Waters SYNAPT G2 Operator's, Overview And Maintenance Manual

Waters SYNAPT G2 Mass

Spectrometry System

Operator’s Overview and Maintenance Guide

Revision A

Copyright notice

© 2009 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.

The information in this document is subject to change without notice and should not be construed as a commitment by Waters Corporation. Waters Corporation assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use.

Trademarks

ACQUITY, ACQUITY UPLC, Connections Insight, ESCi, UPLC, and Waters are registered trademarks of Waters Corporation. IntelliStart, LockSpray, MassLynx, NanoFlow, NanoLockSpray, QuanTof, SYNAPT, T-Wave, “THE SCIENCE OF WHAT'S POSSIBLE.”, Triwave, and ZSpray are trademarks of Waters Corporation.

GELoader is a registered trademark of Cell Technology. Swagelok and snoop are registered trademarks of Swagelok Company. PEEK is a trademark of Victrex plc. Viton is a registered trademark of DuPont Performance Elastomers. Other registered trademarks or trademarks are the sole property of their

respective owners.

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 tech_comm@waters.com.

iii

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

Telephone and fax From the USA or Canada, phone 800

Conventional mail Waters Corporation

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

252-HPLC, or fax 508 872 1990. For other locations worldwide, phone and fax

numbers appear in the Waters Web site.

34 Maple Street Milford, MA 01757 USA

Safety considerations

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

When you develop methods, follow the “Protocol for the Adoption of Analytical Methods in the Clinical Chemistry Laboratory,” American Journal of Medical Technology, 44, 1, pages 30–37 (1978). This protocol addresses good operating procedures and the techniques necessary to validate system and method performance.

Considerations specific to the SYNAPT G2 MS system

Solvent leakage hazard

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

Warning:

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

• To avoid chemical degradation of the source O-rings, which can withstand exposure only to certain solvents (see “Solvents used

to prepare mobile phases” on page C-3), determine whether any

solvents you use that are not listed are chemically compatible with the composition of the O-rings.

Flammable solvents hazard

Warning: To prevent the ignition of accumulated solvent vapors inside

the source, maintain a continuous flow of nitrogen through the source whenever significant amounts of flammable solvents are used during instrument operation.

Never let the nitrogen supply pressure fall below 400 kPa (4 bar, 58 psi) during analyses that require flammable solvents. Connect to the LC output with a gas-fail connector to stop the LC solvent if the nitrogen supply fails.

High temperature hazard

Warning: To avoid burn injuries, avoid touching the source enclosure

with your hand when operating or servicing the instrument.

Mass spectrometer high temperature hazard

Source ion block assembly

Hazards associated with removing an instrument from service

Warning: To avoid personal contamination with

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

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

and borosilicate tips with care.

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

• Source interior

• Waste tubing

• Exhaust system

• Rotary pump oil (where applicable)

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

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

Safety advisories

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

vii

Operating this instrument

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

Applicable symbols

Symbol Definition

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

ABN 49 065 444 751

Audience and purpose

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

Intended use

Waters designed this instrument to be used as a research tool to deliver authenticated, exact-mass measurement. It is not for use in diagnostic procedures.

Australia C-Tick EMC Compliant

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

This product has been tested to the requirements of CAN/CSA-C22.2 No. 61010-1, second edition, including Amendment 1, or a later version of the same standard incorporating the same level of testing requirements

viii

Calibrating

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

When calibrating mass spectrometers, consult the calibration section of the operator’s guide for the instrument you are calibrating. In cases where an overview and maintenance guide, not operator’s guide, accompanies the instrument, consult the instrument’s online Help system for calibration instructions.

Quality control

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

ISM classification

ISM Classification: ISM Group 1 Class A

This classification has been assigned in accordance with CISPR 11 Industrial Scientific and Medical (ISM) instruments requirements. Group 1 products apply to intentionally generated and/or used conductively coupled radio-frequency energy that is necessary for the internal functioning of the equipment. Class A products are suitable for use in commercial, (that is, nonresidential) locations and can be directly connected to a low voltage, power-supply network.

EC Authorized Representative

Waters Corporation (Micromass UK Ltd.) Floats Road Wythenshawe Manchester M23 9LZ United Kingdom

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

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

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

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

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

Considerations specific to the SYNAPT G2 MS system .................................... v

Safety advisories............................................................................................... vii

Operating this instrument .............................................................................. viii

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

Audience and purpose...................................................................................... viii

Intended use..................................................................................................... viii

Calibrating .......................................................................................................... ix

Quality control .................................................................................................... ix

ISM classification ................................................................................................. ix

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

EC Authorized Representative .......................................................................... x

1 System Overview .................................................................................... 1-1

Waters SYNAPT G2 MS .................................................................................... 1-2

SYNAPT G2 MS UPLC/MS/MS systems ........................................................ 1-2

ACQUITY UPLC SYNAPT G2 MS UPLC/MS/MS system............................ 1-2

nanoACQUITY UPLC SYNAPT G2 MS nanoUPLC/MS/MS system ........... 1-3

Software .............................................................................................................. 1-3

IntelliStart ....................................................................................................... 1-3

MassLynx ......................................................................................................... 1-4

Instrument Console ......................................................................................... 1-4

Table of Contents xi

Instrument sources ........................................................................................... 1-5

LockSpray source and ionization modes......................................................... 1-5

NanoLockSpray source.................................................................................... 1-7

Dual-mode ionization source........................................................................... 1-9

Matrix-assisted laser desorption ionization ................................................... 1-9

IntelliStart Fluidics system ............................................................................ 1-9

Overview........................................................................................................... 1-9

IntelliStart Fluidics physical layout............................................................. 1-10

System operation ........................................................................................... 1-11

Ion optics ........................................................................................................... 1-12

Analyzers ........................................................................................................... 1-13

Quadrupole..................................................................................................... 1-13

Triwave technology........................................................................................ 1-14

TOF analyzer ................................................................................................. 1-15

Mass spectrometer configuration ............................................................... 1-17

Triwave device ............................................................................................... 1-17

TOF................................................................................................................. 1-17

Leak sensors ..................................................................................................... 1-18

Vacuum system ................................................................................................ 1-18

Controls on the instrument’s rear panel ................................................... 1-19

2 Starting Up and Shutting Down the Mass Spectrometer ............. 2-1

Starting the mass spectrometer .................................................................... 2-2

Calibration information................................................................................... 2-3

Flow rates for the ACQUITY UPLC SYNAPT G2 MS

UPLC/MS/MS system................................................................................ 2-3

Preparing the IntelliStart Fluidics system ................................................. 2-4

Installing the vials........................................................................................... 2-4

Purging the pump ............................................................................................ 2-5

Shutting down the mass spectrometer ........................................................ 2-6

Putting the mass spectrometer in Standby mode .......................................... 2-6

Fully shutting down the mass spectrometer.................................................. 2-6

xii Table of Contents

Rebooting the embedded PC .......................................................................... 2-7

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

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

Configuring for ESI mode ............................................................................... 3-2

Installing the ESI probe .................................................................................. 3-2

Removing the ESI probe.................................................................................. 3-7

Installing the ESI small bore capillary option ........................................... 3-8

Configuring for APCI mode .......................................................................... 3-14

Installing the APCI probe ............................................................................. 3-14

Installing the corona pin in the source......................................................... 3-18

Removing the corona pin from the source .................................................... 3-18

Removing the APCI probe ............................................................................. 3-18

Configuring for ESCi mode .......................................................................... 3-19

Optimizing the ESI probe for ESCi operation.............................................. 3-19

Installing the corona pin in the source......................................................... 3-19

Removing the corona pin from the source .................................................... 3-19

4 Configuring the NanoLockSpray source .......................................... 4-1

Overview of the NanoLockSpray source ..................................................... 4-2

Sample sprayer ................................................................................................ 4-3

LockSpray sprayer........................................................................................... 4-3

NanoFlow gas supply....................................................................................... 4-4

Purge gas.......................................................................................................... 4-4

Sprayer platform adjuster assembly............................................................... 4-4

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

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

Adjusting the sprayer tip position ................................................................ 4-6

Setting up the camera ...................................................................................... 4-7

Table of Contents xiii

Optional glass capillary sprayer ................................................................... 4-8

Installing the glass capillary sprayer ............................................................. 4-8

Fitting and loading the glass capillary........................................................... 4-9

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

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

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

Troubleshooting using Connections Insight .............................................. 5-5

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

Preparing the instrument for work performed on its source ................ 5-7

Removal and refitting of the source enclosure .......................................... 5-8

Removing the source enclosure from the instrument.................................... 5-8

Fitting the source enclosure to the instrument............................................ 5-11

Installing and removing the corona pin .................................................... 5-12

Installing the corona pin in the source......................................................... 5-12

Removing the corona pin from the source .................................................... 5-14

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

Removing O-rings and seals ......................................................................... 5-17

Cleaning the mass spectrometer case ........................................................ 5-18

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

Cleaning the source components ................................................................ 5-21

Cleaning the sampling cone assembly ....................................................... 5-21

Removing the sampling cone assembly from the source ............................. 5-21

Disassembling the sampling cone assembly................................................. 5-23

Cleaning the sample cone and cone gas nozzle ............................................ 5-26

Assembling the sampling cone assembly...................................................... 5-28

Fitting the sampling cone assembly to the source ....................................... 5-29

Cleaning the extraction cone ....................................................................... 5-31

Removing the ion block assembly from the source assembly...................... 5-31

Removing the extraction cone from the ion block ........................................ 5-33

xiv Table of Contents

Cleaning the extraction cone......................................................................... 5-34

Fitting the extraction cone to the ion block.................................................. 5-36

Fitting the ion block assembly to the source assembly................................ 5-37

Cleaning the ion block assembly ................................................................. 5-38

Disassembling the source ion block assembly.............................................. 5-38

Cleaning the ion block components .............................................................. 5-45

Assembling the source ion block assembly................................................... 5-47

Cleaning the source T-Wave ion guide assembly .................................... 5-49

Removing the T-Wave ion guide assembly from the source assembly........ 5-49

Disassembling the T-Wave ion guide assembly ........................................... 5-51

Cleaning the T-Wave ion guide assembly aperture plate............................ 5-52

Cleaning the T-Wave ion guide..................................................................... 5-52

Assembling the T-Wave ion guide assembly ................................................ 5-54

Fitting the T-Wave ion guide assembly, PEEK ion block support,

and ion block assembly to the source assembly ..................................... 5-54

Replacing the ESI probe tip and gasket .................................................... 5-55

Removing the ESI probe tip and gasket ....................................................... 5-56

Fitting the ESI probe tip and gasket............................................................ 5-58

Replacing the ESI probe sample capillary ............................................... 5-59

Removing the existing capillary.................................................................... 5-59

Installing the new capillary .......................................................................... 5-64

Cleaning the APCI probe tip ........................................................................ 5-67

Replacing the APCI probe sample capillary ............................................ 5-68

Removing the existing capillary.................................................................... 5-68

Installing the new capillary .......................................................................... 5-71

Replacing the LockSpray probe capillary ................................................ 5-74

Removing the existing capillary.................................................................... 5-74

Installing the new capillary .......................................................................... 5-77

Replacing the NanoLockSpray reference probe capillary ................... 5-78

Removing the NanoLockSpray reference probe ........................................... 5-78

Installing the new TaperTip and capillary................................................... 5-80

Table of Contents xv

Cleaning or replacing the corona pin ........................................................ 5-83

Replacing the APCI probe heater ............................................................... 5-84

Removing the APCI probe heater ................................................................. 5-84

Fitting the new APCI probe heater .............................................................. 5-86

Replacing the ion block source heater ...................................................... 5-87

Replacing the LockSpray source assembly seals .................................... 5-91

Removing the probe adjuster assembly probe and source

enclosure seals ......................................................................................... 5-91

Fitting the new source enclosure seals......................................................... 5-93

Replacing the mass spectrometer’s air filter ........................................... 5-95

Replacing the air filter................................................................................... 5-95

Replacing the IntelliStart Fluidics tubing ............................................... 5-98

Removing the IntelliStart Fluidics tubing ................................................... 5-99

Plumbing the IntelliStart Fluidics LockSpray system ................................ 5-99

Plumbing the IntelliStart Fluidics sample delivery system...................... 5-108

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

Warning symbols ............................................................................................... A-2

Task-specific hazard warnings........................................................................ A-2

Specific warnings ............................................................................................. A-3

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

Warnings that apply to all Waters instruments ......................................... A-6

Electrical and handling symbols ................................................................. A-11

Electrical symbols .......................................................................................... A-11

Handling symbols .......................................................................................... A-12

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

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

Connecting the Edwards oil-free roughing pump ................................... B-3

Making the electrical connections to the Edwards oil-free

roughing pump........................................................................................... B-7

xvi Table of Contents

Connecting to the nitrogen gas supply ....................................................... B-7

Connecting to the collision cell gas supply ............................................... B-9

Connecting the nitrogen exhaust line ...................................................... B-10

Connecting the liquid waste line ............................................................... B-13

Input/output signal connectors .................................................................. B-15

Signal connections ......................................................................................... B-18

Connecting the workstation (system without ACQUITY UPLC) ........ B-21

Connecting Ethernet cables (system with ACQUITY UPLC) .............. B-21

Connecting to the electricity source ......................................................... B-22

Connecting the NanoLockSpray source camera .................................... B-23

Installing the camera driver software .......................................................... B-23

C Materials of construction and compliant solvents ....................... C-1

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

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

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

Index ..................................................................................................... Index-1

Table of Contents xvii

xviii Table of Contents

1 System Overview

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

Contents

Topic Page

Waters SYNAPT G2 MS 1-2 SYNAPT G2 MS UPLC/MS/MS systems 1-2 Software 1-3 Instrument sources 1-5 IntelliStart Fluidics system 1-9 Ion optics 1-12 Analyzers 1-13 Mass spectrometer configuration 1-17 Leak sensors 1-18 Vacuum system 1-18 Controls on the instrument’s rear panel 1-19

1-1

Waters SYNAPT G2 MS

The SYNAPT™ G2 Mass Spectrometry (MS) system is a hybrid, quadrupole/orthogonal acceleration, time-of-flight (oa-TOF) mass spectrometer controlled by MassLynx™ software.

Either of the following high-performance, ZSpray™, dual-orthogonal, API sources is fitted as standard equipment:

• LockSpray™ ESI/APCI/ESCi

• NanoLockSpray™ ESI source (see page 1-7).

You can also use the following optional sources:

• Dual-mode APPI/APCI (see the Waters Dual-Mode (APPI/APCI) Source for Xevo and SYNAPT G2 Instruments Operator’s Guide).

•MALDI (see the Waters MALDI SYNAPT G2 Mass Spectrometry System Overview and Maintenance Guide).

For the instrument’s specifications, see the Waters SYNAPT G2 MS Site Preparation Guide.

source (see page 1-5).

SYNAPT G2 MS UPLC/MS/MS systems

The Waters SYNAPT G2 MS is compatible with the ACQUITY UPLC® and nanoACQUITY UPLC refer to the documentation relevant to your LC system.

systems. If you are not using either of those systems,

ACQUITY UPLC SYNAPT G2 MS UPLC/MS/MS system

The ACQUITY UPLC SYNAPT G2 MS UPLC®/MS/MS system includes an ACQUITY UPLC system and the Waters SYNAPT G2 MS fitted with the LockSpray ESI/APCI/ESCi source.

The ACQUITY UPLC system includes a binary solvent manager, sample manager, column heater, sample organizer, detectors, and a specialized ACQUITY UPLC column. MassLynx software controls the system.

1-2 System Overview

See also: The ACQUITY UPLC System Operator’s Guide or Controlling

Contamination in LC/MS Systems (part number 715001307). You can find the

latter document online at http://www.waters.com; click Services and Support > Support.

nanoACQUITY UPLC SYNAPT G2 MS nanoUPLC/MS/MS system

The nanoACQUITY UPLC SYNAPT G2 MS nanoUPLC/MS/MS system includes a nanoACQUITY UPLC system and the Waters SYNAPT G2 MS fitted with the NanoLockSpray source.

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. MassLynx software controls the system.

See also: The nanoACQUITY UPLC System Operator’s Guide or Controlling

Contamination in LC/MS Systems (part number 715001307). You can find the

latter document online at http://www.waters.com; click Services and Support > Support.

Software

IntelliStart

IntelliStart software monitors the mass spectrometer’s performance and reports when the instrument is ready for use. The software automatically mass calibrates the instrument and displays performance readbacks. Integrated with MassLynx software and Instrument Console software, IntelliStart software enables simplified setup of the system for use in routine analytical and open-access applications. See the mass spectrometer’s online Help for further details on IntelliStart technology.

The IntelliStart Fluidics system is built into the mass spectrometer. It delivers sample directly to the MS probe from the LC column or from three integral vials. The vials 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. For further details, see “IntelliStart Fluidics

system” on page 1-9.

Software 1-3

MassLynx

MassLynx software, version 4.1, controls the mass spectrometer. A high-performance application, it acquires, analyzes, manages, and distributes mass spectrometry, ultraviolet (UV), evaporative light scattering, and analog data.

MassLynx enables these major operations:

• Configuring the instrument

• Creating LC and MS/MS methods that define operating parameters for a

• Using IntelliStart software to tune and mass calibrate the mass

• Running samples

• Monitoring the run

• Acquiring data

• Processing data

•Reviewing data

• Printing data

See the MassLynx 4.1 user documentation and online Help for more information on installing and using MassLynx software.

run

spectrometer

Instrument Console

Using Instrument Console software, you configure settings, monitor performance, run diagnostic tests, and maintain the system and its modules. The software functions independently of MassLynx software and does not recognize or control the data systems.

See the Instrument Console system online Help for details.

1-4 System Overview

Instrument sources

LockSpray source and ionization modes

The LockSpray source uses lock-mass correction to acquire exact mass data. The sample is introduced into the source through a probe. A lock-spray flow, containing a compound of known mass, flows through a separate ESI probe (the LockSpray sprayer). An oscillating baffle allows the sprays to be analyzed as two separate data functions. The lock-mass correction, calculated from the lock-spray data, is then applied to the sample data set.

You can use the LockSpray source with the following ionization modes:

•ESI

•APCI

•ESCi

• nanoSpray

SYNAPT G2 MS fitted with LockSpray source

Instrument sources 1-5

Electrospray ionization

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

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

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 option, which can accommodate a maximum flow rate of up to 200 µL/min.

Atmospheric pressure chemical ionization

Atmospheric pressure chemical ionization (APCI) produces singly charged protonated or deprotonated molecules for a broad range of nonvolatile samples.

To operate the LockSpray source in APCI mode, you fit the source enclosure with a corona pin and an APCI 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

APCI probe

Sample cone

1-6 System Overview

Corona pin

Hot gas from the APCI probe passes between the sample cone and the corona pin. Mobile phase molecules rapidly react with ions generated by the corona discharge to produce stable reagent ions. Sample 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.

Combined electrospray and atmospheric pressure chemical ionization

In combined electrospray and atmospheric pressure chemical ionization (ESCi) mode, 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 processing and wider compound coverage.

NanoLockSpray source

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 to those in normal flow rate electrospray. However, because sample consumption is greatly reduced, the sensitivity gains are significant when you adopt similar scan parameters. Lock-mass correction with the NanoLockSpray source works in the same way as the LockSpray source does with ESI.

The NanoLockSpray source enclosure consists of a sprayer—either universal, borosilicate glass capillary, or CE (see below)—mounted on a ZSpray, three-axis manipulator.

The combined unit is mounted on the NanoFlow™ stage, which runs on a pair of guide rails, with two defined positions.

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.

Instrument sources 1-7

SYNAPT G2 MS fitted with NanoLockSpray source

The following options are available for the spraying capillary:

• Universal NanoFlow nebulizer sprayer. This option, for flow injection or coupling to nanoACQUITY UPLC, uses

a pump to regulate the flow rate as low as 100 nL/min.

• Borosilicate glass capillary NanoFlow (nanovials). This option uses metal-coated glass capillaries, which allow the lowest

flow rates. Usable for one sample only, they must then be discarded.

• NanoFlow capillary electrophoresis (CE) sprayer. This option uses a make-up liquid at the CE capillary tip, which allows a

stable electrospray to occur. The make-up flow rate is less than 1µL/min.

1-8 System Overview

Dual-mode ionization 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 incorporates an APPI source enclosure used in conjunction with a standard APCI probe. You can operate the source in APPI, APCI, or dual-mode, which switches rapidly between ionization modes, facilitating high-throughput analyses.

See also: The Waters SYNAPT G2 Dual-mode Ionization Source Operator’s

Guide.

Matrix-assisted laser desorption ionization

The matrix-assisted laser desorption ionization (MALDI) interface enables rapid, tool-free switching between API and MALDI modes. A motorized stage moves the MALDI source into position.

See also: The Waters MALDI SYNAPT G2 MS System Operator’s Guide.

IntelliStart Fluidics system

Overview

The IntelliStart Fluidics system is built into the instrument; it controls how sample is delivered to the source.

For standard flow applications, the system delivers sample directly to the mass spectrometer source in one of three ways:

• From the LC column.

• From three integral vials.

• From a wash reservoir that contains solvent for flushing the

Tip: The vials can also deliver sample through direct or combined

infusion to enable optimization at analytical flow rates.

instrument’s solvent delivery system.

IntelliStart Fluidics system 1-9

For nanoACQUITY UPLC, the valves and pumps that make up the IntelliStart Fluidics system introduce dead volume, which causes unacceptable peak broadening. For this reason, the nanoACQUITY UPLC is plumbed directly to the NanoFlow sprayer using a suitably short piece of silica tubing.

For reference flows for both the LockSpray and NanoLockSpray source, the IntelliStart Fluidics system delivers reference solution from vial B or, for extended operating hours, from a separate, external bottle of reference solution.

IntelliStart Fluidics physical layout

The IntelliStart Fluidics system comprises the components shown in the following figure.

System components and configuration

(Tubing connections omitted for clarity)

Access doors

Tubing guides

Lock-spray selector valve

Flow sensor

Sample selector valve

Grounded union

Lock-spray pump

Sample pump

1-10 System Overview

Waters

Diverter valve

Sample vials (A, B, and C)

The IntelliStart Fluidics system consists of these components:

• A sample delivery system, with a rate pump, sample selector valve and diverter valve used for LC and probe connections.

• A lock-spray system, with 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.

• Three, shared, 30-mL sample vials; A, B, and C.

• Plumbing for shared wash and waste bottles.

Sample vials A, B, and C are mounted on the instrument’s front panel. When you select a solvent in the Instrument Console software, its vial is illuminated. You can simultaneously illuminate all three vials, or extinguish the illumination when you are using light-sensitive samples. Generally, vial A contains the sample solution, vial B the reference solution, and vial C the calibrant solution.

The wash reservoir and (optionally) the reservoir containing reference solution are external to the instrument; typically, they are bottles placed on top of the LC system. The waste reservoir is normally a bottle stored under the instrument bench.

During normal operation, the IntelliStart Fluidics system’s access doors must be closed.

System operation

You use the console software to configure the IntelliStart Fluidics system. 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 operating the IntelliStart Fluidics system.

During auto-calibration, the software automatically controls reference solution and sample delivery.

IntelliStart Fluidics system 1-11

Ion optics

The mass spectrometer’s ion optics operate as follows:

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

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

3. The ions pass through the T-Wave™ ion guide to the quadrupole, where they are filtered according to their mass-to-charge ratio.

4. The mass-separated ions pass into the Triwave™ region, where they can undergo collision-induced dissociation (CID).

5. The ions then pass into the time-of-flight (TOF) analyzer. A high-voltage pulse orthogonally accelerates the ions down the flight tube, where the dual-stage reflectron reflects them towards the ion mirror, which, in turn, reflects the ions back to the dual-stage reflectron. The dual-stage reflectron then reflects the ions to the detector. Ions of different mass-to-charge ratios arrive at the detector at different times, hence a mass spectrum can be created.

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

1-12 System Overview

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