. In a client/server system, the service agent must also be installed on the
computer from which you control the system. The service agent software automatically
and securely captures and sends information about the support needs of your system
directly to Waters.

If you encounter a performance issue when using the Instrument Console, you can
manually submit a Connections INSIGHT request to Waters customer support.
Alternatively, you can use Remote Desktop, a real-time collaboration option that controls
the two-way connection with the ACQUITY UPLC system by enabling the Connections
INSIGHT iAssist service level.

Consult these sources for more information about Connections INSIGHT and Connections
INSIGHT iAssist:

• http://www.waters.com

• Connections INSIGHT Installation Guide (part number 715001399)

• Connections INSIGHT User's Guide (part number 715001400)

• Your sales representative

• Your local Waters subsidiary

• Waters Customer Support

To submit a Connections INSIGHT request:

1. Open the Connections INSIGHT software tray application, and select the iHelp tab.

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

3. Click Submit, and allow approximately 5 minutes to save the service profile.

Result: A .zip file containing your Connections INSIGHT profile is forwarded to

Waters customer support for review.

Note: Saving a service profile or plot file from the Instrument Console can require

as much as 150 MB of file space.

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Safety and handling

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

Warning: To avoid personal contamination, always wear

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

Warning: To prevent injury, always observe Good Laboratory Practice

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

Warning: To avoid electric shock,

• do not remove the instrument’s panels. There are no user-serviceable
parts inside the instrument.

• ensure that the instrument is in Standby mode before commencing any
maintenance.

Safety and handling

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

probe and source; they can be hot.

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

performing maintenance inside the source enclosure:

• The instrument is in Standby mode.

• LC flow is diverted to waste or set to Off.

• Desolvation gas flow is stopped.

January 11, 2016, 715004599 Rev. B 95

4 Maintenance Procedures

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 Appendix A for safety advisory information.

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Preparing the instrument for operations on or inside its source

Preparing the instrument for operations on or inside its
source

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

To use MassLynx software to prepare the instrument for operations on or
inside its source:

1. In the Instrument Console, click Stop Flow to stop the LC flow or, if column
flow is required, divert the LC flow to waste as follows:

a. In the Instrument Console system tree, expand Xevo TQ-S micro, Interactive

Fluidics.

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

2. In the Instrument Console, click Standby , and confirm that the Operate
indicator is not illuminated.

3. Wait 3 minutes to allow the desolvation gas flow to cool the probe and source.

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

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

January 11, 2016, 715004599 Rev. B 97

4 Maintenance Procedures

Removing and refitting the source enclosure

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

Removing the source enclosure from the instrument

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biohazardous and/or toxic

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

To remove the source enclosure:

1. Prepare the instrument according to the procedure on page 97.

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

probe and source; they can be hot.

2. Remove the probe from the source.

• If you are removing an ESI probe, see page 59.

• If you are removing an IonSABRE II probe, see page 64.

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

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

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

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

98 Janua ry 11 , 20 16 , 71 50 0 459 9 R ev . B

Removing and refitting the source enclosure

TP03164

Supporting stud

Source enclosure

Cable storage positions

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

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

January 11, 2016, 715004599 Rev. B 99

4 Maintenance Procedures

Fitting the source enclosure to the instrument

Required material

Chemical-resistant, powder-free gloves

Warning: To avoid personal contamination with biologically hazardous, or

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

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

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

To fit the source enclosure:

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

Notice: To prevent the sprayer from colliding with the cone and,

consequently, breaking when you use a NanoFlow source, always retract the
stage before closing the source enclosure door.

2. Close the source enclosure.

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

100 January 11, 2016, 71500459 9 Rev . B