waters xevo g2-s qtof · 2012. 8. 7. · v glass-breakage hazard high-temperature hazard xevo g2-s...

Waters Xevo G2-S QTofOperator’s Overview and Maintenance Guide

715003596 Revision A

Copyright © Waters Corporation 2012All rights reserved

Copyright notice

© 2011–2012 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.The information in this document is subject to change without notice and should not be construed as a commitment by Waters Corporation. Waters Corporation assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use.

Trademarks

ACQUITY, ACQUITY UPLC, Connections INSIGHT, ESCi, UPLC, and Waters are registered trademarks of Waters Corporation.IntelliStart, LockSpray, MassLynx, NanoFlow, NanoLockSpray, StepWave, T-Wave, THE SCIENCE OF WHAT'S POSSIBLE., UNIFI, Xevo, and ZSpray are trademarks of Waters Corporation.GELoader is a registered trademark of Eppendorf-Netheler-Hinz GmbH.PEEK is a trademark of Victrex plc.POZIDRIV is a registered trademark of Phillips Screw Company, Inc.Swagelok is a registered trademark of Swagelok Company.Super Flangeless and SealTight are trademarks of Upchurch Scientific, Inc.TaperTip is a trademark of New Objective, Inc.Teflon and Viton are registered trademarks of E. I. du Pont de Nemours and Company.Valco is a trademark of Valco Instruments, Inc.Xylan is a registered trademark of Whitford Corporation.Other trademarks or registered trademarks are the sole property of their respective owners.

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Customer comments

Waters’ Technical Communications department invites you to tell us of any errors you encounter in this document or to suggest ideas for otherwise improving it. Please help us better understand what you expect from our documentation so that we can continuously improve its accuracy and usability.We seriously consider every customer comment we receive. You can reach us at [email protected].

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 InformationInternet The Waters Web site includes contact

information for Waters locations worldwide. Visit www.waters.com.

Telephone From the USA or Canada, phone 800 252-HPLC, or fax 508 872-1990.For other locations worldwide, phone and fax numbers appear on the Waters Web site.

Conventional mail Waters Corporation34 Maple StreetMilford, MA 01757USA

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Safety considerations

Some reagents and samples used with Waters instruments and devices can pose chemical, biological, and radiological hazards. You must know the potentially hazardous effects of all substances you work with. Always follow Good Laboratory Practice, and consult your organization’s safety representative for guidance.

Considerations specific to the Xevo G2-S QTof

Solvent-leakage hazard

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

Flammable-solvents hazard

Never let the nitrogen supply pressure fall below 414 kPa (4.0 bar, 60 psi) during analyses that require flammable solvents. Connect to the LC output with a gas-fail connector to stop the LC solvent if the nitrogen supply fails.

Warning: To avoid personal contamination with toxic or biologically hazardous materials, you must follow these safety measures:• To confirm the integrity of the source exhaust system, renew

the source O-rings at intervals not exceeding one year.• To avoid chemical degradation of the source O-rings, which can

withstand exposure only to certain solvents (see “Solvents used to prepare mobile phases” on page C-3), determine whether any solvents you use that are not listed are chemically compatible with the composition of the O-rings.

Warning: To prevent the ignition of accumulated solvent vapors inside the source, maintain a continuous flow of nitrogen through the source whenever significant amounts of flammable solvents are used during the instrument’s operation.

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Glass-breakage hazard

High-temperature hazard

Xevo G2-S QTof high-temperature hazard:

Warning: To avoid injuries from broken glass, falling objects, or exposure to toxic substances, never place containers on top of the instrument or on its front covers. Instead, use the bottle tray.

Warning: To avoid burn injuries, do not touch the source ion block assembly when operating or servicing the instrument.

Source ion block assembly

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Hazards associated with removing an instrument from service

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

• Source interior• Waste tubing• Exhaust system• Rotary pump oil (where applicable)

The need to decontaminate other vacuum areas of the instrument depends on the kinds of samples the instrument analyzed and their levels of concentration. Do not dispose of the instrument or return it to Waters for repair until the authority responsible for approving its removal from the premises specifies the extent of decontamination required and the level of residual contamination permissible. Management must also prescribe the method of decontamination to be used and the appropriate protection for personnel undertaking the decontamination process.You must handle items such as syringes, fused silica lines, and borosilicate tips used to carry sample into the source area in accordance with laboratory procedures for contaminated vessels and sharps. To avoid contamination by carcinogenic, toxic, or biohazardous substances, you must wear chemical-resistant gloves when handling or disposing of used oil.

Safety advisoriesConsult Appendix A for a comprehensive list of warning and caution advisories.

Warning: To avoid personal contamination with biologically hazardous, corrosive, or toxic materials, wear chemical-resistant gloves during all phases of instrument decontamination.

Warning: To avoid puncture injuries, handle syringes, fused silica lines, and borosilicate tips with care.

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Operating this instrument

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

Applicable symbols

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

Symbol DefinitionManufacturer

Date of manufacture

Part number

Serial number

Supply ratings

Authorized representative of the European Community

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

Australia C-Tick EMC compliant

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

ABN 49 065 444 751

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Intended useWaters designed the orthogonal acceleration, time-of-flight Xevo™ G2-S QTof for use as a research tool to deliver authenticated mass measurement. The Xevo G2-S QTof is for research use only and is not intended for use in diagnostic applications.

CalibratingTo calibrate LC systems, follow acceptable calibration methods using at least five standards to generate a standard curve. The concentration range for standards should cover the entire range of QC samples, typical specimens, and atypical specimens.When calibrating mass spectrometers, consult the calibration section of the operator’s guide for the instrument you are calibrating. In cases where an overview and maintenance guide, not operator’s guide, accompanies the instrument, consult the instrument’s online Help system for calibration instructions.

Quality controlRoutinely run three QC samples that represent subnormal, normal, and above-normal levels of a compound. Ensure that QC sample results fall within an acceptable range, and evaluate precision from day to day and run to run. Data collected when QC samples are out of range might not be valid. Do not report these data until you are certain that the instrument performs satisfactorily.

ISM classification

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

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EC authorized representative

Waters Corporation (Micromass UK Ltd.)Floats RoadWythenshaweManchester M23 9LZUnited Kingdom

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

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Table of Contents

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

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

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

Contacting Waters ............................................................................................... iii

Safety considerations .......................................................................................... iv Considerations specific to the Xevo G2-S QTof ................................................. iv Safety advisories ................................................................................................. vi

Operating this instrument ................................................................................ vii Applicable symbols ........................................................................................... vii Audience and purpose....................................................................................... vii Intended use..................................................................................................... viii Calibrating ....................................................................................................... viii Quality control ................................................................................................. viii

ISM classification .............................................................................................. viii ISM Classification: ISM Group 1 Class A ...................................................... viii

EC authorized representative ........................................................................... ix

1 Waters Xevo G2-S QTof Overview ...................................................... 1-1

Waters Xevo G2-S QTof .................................................................................... 1-2 IntelliStart technology..................................................................................... 1-2 ACQUITY and nanoACQUITY Xevo G2-S QTof UPLC/MS systems ........... 1-3 Software and data system ............................................................................... 1-6

LockSpray source and ionization modes .................................................... 1-6 Electrospray ionization (ESI) .......................................................................... 1-7 Atmospheric pressure chemical ionization (APCI) ........................................ 1-8 Combined electrospray/atmospheric pressure chemical ionization (ESCi) . 1-9 Atmospheric solids analysis probe (ASAP)..................................................... 1-9

Table of Contents xi

NanoLockSpray source and ionization modes .......................................... 1-9 TRIZAIC UPLC source .................................................................................. 1-11

Combined APPI/APCI source ....................................................................... 1-11

IntelliStart Fluidics system .......................................................................... 1-12 IntelliStart Fluidics system physical layout ................................................ 1-13 System operation ........................................................................................... 1-14

Ion optics ........................................................................................................... 1-15

Leak sensors .................................................................................................... 1-16

Vacuum system ................................................................................................ 1-16

2 Preparing the Mass Spectrometer for Operation ........................... 2-1

Starting the mass spectrometer .................................................................... 2-2 Verifying the instrument’s state of readiness ................................................ 2-3 Monitoring the mass spectrometer LEDs....................................................... 2-3 Calibration ....................................................................................................... 2-3 Flow rates for the Xevo G2-S QTof system..................................................... 2-4

Preparing the IntelliStart Fluidics system ................................................. 2-4 Installing the reservoir bottles........................................................................ 2-4 Adjusting the solvent delivery tube positions ................................................ 2-7 Purging the pump ............................................................................................ 2-8

Rebooting the mass spectrometer ................................................................. 2-8

Leaving the mass spectrometer ready for operation ............................... 2-8

Emergency shutdown of the mass spectrometer ....................................... 2-9

3 Configuring the LockSpray Source ................................................... 3-1

Configuring the LockSpray source ............................................................... 3-2

Configuring for ESI mode ............................................................................... 3-2 Installing the ESI probe .................................................................................. 3-2 Removing the ESI probe.................................................................................. 3-7

Configuring for APCI mode ............................................................................ 3-8 Installing the IonSABRE II probe .................................................................. 3-8

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Removing the IonSABRE II probe ................................................................ 3-11

Configuring for ESCi mode .......................................................................... 3-12 Optimizing the ESI probe for ESCi operation.............................................. 3-12

4 Configuring the NanoLockSpray Source ......................................... 4-1

Overview of the NanoLockSpray source ..................................................... 4-2 Sample sprayer ................................................................................................ 4-3 LockSpray sprayer ........................................................................................... 4-3 NanoFlow gas supply....................................................................................... 4-4 Purge gas.......................................................................................................... 4-4 Sprayer platform adjuster assembly............................................................... 4-4

Selecting and configuring the NanoLockSpray source ........................... 4-4

Deploying the sprayer platform adjuster assembly ................................. 4-5

Adjusting the sprayer tip position ................................................................ 4-7

Setting up the camera ...................................................................................... 4-8

Optional glass capillary sprayer ................................................................... 4-9

5 Maintenance Procedures ..................................................................... 5-1

Maintenance schedule ..................................................................................... 5-3

Spare parts ......................................................................................................... 5-4

Troubleshooting with Connections INSIGHT ............................................ 5-5

Safety and handling ......................................................................................... 5-6

Preparing the instrument for working on the source ............................. 5-7

Removing and refitting the source enclosure ............................................ 5-7 Removing the source enclosure from the instrument .................................... 5-7 Fitting the source enclosure to the instrument............................................ 5-10

Installing and removing the corona pin .................................................... 5-11 Installing the corona pin in the source ......................................................... 5-11 Removing the corona pin from the source .................................................... 5-14

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Operating the source isolation valve ......................................................... 5-15

Removing O-rings and seals ......................................................................... 5-18

Cleaning the instrument case ...................................................................... 5-19

Emptying the nitrogen exhaust trap bottle .............................................. 5-19

Maintaining the roughing pump ................................................................. 5-21

Maintaining the Oerlikon Leybold oil-filled roughing pump ............... 5-21 Gas ballasting the Oerlikon Leybold roughing pump.................................. 5-23 Inspecting the roughing pump oil level ........................................................ 5-23 Adding oil to the roughing pump .................................................................. 5-24 Replacing the roughing pump’s oil and oil demister elements.................... 5-26

Cleaning the source components ................................................................ 5-33

Cleaning the sampling cone assembly ....................................................... 5-34 Removing the sampling cone assembly from the source ............................. 5-34 Disassembling the sampling cone assembly................................................. 5-36 Cleaning the sample cone and cone gas nozzle ............................................ 5-39 Assembling the sampling cone assembly...................................................... 5-41 Fitting the sampling cone assembly to the source ....................................... 5-42

Cleaning the ion block assembly ................................................................. 5-44 Removing the ion block assembly from the source assembly ...................... 5-44 Disassembling the source ion block assembly.............................................. 5-47 Cleaning the ion block components .............................................................. 5-53 Assembling the source ion block assembly................................................... 5-55 Fitting the ion block assembly to the source assembly................................ 5-56

Cleaning the StepWave ion guide assembly ............................................. 5-58 Handling the StepWave ion guide assembly................................................ 5-58 Removing the ion block support from the source assembly......................... 5-58 Removing the StepWave assembly from the source assembly .................... 5-60 Disassembling the StepWave ion guide assembly ....................................... 5-63 Cleaning the StepWave ion guide assembly................................................. 5-68 Assembling the StepWave ion guide assembly ............................................ 5-73 Fitting the StepWave assembly to the source assembly.............................. 5-75 Fitting the ion block support to the source................................................... 5-77

xiv Table of Contents

Replacing the ESI probe tip and gasket .................................................... 5-78 Removing the ESI probe tip and gasket ....................................................... 5-78 Fitting the ESI probe tip and gasket ............................................................ 5-81

Replacing the ESI probe sample capillary ............................................... 5-82 Removing the existing capillary.................................................................... 5-82 Installing the new capillary .......................................................................... 5-86

Cleaning the IonSABRE II probe tip .......................................................... 5-90

Replacing the IonSABRE II probe sample capillary .............................. 5-90 Removing the existing capillary.................................................................... 5-90 Installing the new capillary .......................................................................... 5-93

Replacing the LockSpray reference probe capillary ............................. 5-97 Removing the existing capillary.................................................................... 5-97 Installing the new capillary .......................................................................... 5-99

Replacing the NanoLockSpray reference probe capillary ................. 5-100 Removing the reference probe from the NanoLockSpray source .............. 5-100 Installing the new TaperTip and capillary................................................. 5-103

Cleaning or replacing the corona pin ...................................................... 5-105

Replacing the IonSABRE II probe heater ............................................... 5-106 Removing the IonSABRE II probe heater .................................................. 5-106 Fitting the new IonSABRE II probe heater................................................ 5-108

Replacing the ion block source heater .................................................... 5-109

Replacing the LockSpray source’s assembly seals ............................... 5-113 Removing the probe adjuster assembly probe and source

enclosure seals ....................................................................................... 5-113 Fitting the new source enclosure and probe adjuster assembly

probe seals.............................................................................................. 5-115

Replacing the mass spectrometer’s air filters ........................................ 5-117 Replacing the air filter inside the front door.............................................. 5-117 Replacing the air filters on the sides of the instrument ............................ 5-119

Table of Contents xv

Replacing the IntelliStart Fluidics tubing ............................................. 5-121

Replacing IntelliStart Fluidics tubing (Standard configuration) ..... 5-122 Removing the IntelliStart Fluidics tubing ................................................. 5-123 Plumbing the IntelliStart Fluidics lock-spray system............................... 5-124

Replacing IntelliStart Fluidics tubing (NanoLockSpray) ................... 5-132 Plumbing the IntelliStart Fluidics sample delivery system...................... 5-132

Plumbing the IntelliStart Fluidics for low flow sample delivery ...... 5-138

A Safety Advisories .................................................................................. A-1

Warning symbols ............................................................................................... A-2 Task-specific hazard warnings........................................................................ A-2 Specific warnings ............................................................................................. A-3

Caution symbol .................................................................................................. A-5

Prohibition symbol ........................................................................................... A-6

Warnings that apply to all Waters instruments ......................................... A-7

Electrical and handling symbols ................................................................. A-12 Electrical symbols .......................................................................................... A-12 Handling symbols .......................................................................................... A-13

B External Connections .......................................................................... B-1

Mass spectrometer external wiring and vacuum connections ............. B-2

Connecting the Oerlikon Leybold oil-filled roughing pump ................. B-3 Making the electrical connections to the Oerlikon Leybold oil-filled roughing

pump........................................................................................................... B-6

Connecting the Edwards oil-free roughing pump ................................... B-7 Making the electrical connections to the Edwards oil-free roughing pump B-10

xvi Table of Contents

Connecting to the nitrogen gas supply ..................................................... B-10

Connecting to the collision cell gas supply ............................................. B-12

Connecting the nitrogen exhaust line ...................................................... B-13

Connecting liquid waste lines ..................................................................... B-15

Connecting the workstation (systems with no ACQUITY LC) ............ B-17

Connecting Ethernet cables (systems with ACQUITY LC) .................. B-18

Input/output signal connectors .................................................................. B-19 Signal connections ......................................................................................... B-22

Connecting to the electricity source ......................................................... B-25

Connecting the NanoLockSpray source camera .................................... B-25 Installing the camera driver software .......................................................... B-26

C Materials of Construction and Compatible Solvents ................... C-1

Preventing contamination ............................................................................. C-2

Items exposed to solvent ................................................................................ C-2

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

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xviii Table of Contents

1 Waters Xevo G2-S QTof Overview

This chapter describes the instrument, including its controls, sources and IntelliStart™ Fluidics system.Contents:

Topic PageWaters Xevo G2-S QTof 1-2LockSpray source and ionization modes 1-6NanoLockSpray source and ionization modes 1-9Combined APPI/APCI source 1-11IntelliStart Fluidics system 1-12Ion optics 1-15Leak sensors 1-16Vacuum system 1-16

1-1

Waters Xevo G2-S QTof

The Xevo™ G2-S QTof Mass Spectrometry (MS) system is a hybrid, quadrupole, orthogonal acceleration, time-of-flight (TOF) mass spectrometer operated by Waters® informatics software.Either of the following high-performance, ZSpray™, dual-orthogonal, API sources is fitted as standard equipment:

• LockSpray™ (ESI/APCI/ESCi®) source, which combines these ionization modes:

– Electrospray– Atmospheric pressure chemical– Combined electrospray and atmospheric pressure chemical

See “NanoLockSpray source and ionization modes” on page 1-9.• NanoLockSpray™ ESI source, see “NanoLockSpray source and

ionization modes” on page 1-9.The following optional sources are compatible with the Xevo G2-S QTof:

• Combined APPI/APCI source, with the Xevo G2-S QTof (see the Waters APPI Source Operator’s Guide Supplement, part number 71500137602).

• Atmospheric Solids Analysis Probe (ASAP) (see the Atmospheric Solids Analysis Probe Operator’s Guide Supplement).

• Atmospheric Pressure Gas Chromatography (APGC) source (see the Atmospheric Pressure GC Operator’s Guide Supplement).

• TRIZAIC UPLC source (see the TRIZAIC UPLC System Guide).For the instrument’s specifications, consult the Waters Xevo G2-S QTof Site Preparation Guide (part number 715001948).

IntelliStart technologyIntelliStart technology monitors instrument performance and reports when it is ready for use.The console software automatically mass calibrates the mass spectrometer and displays performance readbacks to enable simplified setup of the system for use in routine analytical and open access applications.

1-2 Waters Xevo G2-S QTof Overview

The IntelliStart Fluidics1 system is built into the mass spectrometer. It delivers sample directly to the MS probe from the LC column or from three integral reservoirs. The reservoirs can also deliver sample through direct or combined infusion so that you can optimize instrument performance at analytical flow rates. An additional reservoir contains solvent for the automated flushing of the solvent delivery system.

ACQUITY and nanoACQUITY Xevo G2-S QTof UPLC/MS systemsThe Waters Xevo G2-S QTof is compatible with ACQUITY UPLC® and nanoACQUITY UPLC® systems, including the H-Class and I-Class systems. If you are not using either system, refer to the documentation specific to your LC system.

The ACQUITY® Xevo G2-S QTof UPLC®/MS system includes an ACQUITY UPLC system and the Waters Xevo G2-S QTof fitted with the LockSpray ESI/APCI/ESCi source.The nanoACQUITY Xevo G2-S QTof UPLC/MS system includes a nanoACQUITY UPLC system and the Waters Xevo G2-S QTof fitted with the NanoLockSpray source.

ACQUITY UPLC system

The ACQUITY UPLC system includes a binary or quaternary solvent manager, sample manager, column heater, sample organizer, detectors, and a specialized ACQUITY UPLC column. Watersinformatics software controls the system.For further information, see the ACQUITY UPLC System Operator’s Guide or Controlling Contamination in UPLC/MS and HPLC/MS Systems (part number 715001307). You can find the latter document on http://www.waters.com; click Services & Support > Support.

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

Waters Xevo G2-S QTof 1-3

Waters ACQUITY Xevo G2-S QTof UPLC/MS system:

Sample organizer (optional)Solvent tray

Xevo G2-S QTof

Sample manager

Binary solvent manager

Access door to the fluidics pump

High voltage connector for the ESI probe

Probe

Source interface sliding door

LockSpray source enclosure

Access door to the fluidics valves

Column heater


nanoACQUITY UPLC system

The nanoACQUITY UPLC system includes a binary solvent manager, auxiliary solvent manager, sample manager, column heater, sample organizer, detectors, and a specialized nanoACQUITY UPLC column. Watersinformatics software controls the system.For further information, see the nanoACQUITY UPLC System Operator’s Guide or Controlling Contamination in UPLC/MS and HPLC/MS Systems (part number 715001307). You can find the latter document on http://www.waters.com; click Services & Support > Support.

Waters nanoACQUITY Xevo G2-S QTof UPLC/MS system:

Solvent tray

Column heater

Xevo G2-S QTof

Sample manager

Access door to the fluidics pump

Access door to the fluidics valve

Source interface sliding door

NanoLockSpray source enclosure

Binary solvent manager

Waters Xevo G2-S QTof 1-5

Software and data systemWaters informatics software controls the mass spectrometer. The software acquires, analyzes, manages, and distributes data from mass spectrometry, ultraviolet (UV), evaporative light scattering, and other sources.Waters informatics software enables these major operations:

• Configuring the instrument.• Creating LC and MS methods that define operating parameters for a

run.• Tuning and mass calibrating the mass spectrometer.• Running samples.• Monitoring sample runs.• Acquiring data.• Processing data.• Reviewing data.• Printing data.

See the online Help for more information

LockSpray source and ionization modes

The LockSpray source uses lock-mass correction to acquire exact mass data. The analyte is introduced into the source through a probe. A reference flow containing a compound of known mass flows through a separate ESI probe. An oscillating baffle allows the sprays to be analyzed as two separate data functions. The lock-mass correction calculated from the reference data is then applied to the analyte data set.You can use the LockSpray source with the ESI, APCI, ESCi, and ASAP ionization modes. See Chapter 3 “Configuring the LockSpray source”.


Xevo G2-S QTof fitted with LockSpray source:

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.To operate the LockSpray source in ESI mode, you fit the source enclosure with an ESI probe.

LockSpray source and ionization modes 1-7

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

Atmospheric pressure chemical ionization (APCI)Atmospheric pressure chemical ionization (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. Mobile phase from the LC column enters the probe, where it is pneumatically converted to an aerosol, rapidly heated, and vaporized or gasified at the probe tip.

APCI mode:

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 pass through the sample cone and into the mass spectrometer.

IonSABRE II probe

Sample cone

Corona pin


Combined electrospray/atmospheric pressure chemical ionization (ESCi)

In combined electrospray and atmospheric pressure chemical ionization (ESCi©) mode, the standard ESI probe is used in conjunction with a corona pin. The design allows alternating acquisition of ESI and APCI ionization data, facilitating high-throughput processing and wider compound coverage.

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.

NanoLockSpray source and ionization modes

The NanoLockSpray source allows electrospray ionization performed in the flow rate range of 5 to 1000 nL/min. For a given sample concentration, the ion currents for similar experiments approximate those in normal flow rate electrospray. However, because sample consumption is greatly reduced, the sensitivity gains are significant when similar scan parameters are used.Lock-mass correction with the NanoLockSpray source works as the LockSpray source does in electrospray ionization mode.The NanoLockSpray source enclosure consists of a sprayer — universal, borosilicate glass capillary, or CE (see below) — mounted on a ZSpray three-axis manipulator.A light within the source provides illumination for the spray, which you can observe using the video camera mounted on the corner of the source housing.See Chapter 4 “Configuring the NanoLockSpray Source”.

NanoLockSpray source and ionization modes 1-9

Xevo G2-S QTof fitted with NanoLockSpray source:

Options shown in the following table are available for the spraying capillary:

Spraying-capillary options:

Option DescriptionUniversal NanoFlow™ nebulizer sprayer

For flow injection or coupling to nanoACQUITY systems. A pump regulates flow rate to as low as 100 nL/min.

Borosilicate glass capillary NanoFlow (nanovials)

Uses metal-coated glass capillaries, permitting the lowest flow rates. Usable for one sample only, after which you must discard them.


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

Combined APPI/APCI source

Atmospheric pressure photoionization (APPI) uses photons generated by a discharge UV lamp (~10.2 eV) to produce sample ions from vaporized LC eluent. Direct photoionization of the sample molecule occurs when the photon energy exceeds the ionization potential of the sample molecule.The optional dual-mode (APPI/APCI) ionization source comprises an APPI source enclosure, which is used in conjunction with a standard APCI probe. You can operate the source in APPI or dual mode. The latter mode involves rapid alternation of the APPI and APCI ionization modes, facilitating high-throughput analyses.For further details, see the Waters APPI Source Operator’s Guide Supplement (part number 71500137602).

Combined APPI/APCI source 1-11

IntelliStart Fluidics system

The IntelliStart Fluidics system is built into the instrument; it controls how sample is delivered to the source. System connections differ according to whether you are using a LockSpray or NanoLockSpray source. See page 5-121.For standard flow applications, the system delivers sample directly to the mass spectrometer’s source in one of three ways:

• From the LC column.• From three integral reservoir bottles. Use standard reservoir bottles

(30 mL) for instrument setup and calibration. Use low-volume vials (1.5 mL) to infuse smaller volumes.The reservoir bottles can also deliver sample through direct or combined infusion, permitting optimization at analytical flow rates.

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

For nanoACQUITY, the valves and pumps of the IntelliStart Fluidics system introduce dead volume, which can cause unacceptable peak broadening. For this reason, the nanoACQUITY is plumbed directly to the NanoFlow sprayer using a suitable, short piece of silica tubing.For reference flows for both the LockSpray and NanoLockSpray source, the IntelliStart Fluidics system delivers lock-mass solution from reservoir bottle B or, for extended operating hours, from a separate, external bottle of lock-mass solution.


IntelliStart Fluidics system physical layoutThe IntelliStart Fluidics system comprises the components shown in the following figure.

IntelliStart Fluidics system components:

A B C

AA

BB

C

AA BB C

W atersW aters

AA

BB

CC

Lock-spray selector valve

Sample selector valve

Divert valve

Sample pump

Lock-spray pump

Sample reservoir bottles (A, B and C)

Tube guides Optional Flow sensorGrounded union

Access doors

IntelliStart Fluidics system 1-13

The IntelliStart Fluidics system consists of these components:• A sample delivery system composed of a pump, sample selector valve,

and a divert valve used for LC and probe connections.• A lock-spray system, composed of a pump capable of ultra-low flow rates,

a lock-spray selector valve, flow sensor, and grounded union. The grounded union protects the flow sensor from probe voltages. The flow sensor regulates flow rate, reducing it to accommodate the very low volumes required by the NanoLockSpray source. The flow sensor and grounded union are optional fittings when used with the lock-spray system. They are, however, standard fittings when used with the NanoLockSpray source.

• Three shared 30-mL sample reservoir bottles: A, B, and C.• Plumbing for shared wash and waste bottles.

The sample reservoirs are mounted on the instrument’s front panel. When you select a solvent in the instrument software, a light-emitting diode (LED) illuminates the appropriate reservoir. You can simultaneously illuminate all three reservoirs or extinguish the LEDs, for light-sensitive samples.Recommendation: Use reservoir A for the sample solution, reservoir B for the lock-spray solution, and reservoir C for the calibrant solution.The wash reservoir and (optionally) the reservoirs containing the lock-mass reference solutions are external to the instrument; typically they are bottles on the LC system. The waste reservoir is normally a bottle stored under the instrument bench.During normal operation the instrument access doors must be kept closed.

System operationYou configure the IntelliStart Fluidics system using the instrument software, in which you can edit parameter settings, frequency, and the extent of the automation. During auto-calibration, the software automatically controls lock-mass and sample delivery.Consult the mass spectrometer’s online Help for further details on operating the IntelliStart Fluidics system.


Ion optics

The mass spectrometer’s ion optics operate in the following sequence:1. Samples from the LC or instrument’s solvent delivery system are

introduced at atmospheric pressure into the ionization source.2. The ions pass through the sample cone and into the vacuum system.3. The ions pass through the StepWave ion guide to the quadrupole, where

they are filtered according to their mass-to-charge ratio.4. The mass-separated ions pass into the T-Wave™ collision cell, where

they can undergo collision-induced dissociation (CID).5. The ions pass into the time-of-flight (ToF) analyzer. A high voltage pulse

orthogonally accelerates the ions up the flight tube, where a reflectron reflects them back towards the detector. Ions of different mass-to-charge ratios arrive at the detector at different times. The difference in the arrival times provides the basis for a mass spectrum.

6. The signal from the detector is amplified, digitized, and transmitted to the software.

Ion optics overview:

Pusher

DRE lens

Quadrupole

StepWave ion guide

Lock-spray sprayer

Transfer lenses

T-Wave collision cellIsolation valve

Reflectron

Flight tubeSample sprayer

Detector

Sample cone

Ion optics 1-15

Leak sensors

Leak sensors in the instrument’s drip trays continuously monitor for liquid leaks. A leak sensor stops system flow when its optical sensor detects about 1.5 mL of accumulated leaked liquid in its surrounding reservoir. At the same time, the software displays an error message alerting you that a leak has developed. Consult the Waters ACQUITY UPLC Leak Sensor maintenance instructions (part number 71500082506) for complete details.

Vacuum system

An external roughing pump and three internal turbomolecular pumps maintain therequired vacuum.Protective interlocks guard against vacuum leaks and electrical or vacuum pump failure. The system monitors the turbomolecular pump speeds and continuously measures vacuum pressure via built-in gauges. The gauges also serve as switches, stopping operation when vacuum loss is sensed.A vacuum isolation valve isolates the source from the mass analyzer, allowing cleaning of the sample cone without the need to vent the instrument to atmospheric pressure.


2 Preparing the Mass Spectrometer for Operation

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

Contents:

Topic PageStarting the mass spectrometer 2-2Preparing the IntelliStart Fluidics system 2-4Rebooting the mass spectrometer 2-8Leaving the mass spectrometer ready for operation 2-8Emergency shutdown of the mass spectrometer 2-9

2-1

Starting the mass spectrometer

The Waters Xevo G2-S QTof is compatible with the ACQUITY UPLC and nanoACQUITY UPLC systems. If you are not using either system, refer to the documentation relevant to your LC system (see “Software and data system” on page 1-6).

Requirement: Power-on the instrument server or workstation PC first, to ensure that it can assign IP addresses to LCMS system modules.See the mass spectrometer’s online Help for details.

To start the mass spectrometer:

1. On the rear panel, ensure the nitrogen supply is connected to the instrument’s nitrogen inlet connection (see the figure on page B-2).Requirement: The nitrogen must be dry and oil-free, with a purity of at least 95%. Regulate the supply at 600 to 690 kPa (6.5 to 7.0 bar, 94 to 100 psi).

2. Ensure that the collision gas supply is connected to the instrument’s collision 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 instrument server or workstation PC.4. Switch on the Xevo G2-S QTof at the power outlet.5. Press the power switches of the ACQUITY instruments.

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

Caution: To avoid damage to the instrument caused by incompatible solvents, refer to the following sources:• Appendix C, “Materials of Construction and Compatible Solvents”,

for mass spectrometer solvent information.• Appendix C of the ACQUITY UPLC System Operator’s Guide for

solvent compatibility with ACQUITY devices.

Warning: To avoid ignition of flammable solvents, never let the nitrogen supply pressure fall below 414 kPa (4.0 bar, 60 psi).

2-2 Preparing the Mass Spectrometer for Operation

6. Allow 4 minutes for the PC to initialize.Tip: The power and status LEDs change as follows:• During initialization, the binary solvent manager’s and sample

manager’s status LED flashes green.• After the instruments are successfully powered-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 status LED remain unlit.

7. Start the software and monitor the instrument console for messages and LED indications.

8. Click Operate.Result: When the mass spectrometer is in good operating condition, the software indicates “Ready” in the instrument console.

Verifying the instrument’s state of readinessWhen the mass spectrometer is in good operating condition, the power and status LEDs show constant green. You can view any error messages in console software.

Monitoring the mass spectrometer LEDsLight-emitting diodes on the mass spectrometer indicate its operational status.Power LED – The power LED, below the mass spectrometer’s source, indicates when the mass spectrometer is powered-on or powered-off.Status LED – The status LED, on the right-hand side of the power LED, indicates the operating condition. See the mass spectrometer’s online Help for details on the status LED indications.

CalibrationCalibrate the mass spectrometer prior to use, see the mass spectrometer’s online Help.

Starting the mass spectrometer 2-3

Flow rates for the Xevo G2-S QTof systemThe Xevo G2-S QTof system can run at high flow rates. To optimize desolvation, and thus sensitivity, run the system at appropriate gas flows and desolvation temperatures.

Preparing the IntelliStart Fluidics system

For additional information, see “Connecting liquid waste lines” on page B-15.

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

Required materials

Chemical-resistant, powder-free gloves

Flow rate versus temperature and gas flow:

Flow rate (mL/min)

Source temperature (°C)

Desolvation temperature (°C)

Desolvation gas flow (L/h)

0.000 to 0.020 100 200 8000.020 to 0.100 120 350 8000.101 to 0.300 120 450 8000.301 to 0.500 150 500 1000>0.500 150 0 1200

Warning: To avoid injuries from broken glass, falling objects, or exposure to toxic substances, do not place containers on top of the instrument or on its front covers.Instead use the bottle tray.


To install the reservoir bottles:

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

3. For each reservoir bottle, ensure that the ends of the solvent delivery tubes are positioned so that they are close to, but do not touch, the bottom of the bottle (see page 2-7).

Warning: To avoid personal contamination with biologically hazardous, toxic, or corrosive materials, and to avoid spreading contamination to uncontaminated surfaces, wear clean, chemical-resistant, powder-free gloves when working with the reservoir bottles.

Reservoir bottle

Solvent delivery tube

Preparing the IntelliStart Fluidics system 2-5

To install the low-volume vials:

1. If a standard reservoir bottle is fitted, remove it.2. Screw the low-volume adaptors into the manifold and finger-tighten

them.

3. Screw the low-volume vials into the adaptors.4. For each low-volume vial, ensure that the ends of the solvent delivery

tubes are positioned so that they are close to, but do not touch, the bottom of the vial (see page 2-7).

Warning: To avoid personal contamination with biologically hazardous, toxic, or corrosive materials, and to avoid spreading contamination to uncontaminated surfaces, wear clean, chemical-resistant, powder-free gloves when working with the reservoir bottles.

Warning: To avoid laceration injuries caused by the shattering of fragile, low-volume glass vials, take care when screwing them in, and never use force.

Low-volume vial

Low-volume adaptor



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

To adjust the position of a solvent delivery tube:

1. Open the access door to the fluidics pump (see the figure on page 1-13).2. Loosen the finger-tight fitting for the solvent delivery tube you are

adjusting.

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

4. Tighten the finger-tight fitting.5. Close the access door.

Finger-tight fitting


Preparing the IntelliStart Fluidics system 2-7

Purging the pumpWhenever you replace a solution bottle, purge the 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 system can require more than one purge cycle to minimize carryover.

Rebooting the mass spectrometer

Reboot the mass spectrometer when either of these conditions applies:• The console software fails to initialize or connect.• Immediately following a software upgrade.

To reboot the mass spectrometer:

1. Open the sliding door above the instruments source enclosure, and locate the reset button aperture.

2. Insert a short length of PEEK tubing into the aperture to press the reset button.

Leaving the mass spectrometer ready for operation

When you are not using the instrument, stop the LC flow and put the instrument in Standby mode, to conserve energy and reduce nitrogen consumption.Tip: After you return the instrument to Operate mode, the LockSpray source’s temperature requires up to 30 minutes to stabilize at the relatively high temperatures needed for UPLC operation.


Emergency shutdown of the mass spectrometer

To shut down the mass spectrometer in an emergency:

Note: Data can be lost during an emergency shutdown.1. Switch off the power at the electrical outlet.

Result: The instrument turns off and vents.2. Disconnect the power cable from the instrument’s rear panel.

Warning: To avoid electric shock, isolate the instrument from the electrical supply, disconnect the power cable from the instrument’s rear panel.

Emergency shutdown of the mass spectrometer 2-9

3 Configuring the LockSpray Source

This chapter explains how to configure the LockSpray source for the following ionization modes:• ESI (electrospray ionization)• APCI (atmospheric pressure ionization)• ESCi (combined electrospray and atmospheric pressure ionization)

Contents:

Topic PageConfiguring the LockSpray source 3-2Configuring for ESI mode 3-2Configuring for APCI mode 3-8Configuring for ESCi mode 3-12

3-1

Configuring the LockSpray source

The following table summarizes how you configure the LockSpray source for the various ionization modes.

Configuring for ESI mode

To operate in ESI mode, you must fit the ESI probe to the LockSpray source enclosure. For more information on using ESI mode, see the Xevo G2-S QTof system online Help.

Installing the ESI probe

Required materials

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

Configuring the LockSpray source:

Ionization mode Probe type Corona pin fitted?ESI ESI NoAPCI APCI YesESCi ESI Yes

3-2 Configuring the LockSpray Source

To install the ESI probe:

1. Prepare the instrument for working on the source (see page 5-7).

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

Warning: To avoid personal contamination with biologically hazardous, toxic, or corrosive materials, and to avoid spreading contamination to uncontaminated surfaces, wear clean, chemical-resistant, powder-free gloves when working with the LC system connections, ESI probe, and source.

Warning: To avoid electric shock, ensure that the instrument is prepared for working on the source before commencing this procedure.

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

Configuring for ESI mode 3-3

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 in the probe adjuster assembly.

TP03129

Location hole of the probe adjuster assembly

Probe location dowel

Probe label


ESI probe, mounted on the LockSpray source enclosure:

4. Tighten the probe locking ring to secure the probe in place.Tip: An automatic pressure test is performed when the probe is correctly seated in position.

5. Connect the ESI probe’s cable to the high voltage connector.6. Open the access door to the IntelliStart Fluidics system (see the figure

on page 1-13).

7. Using a long “finger-tight” fitting, connect 0.004-inch ID (or greater) tubing, from port 2 (the top port) of the diverter valve to the ESI probe, where you use a PEEK, “finger-tight” nut and ferrule to connect to the union.

Caution: To avoid nitrogen leakage, fully tighten the probe locking ring.

Warning: To avoid electric shock, do not use stainless steel tubing to connect the diverter valve to the ESI probe; use the PEEK tubing supplied with the instrument.

TP03128

ESI probe cable

ESI probe

Vernier probe adjuster

Probe locking ring

Source window

High voltage connector

Source enclosure release


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 supplied with the instrument, you

must minimize the length of the tube connecting the diverter valve to the ESI probe. Doing so minimizes delays and dispersion.

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

Long “finger-tight” fitting and PEEK, “finger-tight” nut and ferrule:

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

Warning: To avoid electric shock, only use natural (beige) PEEK fittings at the top of the probe.

ESI probe

Diverter valve

Tubing connection

Probe adjuster assembly


Removing the ESI probe

Required materials


To remove the ESI probe:

1. Prepare the instrument for working on the source (see page 5-7).2. Disconnect the fluidics tubing from the ESI probe.3. Disconnect the ESI probe’s cable from the high voltage connector.4. Unscrew the probe locking ring.

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



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


Configuring for APCI mode

To operate in APCI mode, you must fit the IonSABRE II probe to the LockSpray source enclosure.For more information on using APCI mode, see the Xevo G2-S QTof system online Help.

Installing the IonSABRE II probe

Required materials

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

To install the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 5-7).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.

Warning: To avoid personal contamination with biologically hazardous, toxic, or corrosive materials, and to avoid spreading contamination to uncontaminated surfaces, wear clean, chemical-resistant, powder-free gloves when working with the LC system connections, IonSABRE II probe, and source.



3. Tighten the probe locking ring to secure the probe in place.Tip: An automatic pressure test is performed when the probe is correctly seated in position.

TP03129

Probe location dowel

Probe adjuster assembly location hole

Probe label

Configuring for APCI mode 3-9

IonSABRE II probe mounted on the source enclosure:

4. Open the access door to the fluidics valve (see the figure on page 1-4).

5. Using tubing greater than or equal to 0.004-inch ID, connect port 2 (the top port) of the diverter 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 rates1.2 mL/min.Requirements:• If you are replacing the tubing supplied with the instrument, you

must minimize the length of the tube connecting the diverter valve to the ESI probe. Doing so minimizes delays and dispersion.

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

6. Close the access door.7. Install the corona pin (see page 5-11).

Warning: To avoid electric shock, do not use stainless steel tubing to connect the diverter valve to the IonSABRE II probe; use the PEEK tubing supplied with the instrument.

Vernier probe adjuster

Source enclosure release

Source window

Vertical probe adjuster

IonSABRE II probe


Removing the IonSABRE II probe

Required materials


To remove the IonSABRE II probe:

1. Prepare the instrument for working on the source (see page 5-7).2. Remove the corona pin (see page 5-11).3. Disconnect the diverter valve tubing from the IonSABRE II probe.4. Unscrew the probe locking ring.5. Carefully remove the probe from the probe adjuster assembly.



Configuring for APCI mode 3-11

Configuring for ESCi mode

To operate in ESCi mode, you must fit an ESI probe and corona pin to the LockSpray source enclosure.The system, with the ESI probe installed and corona discharge pin fitted, can alternate between ESI and ESCi modes, facilitating data acquisition in ESI and ESCi modes in parallel. For more information on using dual ESI and ESCi modes, see the Xevo G2-S QTof system online Help.See “Installing the ESI probe” on page 3-2, “Installing the corona pin in the source” on page 5-11, and “Combined electrospray/atmospheric pressure chemical ionization (ESCi)” on page 1-9.

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


4 Configuring the NanoLockSpray Source

The Waters NanoLockSpray dual, electrospray, ion source enables the optimized co-introduction of sample and lock mass compound directly into the ion source. This feature provides authenticated, exact-mass measurement in MS mode at low flow rates.

Contents:

Topic PageOverview of the NanoLockSpray source 4-2Selecting and configuring the NanoLockSpray source 4-4Deploying the sprayer platform adjuster assembly 4-5Adjusting the sprayer tip position 4-7Setting up the camera 4-8Optional glass capillary sprayer 4-9

4-1

Overview of the NanoLockSpray source

NanoLockSpray source:

The NanoLockSpray source enclosure holds two nanoFlow sprayers positioned orthogonally with respect to one another. The sample flows through one sprayer and the lock-mass reference solution through the other. A motorized baffle rotates to admit spray from either sprayer to the sampling cone.

Sprayer platform adjuster assembly

Thumbscrew

Thumbscrew (on left-hand side of sprayer platform)

Sprayer safety cover

Z-position adjuster

Y-position adjuster

X-position adjuster

LockSpray sprayer inlet

Camera focussing ring

Camera

Sprayer shield

Shield holding screw

4-2 Configuring the NanoLockSpray Source

Schematic of the NanoLockSpray source:

Spray indexing permits acquisition of sample and lock-spray data in separate data channels, and the baffle design ensures negligible cross-talk between the two sprays. The lock-spray data are used to calculate a correction factor for the mass-scale calibration, which is then applied to the sample data, providing exact-mass information.

Sample sprayerYou can use the NanoLockSpray source with different nanoFlow sprayers. For instructions on how to set up these sprayers, see page 4-4.

LockSpray sprayerThe LockSpray™ sprayers for the NanoLockSpray source operate as part of the instrument's IntelliStart™ Fluidics system. Fitted with a 500 µL pump, the LockSpray sprayer operates at 0.5 µL/min. You must choose the concentration of the lock-spray reference solution that gives a suitable ion intensity.

LockSpray inlet

Sample inlet

Sample coneBaffle

Overview of the NanoLockSpray source 4-3

NanoFlow gas supplyThe sample sprayer nebulizer gas supply pressure is electronically controlled from 0 to 2 bar. The optimum pressure is sprayer-dependent, but usually lies between 0.3 bar and 1.0 bar.

Purge gasPurge gas typically flows at 100 L/h. It provides a positive pressure in the source enclosure that reduces the chemical background interference caused by contaminants in the laboratory air. For information on adjusting the purge gas flow, see the mass spectrometer’s online Help.

Sprayer platform adjuster assemblyThe sprayer platform adjuster assembly allows precise X-, Y-, and Z-positioning of the sprayer tip. You can also withdraw the sprayer from the source to obtain access to the sprayer tip.Using the two thumbscrews on the base of the adjuster assembly, you can move the platform in and out of the source (see “Deploying the sprayer platform adjuster assembly” on page 4-5).

Selecting and configuring the NanoLockSpray source

The Universal NanoFlow sprayer is installed as standard equipment on the NanoLockSpray source. For installation and maintenance details, see the Waters Universal NanoFlow Sprayer Installation and Maintenance Guide (part number 71500110107).When fitted, the NanoLockSpray source is automatically recognized by the software.Requirement: The sprayer platform must be inserted in the source enclosure for correct identification of the source.The following table summarizes how you configure the NanoLockSpray source for the various ionization modes.Tip: A corona pin is not used with the NanoLockSpray source.


Deploying the sprayer platform adjuster assembly

To move the sprayer platform out of the source:

1. Confirm that the sprayer’s safety cover is installed (see the figure on page 4-2).

2. Unscrew the thumbscrew on the front of the sprayer platform.3. Pull out the side thumbscrew and withdraw the sprayer platform from

the source.4. Release the side thumbscrew, locking the platform in the withdrawn

position.

NanoLockSpray source configuration:

Sprayer type Used forUniversal NanoFlow sprayer. See Universal NanoFlow Sprayer Installation and Maintenance Guide, (part number 71500110107)

For coupling to nanoACQUITY UPLC with regulated flow rates down to 100 nL/min.

Borosilicate glass capillary NanoFlow (see page 4-9). For details, see the Borosilicate Glass Capillary Sprayer Operator’s Guide (part number 715003371).

Suitable for single shot analyses. This option yields lower flow rates (

To move the sprayer platform into the source:

1. Confirm the clear sprayer shield is in place and secured (see the figure on page 4-2).

2. Confirm that the sprayer’s safety cover is installed.3. Pull out the side thumbscrew, and push the sprayer platform into the

source.4. Release the side thumbscrew, locking the platform in position.5. Tighten the front thumbscrew, securing the adjuster assembly rigidly to

the source.

Warning: To avoid electrical shock, ensure the safety cover is in place over the sprayer.


Adjusting the sprayer tip position

To adjust the tip position:

1. Adjust the X, Y, and Z controls on the adjuster assembly to move the sprayer tip close to the sampling cone and baffle.

2. Adjust the height of the sprayer so that its tip is level with the center of the sampling cone, using the index mark on the adjuster.

3. Adjust the horizontal position of the sprayer so that the tip points toward the left-hand side of the baffle. Tips:• If you observe an electrical discharge between the sprayer tip and

baffle, move the tip farther from the baffle, or reduce the capillary voltage. Note, however, that the capillary voltage must be high enough to maintain a good spray.

• Fine tune the position of the sprayer while acquiring a spectrum of a standard compound. Small adjustments to the sprayer position can make large differences to the source sensitivity.

Adjusting the sprayer tip position 4-7

Setting up the camera

To set up the camera:

1. Click to open the Camera Control dialog box.

Camera Control view of sprayers and sample cone:

2. Rotate the camera’s focusing ring to focus on the sample sprayer (see the figure on page 4-2).

Sample cone

Baffle

Sample spray

Sample sprayer


Optional glass capillary sprayer

The glass capillary sprayer is designed for use with metal-coated borosilicate glass capillaries. They allow extremely low flow rates (less than 100 nL/min). The glass capillaries are used for one sample only and must then be discarded.To use the glass capillary sprayer, complete the procedures described in the Borosilicate Glass Capillary Sprayer Operator’s Guide (part number 715003371).

Optional glass capillary sprayer 4-9

5 Maintenance ProceduresThis 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 PageMaintenance schedule 5-3Spare parts 5-4Troubleshooting with Connections INSIGHT 5-5Safety and handling 5-6Preparing the instrument for working on the source 5-7Removing and refitting the source enclosure 5-7Installing and removing the corona pin 5-11Operating the source isolation valve 5-15Removing O-rings and seals 5-18Cleaning the instrument case 5-19Emptying the nitrogen exhaust trap bottle 5-19Maintaining the roughing pump 5-21Maintaining the Oerlikon Leybold oil-filled roughing pump 5-21Cleaning the source components 5-33Cleaning the sampling cone assembly 5-34Cleaning the ion block assembly 5-44Cleaning the StepWave ion guide assembly 5-58Replacing the ESI probe tip and gasket 5-78Replacing the ESI probe sample capillary 5-82Cleaning the IonSABRE II probe tip 5-90

5-1

Replacing the IonSABRE II probe sample capillary 5-90Replacing the LockSpray reference probe capillary 5-97Replacing the NanoLockSpray reference probe capillary 5-100Cleaning or replacing the corona pin 5-105Replacing the IonSABRE II probe heater 5-106Replacing the ion block source heater 5-109Replacing the LockSpray source’s assembly seals 5-113Replacing the mass spectrometer’s air filters 5-117Replacing the IntelliStart Fluidics tubing 5-121Replacing IntelliStart Fluidics tubing (Standard configuration) 5-122Replacing IntelliStart Fluidics tubing (NanoLockSpray) 5-132Plumbing the IntelliStart Fluidics for low flow sample delivery 5-138

Contents: (Continued)

Topic Page

5-2 Maintenance Procedures

Maintenance schedule

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

Maintenance schedule:

Procedure Frequency For information...Clean the instrument case. As required. See page 5-19.Empty the nitrogen exhaust trap bottle.

Check daily, empty as required.

See page 5-19.

Inspect and adjust the roughing pump’s oil level.

Weekly. See page 5-23.

Replace the roughing pump’s oil and oil mist filter.

Annually. See page 5-26.

Replace the oil-free (scroll) pump’s seals.

Annually. See Edwards document XDS35i Instruction Manual A730-01-880.

Clean the source components. When sensitivity decreases to unacceptable levels.

See page 5-33.

Clean the StepWave ion guide.

When sensitivity is not improved by cleaning source components.

See page 5-58.

Replace the ESI probe tip. When sensitivity decreases to unacceptable levels.

See page 5-78.

Replace the ESI probe capillary.

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

See page 5-82.

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

When sensitivity decreases to unacceptable levels.

See page 5-90.

Maintenance schedule 5-3

Spare parts

Waters recommends that you replace only the parts mentioned in this document. For spare parts details, see the Waters Quality Parts Locator on the Waters Web site’s Services & Support page.

Replace the IonSABRE II probe capillary.

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

See page 5-90.

Replace the LockSpray probe capillary.


Replace the NanoLockSpray reference probe capillary.


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

When the corona pin is corroded or black, or the sensitivity decreases to unacceptable levels.

See page 5-105.

Replace the IonSABRE II probe heater.

If the heater fails to heat the probe.

See page 5-106.

Replace the ion block heater cartridge.

If the heater fails to heat the ion block.

See page 5-109.

Replace the source assembly seals.


Replace the mass spectrometer air filters.


Replace the IntelliStart Fluidics tubing.

In the event of blockage in the tubing connections between the IntelliStart Fluidics system components.

See page 5-121.

Maintenance schedule: (Continued)

Procedure Frequency For information...


Troubleshooting with Connections INSIGHT

Connections INSIGHT® is an “intelligent” device management (IDM) Web service that enables Waters to provide proactive service and support for the ACQUITY UPLC system. To use Connections INSIGHT, you must install its service agent software on your MassLynx™ 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. Select Troubleshoot > Submit Connections INSIGHT request.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. Saving a service profile or plot file from the Instrument Console can require as much as 150 MB of file space.

Troubleshooting with Connections INSIGHT 5-5

Safety and handling

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

See Appendix A for safety advisory information.

Warning: To avoid personal contamination with biologically hazardous, toxic, or corrosive materials, and to avoid spreading contamination to uncontaminated surfaces, wear clean, chemical-resistant, powder-free gloves when working with the LC system connections, ESI probe, and source components.

Warning: To prevent injury, always observe Good Laboratory Practice when handling solvents, changing tubing, or operating the instrument. Know the physical and chemical properties of the solvents used (see the Material Safety Data Sheets for the solvents in use).

Warning: To avoid electric shock,• do not remove the instrument’s panels. There are no user-serviceable

items inside the instrument.• ensure that the instrument is in Standby mode before commencing

any maintenance.

Warning: To avoid burn injuries, take great care when working with the probe and source.

Warning: To avoid puncture wounds, take great care while working with the source enclosure open when one or both of these conditions apply:• An ESI probe is fitted (the probe tip is sharp).• A corona pin is fitted (the pin’s tip is sharp).


Preparing the instrument for working on the source

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

To prepare the instrument for working on the source:

1. In the instrument console, stop the LC flow or, if column flow is required, divert the LC flow to waste.

2. In the instrument console, select source standby and confirm that the operate indicator is not illuminated.

3. Set the source temperature to 30 °C.

4. Wait for the source temperature, desolvation temperature or IonSABRE II probe temperature to cool.

5. Ensure that the API desolvation gas flow is stopped.

Removing and refitting the source enclosure

Before performing certain maintenance procedures, or fitting the optional dual-mode APPI/APCI source to the instrument, you must remove the LockSpray or NanoLockSpray source enclosure from the instrument.Note: The following procedures apply to both the standard and optional source enclosures.

Removing the source enclosure from the instrument

Required materials


Warning: To avoid burn injuries, take great care when working on the source and probe, as they can be hot.

Preparing the instrument for working on the source 5-7

To remove the source enclosure:


2. Remove the probe from the source:• If you are removing an ESI probe, see page 3-7.• If you are removing an IonSABRE II probe, see page 3-11.

3. Slide open the instrument’s source interface door (see the figure on page 1-4).

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

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


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

Warning: To avoid puncture wounds, take great care while working with the source enclosure open if a corona pin is fitted. The pin’s tip is sharp.

Caution: To avoid damaging the sample inlet, when removing a NanoLockSpray source enclosure, you must slide the sprayer platform out of the source enclosure before you open the enclosure (see page 4-5).


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

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

TP03164

Supporting stud

Source enclosure

Cable storage positions

Removing and refitting the source enclosure 5-9

Fitting the source enclosure to the instrument

Required materials


To fit the source enclosure to the instrument:

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

2. Close the source enclosure.3. Connect the probe adjuster and options cables to the instrument’s

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

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


Warning: To avoid puncture wounds, take great care while fitting the source enclosure to the source if a corona pin is fitted. The pin’s tip is sharp.

Caution: To avoid damaging the sample inlet, when removing a NanoLockSpray source enclosure, you must slide the sprayer platform out of the source enclosure before you open the enclosure (see page 4-5).


Installing and removing the corona pin

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

Installing the corona pin in the source

Required materials


To install the corona pin in the source:


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

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


Warning: To avoid electric shock,prepare the instrument for work performed on its source before beginning this procedure.

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

Warning: To avoid puncture wounds, take great care while working with the source enclosure open when an ESI probe is fitted. The probe’s tip is sharp.

Installing and removing the corona pin 5-11

Corona pin mounting contact:

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

Warning: To avoid puncture injury, handle the corona pin with care. Its tip is sharp.

TP03130

Corona pin mounting contact blanking plug


Corona pin:

5. Close the source enclosure.6. Look through the source window, and use the vernier probe adjuster (see

page 3-3) to position the ESI probe tip so that it is pointing approximately midway between the tips of the sample cone and the corona pin.

TP03130

Corona pin

Sample cone orifice

Installing and removing the corona pin 5-13

Removing the corona pin from the source

Required materials


To remove the corona pin from the source:

1. Prepare the instrum

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