Waters SQ Detector

Operator’s Guide
71500126602/Revision D

Copyright © Waters Corporation 2009

All rights reserved
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 UPLC, Connections Insight, ESCi, and Waters are registered
trademarks of Waters Corporation. ACQUITY, Empower, IntelliStart,
IonSABRE, MassLynx, T-Wave, UPLC, and ZSpray and “THE SCIENCE OF
WHAT’S POSSIBLE.” are trademarks of Waters Corporation.
Nalgene is a registered trademark of Nalge Nunc International.
PEEK is a trademark of Victrex Corporation.
snoop and Swagelok are registered trademarks of Swagelok Company.
TORX is a registered trademark of Textron Inc.
Viton is a registered trademark of DuPont Performance Elastomers.
Other trademarks or registered trademarks are the sole property of their
respective owners.

ii
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].

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 e-mail
addresses 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 in the Waters Web site.
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

Safety considerations
Some reagents and samples used with Waters instruments and devices can
pose chemical, biological, 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.

iv
Considerations specific to the SQ Detector
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
the instrument’s operation.

Never let the nitrogen supply pressure fall below 690 kPa (6.9 bar, 100 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.

v
 High temperature hazard

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

with your hand when operating or servicing the instrument.

SQ Detector high temperature hazard

Source enclosure assembly

PO W ER O PER ATE

DESOLVATION NEBULIZER

HV APPI

PROBE

RP00017

vi
 High voltage hazard

Warning:
• To avoid electric shock, do not remove the SQ Detector’s protective
panels. The components they cover are not user-serviceable.
• To avoid non-lethal electric shock, any equipment connected to the
ESI and IonSABRE™ APCI probes must be grounded.
• To avoid nonlethal electric shock when the instrument is in
Operate mode, avoid touching the areas marked with the high
voltage warning symbol. To touch those areas, first put the
instrument in Standby mode.

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 procedures
and the guidelines presented in this section.

Applicable symbols

Symbol Definition
Authorized representative of the European
Community

Confirms that a manufactured product complies

with all applicable European Community
directives.
For in vitro diagnostic use

ABN 49 065 444 751 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

Intended use
Waters designed the Single Quad (SQ) Detector for use as a research tool to
deliver authenticated mass measurement in MS mode.

viii
 The Waters SQ Detector can be used for general in vitro diagnostic
applications. However, only professionally trained and qualified laboratory
personnel can use the instrument for those purposes.
The Waters SQ Detector is CE-marked according to the
European Union In Vitro Diagnostic Device Directive 98/79/EC.

Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards must cover the entire range of quality-control 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 quality-control samples that represent subnormal,
normal, and above-normal levels of a compound. Ensure that quality-control
sample results fall within an acceptable range, and evaluate precision from
day to day and run to run. Data collected when quality control samples are out
of range might not be valid. Do not report these data until you are certain that
the instrument performs satisfactorily.
When analyzing samples from a complex matrix such as soil, tissue,
serum/plasma, whole blood, and so on, note that the matrix components can
adversely affect LC/MS results, enhancing or suppressing ionization. To
minimize these matrix effects, Waters recommends you adopt the following
measures:
• Prior to the instrumental analysis, use appropriate sample
pretreatment such as protein precipitation, liquid/liquid extraction
(LLE), or solid phase extraction (SPE) to remove matrix interferences.
• Whenever possible, verify method accuracy and precision using
matrix-matched calibrators and QC samples.
• Use one or more internal standard compounds, preferably isotopically
labeled analytes.

ix
IVD authorized representative information

IVD authorized representative

Waters Corporation (Micromass UK Limited) is

registered in the United Kingdom with the Medicines
and Healthcare Products Regulatory Agency (MHRA)
at Market Towers, 1 Nine Elms Lane, London,
SW8 5NQ. The reference number is IVD000167.

Waters Corporation (Micromass UK Limited)

Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom

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

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.

x
Table of Contents
Copyright notice ................................................................................................... ii

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

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

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

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

Considerations specific to the SQ Detector ........................................................ v
Safety advisories ............................................................................................... vii

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

Applicable symbols .......................................................................................... viii
Intended use..................................................................................................... viii
Calibrating .......................................................................................................... ix
Quality control .................................................................................................... ix

IVD authorized representative information .................................................. x

IVD authorized representative ........................................................................... x

ISM classification .................................................................................................. x

1 Waters SQ Detector ............................................................................... 1-1

Overview ............................................................................................................. 1-2
Waters SQ Detector ......................................................................................... 1-2
ACQUITY SQD UPLC/MS system.................................................................. 1-4
Software and data system ............................................................................... 1-5
ACQUITY UPLC Console................................................................................ 1-6

Ionization techniques and source probes ................................................... 1-7

Electrospray ionization (ESI) .......................................................................... 1-7
Combined ESI and APCI (ESCi) ..................................................................... 1-7
Atmospheric pressure chemical ionization..................................................... 1-8
Atmospheric pressure photoionization ........................................................... 1-8

Ion optics ............................................................................................................. 1-9

Table of Contents xi
 MS operating modes ....................................................................................... 1-10

Sample inlet ...................................................................................................... 1-10

Leak sensors ..................................................................................................... 1-10

Vacuum system ................................................................................................ 1-10

Rear panel ......................................................................................................... 1-11

IntelliStart Fluidics system .......................................................................... 1-12

Overview......................................................................................................... 1-12

System operation ............................................................................................ 1-13

2 Preparing for Operation ...................................................................... 2-1

Starting the instrument .................................................................................. 2-2
Configuring IntelliStart................................................................................... 2-4
Verifying the instrument’s state of readiness ................................................ 2-4
Tuning and calibration information ............................................................... 2-4
Running the instrument at high flow rates.................................................... 2-5
Monitoring the instrument LEDs ................................................................... 2-5

Preparing the IntelliStart Fluidics system ................................................. 2-6

Installing the solvent manifold drip tray ....................................................... 2-6
Installing the reservoir bottles........................................................................ 2-7
Diverter valve positions................................................................................... 2-8
Purging the infusion syringe......................................................................... 2-11

Rebooting the instrument ............................................................................. 2-11

Rebooting the instrument by pressing the reset button .............................. 2-11

Leaving the mass spectrometer ready for operation ............................. 2-12

Emergency instrument shutdown................................................................. 2-12

3 ESI and ESCi Modes of Operation ..................................................... 3-1

Introduction ....................................................................................................... 3-2

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

Installing the corona pin ................................................................................. 3-5
Optimizing the ESI probe for ESCi operation................................................ 3-7

xii Table of Contents

 Removing the corona pin ................................................................................ 3-7

Removing the ESI probe ................................................................................. 3-9

4 Maintenance Procedures ..................................................................... 4-1

Maintenance schedule ..................................................................................... 4-3

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

Troubleshooting with Connections Insight ................................................ 4-5

Safety and handling ......................................................................................... 4-7

Preparing the instrument for work performed on the source ............... 4-8

Operating the source isolation valve ........................................................... 4-9

Removing O-rings and seals ......................................................................... 4-11

Cleaning the instrument’s exterior ............................................................ 4-12

Emptying the exhaust trap bottle ............................................................... 4-12

Emptying the roughing pump exhaust liquid trap bottle ..................... 4-14

Gas ballasting the roughing pump ............................................................. 4-16

Gas ballasting a pump fitted with a screwdriver-operated
gas ballast valve....................................................................................... 4-17
Gas ballasting a pump fitted with a handle-operated gas ballast valve .... 4-18

Checking the roughing pump oil level ....................................................... 4-19

Adding oil to the roughing pump ................................................................ 4-19

Cleaning the source components ................................................................ 4-21

Cleaning the sample cone and gas cone .................................................... 4-21
Removing the cone gas assembly from the source ....................................... 4-21
Disassembling the cone gas assembly .......................................................... 4-24
Cleaning the sample cone and gas cone........................................................ 4-25
Assembling the cone gas assembly ............................................................... 4-28
Fitting the cone gas assembly to the source................................................. 4-29

Cleaning the ion block, isolation valve, and extraction cone .............. 4-31

Table of Contents xiii

 Removing the ion block assembly from the source assembly ...................... 4-31
Disassembling the source ion block assembly.............................................. 4-33
Cleaning the ion block, isolation valve, and extraction cone....................... 4-40
Assembling the source ion block assembly................................................... 4-42
Fitting the ion block assembly to the source assembly................................ 4-45

Cleaning the source hexapole assembly .................................................... 4-47

Removing the ion block assembly, ion block support,
and hexapole from the source assembly ................................................. 4-47
Cleaning the hexapole assembly ................................................................... 4-49
Fitting the hexapole assembly, PEEK ion block support,
and ion block assembly to the source assembly ..................................... 4-52

Replacing the ESI probe tip ......................................................................... 4-54

Replacing the ESI probe sample capillary ............................................... 4-55

Cleaning the IonSABRE APCI probe tip ................................................... 4-62

Replacing the IonSABRE APCI probe sample capillary ....................... 4-62

Removing the existing capillary.................................................................... 4-62
Installing the new capillary .......................................................................... 4-66

Cleaning or replacing the corona pin ........................................................ 4-70

Replacing the APCI probe heater ............................................................... 4-71

Replacing the ion block source heater ...................................................... 4-75

Replacing the source assembly seals ......................................................... 4-79

Removing the source enclosure from the instrument .................................. 4-79
Disassembling the source enclosure and probe adjuster assembly............. 4-82
Removing the seals from the source enclosure
and probe adjuster assembly................................................................... 4-83
Fitting the new source enclosure and probe adjuster assembly seals ........ 4-86
Assembling the probe adjuster assembly and source enclosure.................. 4-87
Fitting the source enclosure to the instrument............................................ 4-88

Maintaining the instrument air filters ...................................................... 4-90

Cleaning the air filter inside the instrument’s lower bezel ......................... 4-90
Replacing the air filter inside the lower bezel.............................................. 4-91

xiv Table of Contents

 Cleaning the air filter behind the source probe ........................................... 4-92
Replacing the air filter behind the source probe .......................................... 4-94

Replacing the roughing pump oil ............................................................... 4-95

Replacing the roughing pump’s oil demister element ........................... 4-98

5 Optional APCI Mode of Operation ..................................................... 5-1

Atmospheric pressure chemical ionization ................................................ 5-2

IonSABRE APCI probe .................................................................................... 5-2

Installing the IonSABRE APCI probe .......................................................... 5-3

Installing the corona pin ................................................................................. 5-5

Removing the corona pin ................................................................................ 5-5

Removing the IonSABRE APCI probe ......................................................... 5-6

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-5

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

Electrical symbols .......................................................................................... A-11
Handling symbols .......................................................................................... A-12

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

External wiring and vacuum connections ................................................. B-2

Connecting the oil-filled roughing pump ................................................... B-3

Making the electrical connections for a roughing pump
with an external relay box......................................................................... B-8
Making the electrical connections for a roughing pump
without an external relay box ................................................................... B-9

Table of Contents xv
 Connecting the oil-free roughing pump ................................................... B-10
Making the electrical connections for an oil-free roughing pump............... B-17

Connecting to the nitrogen gas supply ..................................................... B-18

Connecting the nitrogen exhaust line ...................................................... B-20

Connecting the liquid waste line ............................................................... B-23

Connecting the workstation ........................................................................ B-25

Connecting Ethernet cables ........................................................................ B-26

I/O signal connectors ..................................................................................... B-26

Signal connections ......................................................................................... B-28

Connecting to the electricity source ......................................................... B-31

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

D Preparing Samples for LC/MS System Check

with Empower software .................................................................. D-1
Assembling required materials .................................................................... D-2

Preparing the sulfadimethoxine standard ................................................ D-2

Storing the solutions ....................................................................................... D-3

Using the solution in an LC/MS System Check run ................................. D-3

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

xvi Table of Contents

1 Waters SQ Detector

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

Topic Page
Overview 1-2
Ionization techniques and source probes 1-7
Ion optics 1-9
MS operating modes 1-10
Sample inlet 1-10
Leak sensors 1-10
Vacuum system 1-10
Rear panel 1-11
IntelliStart Fluidics system 1-12
System operation 1-13

1-1
Overview

Waters SQ Detector
The Waters® SQ Detector is a single-quadrupole, atmospheric pressure
ionization (API) mass spectrometer. Designed for routine ACQUITY
®
UPLC /MS analyses, it can scan at speeds up to 10,000 Da/s.
Waters provides these ion sources with the instrument as standard
equipment:
• ZSpray™ (dual orthogonal sampling) interface.
®
• Multi-mode ESCi ionization switching for atmospheric pressure
chemical ionization (APCI) and electrospray ionization (ESI).
Optional ionization modes are IonSABRE™ APCI and APPI (atmospheric
pressure photoionization).
For instrument specifications, see the Waters SQ Detector Site Preparation
Guide.

Waters SQ Detector

TP02592

1-2 Waters SQ Detector

Waters SQ Detector, with doors open

PO W ER O PER ATE

DESOLVATION NEBULIZER

HV APPI

PROBE

RP00016

IntelliStart technology
IntelliStart™ technology monitors LC/MS performance and reports when the
instrument is ready for use.
The software automatically tunes and mass calibrates the instrument and
displays performance readbacks. Integrated with Empower™
chromatography software, MassLynx™ mass spectrometry software, and
ACQUITY UPLC® Console software, it enables simplified setup of the system
for use in routine analytical and open access applications. (See “Software and
data system” on page 1-5).
The IntelliStart Fluidics system is built into the instrument. It delivers
sample directly to the MS probe from the LC column or from two integral
reservoirs. The integral reservoirs can also deliver sample through direct or
combined infusion so that you can optimize instrument performance at
analytical flow rates. See the instrument’s online Help for further details of
IntelliStart.

Overview 1-3
ACQUITY SQD UPLC/MS system
The ACQUITY SQD UPLC/MS system includes an ACQUITY UPLC system
and the Waters SQ Detector.
If you are not using your instrument as part of an ACQUITY UPLC system,
refer to the documentation for your LC system.

ACQUITY UPLC system

The ACQUITY UPLC system includes a binary solvent manager, sample
manager, column heater, optional sample organizer, optional detectors, and a
specialized ACQUITY UPLC column. WatersEmpower™ chromatography
software or MassLynx mass spectrometry software controls the system.
For further instruction, see the ACQUITY UPLC System Operator’s Guide or
Controlling Contamination in LC/MS Systems (part number 715001307). You
can find the latter document on http://www.waters.com; click Services and
Support and then Support Center.
A booster is also available for the instrument, to allow stacking of other units
on top of the instrument. Contact Waters for more details.

1-4 Waters SQ Detector

 Waters ACQUITY SQD
Sample organizer (optional)

Solvent tray

Column heater

SQ Detector

TP02597
Binary solvent Sample manager
manager

Software and data system

The instrument is controlled by either Empower chromatography software or
MassLynx mass spectrometry software. Each is a high-performance
application that acquires, analyzes, manages, and distributes ultraviolet
(UV), evaporative light scattering, analog, and mass spectrometry data.
Both Empower and MassLynx software enable these major operations:
• Configuring the instrument.
• Creating LC and MS methods that define operating parameters for a
run.
• Using IntelliStart software to tune and mass calibrate the instrument.
• Running samples.
• Monitoring the run.
• Acquiring data.

Overview 1-5
 • Processing data.
• Reviewing data.
• Printing data.
See Empower and MassLynx 4.1 user documentation and online Help for more
information on installing and using Empower or MassLynx software.

ACQUITY UPLC Console

The ACQUITY UPLC Console is a software application with which you
configure settings, monitor performance, run diagnostic tests, and maintain
the system and its modules. The ACQUITY UPLC Console functions
independently of Empower and MassLynx software and does not recognize or
control the data systems.
See the ACQUITY UPLC System console online Help for details.

1-6 Waters SQ Detector

Ionization techniques and source probes

Electrospray ionization (ESI)

In electrospray ionization (ESI), a strong electrical charge is given the eluent
as it emerges from a nebulizer. The droplets that compose the resultant
aerosol undergo a reduction in size (solvent evaporation). As solvent continues
to evaporate, the charge density increases until the droplet surfaces eject ions
(ion evaporation). The ions can be singly or multiply charged. The multiply
charged ions are of particular interest because the instrument separates them
according to their mass-to-charge ratios (m/z), permitting the detection of
high-molecular-weight compounds.
The instrument can accommodate eluent flow rates of up to 1 mL/min.

Combined ESI and APCI (ESCi)

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

ESCi mode
RP00029 ESI probe tip

Corona pin

Sample cone tip

Ionization techniques and source probes 1-7

Atmospheric pressure chemical ionization
A dedicated, high-performance, atmospheric-pressure, chemical ionization
(APCI) probe is offered as an option. See Chapter 5, “Optional APCI Mode of
Operation”, for full details.

Atmospheric pressure photoionization

Atmospheric pressure photoionization (APPI) is offered as an option. It uses
photons generated by a krypton-discharge ultraviolet (UV) lamp (10.2 eV) to
produce sample ions from vaporized LC eluent.

1-8 Waters SQ Detector

Ion optics
The instrument’s ion optics operate as follows:
1. Samples from the LC or Intellistart fluidics system are introduced at
atmospheric pressure into the ionization source.
2. The ions pass through the sample cone into the vacuum system.
3. Ions are filtered according to their mass-to-charge ratio (m/z).
4. The transmitted ions are detected by the photomultiplier detection
system.
5. The signal is amplified, digitized, and sent to the Empower
chromatography or MassLynx mass spectrometry software.

Ion optics overview

Sample cone
Sample inlet Transfer optics Conversion dynode

Isolation valve

Z-Spray ion source Quadrupole Detector

Ion optics 1-9

MS operating modes
The instrument runs in either of two operating modes:
• Scanning, where scanning occurs to separate the ions in the ion beam
according to their mass-to-charge (m/z) ratios, producing a mass
spectrum.
• Selected Ion Recording (SIR), where the instrument is tuned to detect an
ion, or ions, with specific m/z ratios.

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

Leak sensors
Where fitted, leak sensors in the drip trays of the ACQUITY UPLC system
and the SQ Detector continuously monitor system components for leaks. A
leak sensor stops system flow when its optical sensor detects about 1.5 mL of
accumulated, leaked liquid in its surrounding reservoir. At the same time, the
ACQUITY UPLC Console displays an error message alerting you that a leak
has developed.
Tip: If you are using MassLynx software, refer to the software release notes
provided at installation to confirm whether the leak sensors are enabled.
See Waters ACQUITY UPLC Leak Sensor maintenance instructions for
complete details.

Vacuum system
An external roughing (rotary vane) pump and an internal split-flow
turbomolecular pump combine to create the source vacuum. The
turbomolecular pump evacuates the analyzer and ion transfer region.

1-10 Waters SQ Detector

 Vacuum leaks and electrical or vacuum pump failures cause vacuum loss,
which protective interlocks guard against. The system monitors
turbomolecular pump speed and continuously measures vacuum pressure
with a built-in Pirani gauge. The gauge also serves as a switch, stopping
operation when it senses vacuum loss.
A vacuum isolation valve isolates the source from the mass analyzer, allowing
routine source maintenance without venting.

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

Instrument rear panel

!
Event inputs
and outputs
RS 232

1 1
Analog O ut InjectS tart In
2 2
3 G round 3 G round
4 4
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9

Shielded
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

Power cord V ~ 200 - 240 !

Hz 50 - 60
VA 900 Ethernet
PUMP
API Gas
6.9 Bar Maximum
Roughing pump
Nitrogen inlet relay switch
VACUUM
SOURCE VENT

Source vent
VACUUM

Turbo vacuum 01757 U.S.A.

Source
vacuum

RP00001

Rear panel 1-11

IntelliStart Fluidics system

Overview
The IntelliStart Fluidics system is built into the instrument. The system
delivers sample directly to the MS probe in one of two ways:
• From the LC column.
• From two integral reservoirs.
Tip: The integral reservoirs can also deliver sample through direct or
combined infusion to enable optimization at analytical flow rates.
The system incorporates a multi-position valve with these attributes:
• An input connection from an external LC column.
• An input connection from the instrument’s infusion syringe. (The
infusion syringe is also connected to two reservoirs, A and B. In the
software, you specify which reservoir to draw from.)
• An output connection to the probe.
• An output connection to a waste line.

IntelliStart Fluidics system

Probe

B
LC Idle Off
A
Off

Column
Syringe

LC Waste Reservoir A Reservoir B

1-12 Waters SQ Detector

System operation
Control of solvent and sample delivery during auto-tuning, auto-calibration,
and method development is automatically performed by the software.
IntelliStart Fluidics configuration requirements can be set in the system
console. You can edit the parameters, frequency, and extent of the automation
you want IntelliStart to perform. See the instrument’s online Help for further
details on IntelliStart software and operation of the instrument’s solvent
delivery system.

System operation 1-13

1-14 Waters SQ Detector
2 Preparing for Operation

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

Contents

Topic Page
Starting the instrument 2-2
Preparing the IntelliStart Fluidics system 2-6
Rebooting the instrument 2-11
Leaving the mass spectrometer ready for operation 2-12

2-1
Starting the instrument
The Waters SQ Detector is designed for compatibility with the ACQUITY
UPLC system. If you are not using an ACQUITY UPLC system, refer to the
documentation relevant to the system being used.

Caution: Using incompatible solvents can cause severe damage to the

instrument. For more details, refer to the following sources:
• Appendix C, “Materials of Construction and Compliant Solvents”,
for solvent information.
• Appendix C of the ACQUITY UPLC System Operator’s Guide for on
solvent compatibility with ACQUITY™.

Starting the instrument entails powering-on the ACQUITY workstation,

logging into the workstation, powering-on the SQ Detector and all the other
ACQUITY instruments and devices, and starting the Empower or MassLynx
software.
Requirement: You must power-on and log in to the ACQUITY workstation
first to ensure that it obtains the IP addresses of the system instruments.

To start the instrument

Warning: During analyses that require flammable solvents, to avoid

ignition of the solvents, never let the nitrogen supply pressure fall
below 690 kPa (6.9 bar, 100 psi).

1. Ensure the nitrogen supply is connected to the instrument’s API gas

connection.
Requirement: The nitrogen must be dry and oil-free, with a purity of at
least 95%. Regulate the supply at 600 to 690 kPa (6.0 to 6.9 bar, 90 to
100 psi).
For more information on connections, see the figure “Instrument rear
panel” on page 1-11.
2. Power-on the ACQUITY UPLC system workstation, and log in before
powering-on the other instruments.
3. Press the power switch on the top, left-hand side of the instrument and
ACQUITY instruments.

2-2 Preparing for Operation

 Result: Each system instrument “beeps” and runs a series of startup
tests.
4. Allow 3 minutes for the embedded PC to initialize.
Tip: An audible alert sounds when the PC is ready.
The power and status LEDs change as follows:
• Each system instrument’s power LED shows green.
• 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 SQ Detector’s Operate LED
remain off.
5. Start Empower or MassLynx software.
Tip: You can monitor the ACQUITY Console for messages and LED
indications.
6. Launch IntelliStart using one of the following methods.
• MassLynx – In the MassLynx main window’s lower left-hand corner,
click IntelliStart.
• Empower – In the Run Samples window, right-click the SQ
Detector’s control panel, and then click Launch Intellistart.
Result: The SQ Detector’s console appears. The instrument is in
Standby mode.
7. Click Control > Pump to start the roughing pump. The Operate LED
remains off.
Tip: There is a 20-second delay, during which the turbopump is starting,
before the roughing pump starts. IntelliStart displays “Instrument in
standby”.
8. Click Resolve or Operate to put the instrument into Operate
mode. When the instrument is in good operating condition, IntelliStart
displays “Ready”.
Tip: Clicking Resolve prepares the system for operation, putting the
instrument into Operate mode. If clicking Resolve fails to put the
instrument into Operate mode, IntelliStart displays corrective actions.

Starting the instrument 2-3

Configuring IntelliStart
To configure IntelliStart
1. In the ACQUITY UPLC Console system tree, expand SQ Detector.
2. Click IntelliStart.
3. Click Configure > IntelliStart Configuration.
4. In the IntelliStart Configuration dialog box, in the Checks list, select the
check boxes for the items you want checked during SQ Detector startup.
Clear the check boxes of items you do not want checked.
Tip: To display detailed information for an item, highlight it and then
click Properties.
5. Click OK.

Verifying the instrument’s state of readiness

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

To access IntelliStart
1. In the ACQUITY UPLC Console system tree, expand SQ Detector.
2. Click IntelliStart.

Tuning and calibration information

The instrument must be tuned and calibrated prior to use, tasks normally
performed from IntelliStart.
For further instruction, see the instrument’s online Help topic “Instrument
Setup” and Chapter 4, “Operating the Instrument”.

2-4 Preparing for Operation

Running the instrument at high flow rates
ACQUITY UPLC is run at high flow rates. To optimize desolvation, and thus
sensitivity, you must run the ACQUITY SQD system at appropriate gas flows
and desolvation temperatures. IntelliStart automatically sets these
parameters when you enter a flow rate, according to the following table.

Flow rate versus temperature and gas flow

Flow rate Desolvation Desolvation gas

Source temp (°C)
(mL/min) temp (°C) flow (L/h)
0.000 to 0.100 150 250 500
0.101 to 0.300 150 350 600
0.301 to 0.500 150 400 800
>0.500 150 0 00

Note: Under low ambient temperature, high moisture, and high flow rate
conditions, condensation can occur in the instrument’s source.

Monitoring the instrument LEDs

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

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

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

Starting the instrument 2-5

Preparing the IntelliStart Fluidics system
For additional information, see “Connecting the liquid waste line” on
page B-23.

Installing the solvent manifold drip tray

Required material
Chemical-resistant, powder-free gloves

To install the solvent manifold drip tray

Warning: The solvent manifold drip tray can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Install the solvent manifold drip tray as shown below:

TP02685

2-6 Preparing for Operation

Installing the reservoir bottles
An optional Low-volume Adaptor Kit is available for infusing smaller
volumes. The low-volume vials have a volume of 1.5 mL.
Required material
Chemical-resistant, powder-free gloves

To install the reservoir bottles

Warning: The reservoir bottles can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Remove the reservoir bottle caps.

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

TP02630

To install low-volume vials

Warning: The reservoir bottles can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

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

Preparing the IntelliStart Fluidics system 2-7

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

TP02630

Diverter valve positions

Column and syringe in home position after power-up
After power-up, the flow path between the column and waste is open. The
syringe is empty, and the flow path between it and waste is open.

Probe

B
Waste Idle Off
A
Off

Column

Syringe

LC Waste Reservoir A Reservoir B

2-8 Preparing for Operation

LC position
In the LC position, the flow path between the LC and probe is open, and the
flow path between the syringe and waste is also open.

Probe

B
LC Idle Off
A
Off

Column

Syringe

LC Waste Reservoir A Reservoir B

Infusion position

Probe

Infusion B

Infusion Off
A
On

Column

Syringe

LC Waste Reservoir A Reservoir B

Preparing the IntelliStart Fluidics system 2-9

 Combined position with LC flow and syringe in idle mode

Probe

Combined B
Idle Off
A
Off

Column

Syringe

LC Waste Reservoir A Reservoir B

Waste position
In the waste position, both the LC flow and the infusion syringe flow are
directed to waste. The syringe mode can be only static or dispensing (that is,
never drawing).

Probe

Waste B
Idle Off
A
Off

Column

Syringe

LC Waste Reservoir A Reservoir B

2-10 Preparing for Operation

Purging the infusion syringe
Whenever you replace a solution bottle, purge the infusion syringe with the
solution that you are going to use next. See the mass spectrometer’s online
Help for details.
Tip: Depending on the solutions used, the IntelliStart Fluidics system can
require more than one purge cycle to minimize carryover.

Rebooting the instrument

Reboot the instrument when any of these conditions applies
• The Tune window fails to respond.
• Empower or MassLynx software fails to initialize.
• Immediately following a software upgrade.

Rebooting the instrument by pressing the reset button

The reset button shuts down the electronics momentarily and causes the
instrument to reboot.

To reboot the instrument by pressing the reset button

1. Open the instrument’s front, left-hand door.
2. Press the red, reset button at the top, left-hand side of the instrument.
Reset button

PO W ER O PER ATE

DESOLVATION NEBULIZER

RP00026

Rebooting the instrument 2-11

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

Emergency instrument shutdown

To shut down the instrument in an emergency

Warning: The SQ Detector’s power switch does not isolate the

instrument from the main power supply. To isolate the instrument,
you must disconnect the power cable from the back of the instrument.

Caution: Data can be lost during an emergency shutdown.

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

2. Disconnect the power cable from the back of the instrument.

2-12 Preparing for Operation

3 ESI and ESCi Modes of
Operation
This chapter describes how to prepare the instrument for the following
modes of operation:
• ESI (electrospray ionization).
• ESCi (combined electrospay and atmospheric pressure chemical
ionization).
If your system uses APCI mode, see Chapter 5, “Optional APCI Mode of
Operation”.
Contents

Topic Page
Introduction 3-2
Installing the ESI probe 3-2
Installing the corona pin 3-5
Removing the corona pin 3-7
Removing the ESI probe 3-9

3-1
Introduction
The ESI and ESCi ionization mode options use the standard ESI probe that is
fitted to the instrument when it is shipped from the factory. For ESCi
operation, the corona pin is used in conjunction with the ESI probe. The
following sections explain how to install and remove the ESI probe and corona
pin.
For further instruction, see “Electrospray ionization (ESI)” on page 1-7 and
“Combined ESI and APCI (ESCi)” on page 1-7.

Installing the ESI probe

Required material: Chemical-resistant, powder-free gloves

To install the ESI probe

Warning: The ACQUITY UPLC system connections, ESI probe,

and source can be contaminated with biohazardous and/or toxic
materials. Always wear chemical-resistant, powder-free gloves
while performing this procedure.

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

suitably prepared before commencing this procedure.

1. Prepare the instrument for working on the source (see “Preparing the
instrument for work performed on the source” on page 4-8).

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

Warning: The ESI probe tip is sharp. To avoid puncture wounds,

handle the ESI probe with care.

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

3-2 ESI and ESCi Modes of Operation

4. Ensure that the contacts on the ESI probe align with the probe adjuster
assembly contacts, and carefully slide the ESI probe into the hole in the
probe adjuster assembly.
ESI probe

Probe adjuster assembly

Probe adjuster
assembly contacts

TP02632

5. Secure the ESI probe by tightening the 2 thumbscrews.

Installing the ESI probe 3-3

 ESI probe mounted on the source enclosure, showing the connections

Vernier probe adjuster Thumbscrew

Nebulizer gas connection Diverter valve

POWER OPERATE

Desolvation gas DESOLVATION NEBULIZER

connection
HV APPI
ESI probe
electrical lead
PROBE

Probe adjuster
assembly
electrical lead

RP00017
Probe adjuster assembly ESI probe

6. Connect the ESI probe’s PTFE tube to the nebulizer gas connection.
7. Ensure that the probe adjuster assembly’s electrical lead is connected to
the instrument’s probe connection.
8. Connect the ESI probe’s electrical lead to the instrument’s HV
connection.

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.

9. Using tubing greater than or equal to 0.004-inch (ID), connect the

diverter valve to the ESI probe.
Tip: Two tubes of different ID are supplied with the instrument.
Requirement: 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.
10. Close the instrument’s access door.

3-4 ESI and ESCi Modes of Operation

Installing the corona pin
Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers

To install the corona pin

Warning: The ACQUITY UPLC system connections, ESI probe,

and source can be contaminated with biohazardous and/or toxic
materials. Always wear chemical-resistant, powder-free gloves
while performing this procedure.

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

Standby mode when commencing this procedure.

1. In the ACQUITY UPLC Console, click Standby , and confirm that

the Operate indicator is not illuminated.

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

Warning: The probe tip is sharp. To avoid puncture wounds, take

great care while working with the source enclosure door open if
an ESI probe is fitted.

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.
4. Use the needle-nose pliers to remove the blanking plug from the corona
pin mounting contact. Store the blanking plug in a safe location.

Installing the corona pin 3-5

 Corona pin mounting contact

RP00028

Corona pin mounting

contact blanking plug

Warning: The corona pin tip is sharp. To avoid puncture wounds,

handle the corona pin with care.

Caution: To avoid damaging to the corona pin’s tip and bending

the pin, use the needle-nose pliers to grip the corona pin at the
end that fits into the mounting contact.

5. Use the needle-nose pliers to fit the corona pin to the mounting contact.
Requirement: Ensure that the corona pin is securely mounted and that
its tip aligns with the sample cone aperture.

3-6 ESI and ESCi Modes of Operation

 Source, showing the corona pin, ESi probe tip, and sample cone

ESI probe tip

RP00029

Corona pin

Sample cone tip

6. Use the vernier probe adjuster to position the ESI probe tip so that it is
pointing approximately midway between the tips of the sample cone and
corona pin. (See the figure page 3-4.)
7. Close the source enclosure door, and secure it with both spring-clips.
8. Close the instrument’s access door.

Optimizing the ESI probe for ESCi operation

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

Removing the corona pin

Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers

Removing the corona pin 3-7

 To remove the corona pin

Warning: The ACQUITY UPLC system connections, corona pin,

ESI probe, and source can be contaminated with biohazardous
and/or toxic materials. Always wear chemical-resistant,
powder-free gloves while performing this procedure.

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

Standby mode when commencing this procedure.

1. In the ACQUITY UPLC Console, click Standby , and confirm that

the Operate indicator is not illuminated.

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

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

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.

Warning: The corona pin tip is sharp. To avoid puncture wounds,

handle the corona pin with care.

Caution: To avoid damaging to the corona pin’s tip and bending

the pin, use the needle-nose pliers to grip the corona pin at the
end that fits into the mounting contact.

4. Use the needle-nose pliers to remove the corona pin from its mounting
contact. Store the corona pin in a safe location. (See the figure “Source,
showing the corona pin, ESi probe tip, and sample cone” on page 3-7.)

3-8 ESI and ESCi Modes of Operation

 5. Use the needle-nose pliers to fit the blanking plug to the corona pin
mounting contact. (See the figure “Corona pin mounting contact” on
page 3-6.)
6. Close the source enclosure door, and secure it with both spring-clips.
7. Close the instrument’s access door.

Removing the ESI probe

Required material: Chemical-resistant, powder-free gloves

To remove the ESI probe

Warning: The ACQUITY UPLC system connections, ESI probe,

and source can be contaminated with biohazardous and/or toxic
materials. Always wear chemical-resistant, powder-free gloves
while performing this procedure.

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

suitably prepared before commencing this procedure.

1. Prepare the instrument for working on the source (see “Preparing the
instrument for work performed on the source” on page 4-8).

Warning: The ESI probe and source can be hot. To avoid burn
injuries, take great care while working with the instrument’s
access door open.

2. Open the instrument’s access door.

3. Disconnect the diverter valve tubing from the ESI probe.
4. Disconnect the ESI probe’s electrical lead from the high voltage
connection.
5. Ensure that the API gas is turned off.
6. Disconnect the ESI probe’s PTFE tube from the nebulizer gas
connection.

Removing the ESI probe 3-9

 7. Undo the 2 thumbscrews securing the ESI probe to the probe adjuster
assembly.

Warning: The ESI probe tip is sharp. To avoid puncture wounds,

handle the probe with care.

8. Carefully remove the ESI probe from the probe adjuster assembly.
9. If available, fit the protective sleeve to the ESI probe tip.
10. Close the instrument’s access door.

3-10 ESI and ESCi Modes of Operation

4 Maintenance Procedures

This chapter provides the maintenance guidelines and procedures

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

Topic Page
Maintenance schedule 4-3
Spare parts 4-5
Troubleshooting with Connections Insight 4-5
Safety and handling 4-7
Preparing the instrument for work performed on the source 4-8
Operating the source isolation valve 4-9
Removing O-rings and seals 4-11
Cleaning the instrument’s exterior 4-12
Emptying the exhaust trap bottle 4-12
Emptying the roughing pump exhaust liquid trap bottle 4-14
Gas ballasting the roughing pump 4-16
Checking the roughing pump oil level 4-19
Adding oil to the roughing pump 4-19
Cleaning the source components 4-21
Cleaning the sample cone and gas cone 4-21
Cleaning the ion block, isolation valve, and extraction cone 4-31
Cleaning the source hexapole assembly 4-47
Replacing the ESI probe tip 4-54
Replacing the ESI probe sample capillary 4-55
Cleaning the IonSABRE APCI probe tip 4-62
Replacing the IonSABRE APCI probe sample capillary 4-62

4-1
 Contents

Topic Page
Cleaning or replacing the corona pin 4-70
Replacing the APCI probe heater 4-71
Replacing the ion block source heater 4-75
Replacing the source assembly seals 4-79
Maintaining the instrument air filters 4-90
Replacing the roughing pump oil 4-95
Replacing the roughing pump’s oil demister element 4-98

4-2 Maintenance Procedures

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

Maintenance schedule

Procedure Frequency For information...

Clean the instrument case. As required. See page 4-12.
Empty the exhaust trap bottle Check daily, empty as See page 4-12.
in the instrument exhaust required.
line.
Empty the liquid trap bottle Check daily, empty as See page 4-14.
in the roughing pump exhaust required.
line.
Gas ballast the roughing ESI – weekly; See page 4-16.
pump. APCI – daily.
Inspect and adjust the Weekly. See page 4-19.
roughing pump oil level.
Clean the source components. When sensitivity See page 4-21.
decreases to
unacceptable levels.
Clean or replace the ESI When sensitivity See page 4-54.
probe tip. decreases to
unacceptable levels.
Replace the ESI probe When sensitivity See page 4-55.
capillary. decreases to
unacceptable levels or
sample flow is
inconsistent.
Clean the APCI probe tip. When sensitivity See page 4-62.
(Options using the APCI decreases to
IonSABRE probe only.) unacceptable levels.

Maintenance schedule 4-3

 Maintenance schedule

Procedure Frequency For information...

Replace the APCI probe When sensitivity See page 4-62.
capillary. decreases to
unacceptable levels or
sample flow is
inconsistent.
Clean or replace the corona When the corona pin is See page 4-70.
pin (APCI and ESCi modes). corroded or black, or
the sensitivity
decreases to
unacceptable levels.
Replace the APCI probe If the heater fails when See page 4-71.
heater. the instrument is
pumped down
(evacuated).
Replace the ion block heater If the heater fails to See page 4-75.
cartridge. heat when the
instrument is pumped
down (evacuated).
Replace the source assembly Annually. See page 4-79.
seals.
Clean or replace the Annually. See page 4-90.
instrument’s air filters.
Change the roughing pump Annually. See page 4-95.
oil.
Replace the roughing pump’s Annually. See page 4-98.
demister element. Tip: Applications that
contaminate the
roughing pump oil
reduce this period,
which must be
determined from
experience.

4-4 Maintenance Procedures

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.

Troubleshooting with Connections Insight

®
Connections Insight is an intelligent device management (IDM) Web service
by which Waters provides proactive service and support for the ACQUITY
UPLC system. To use Connections Insight, a Waters technician must install
the Connections Insight service agent software on the system’s Empower or
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 as you are using the ACQUITY UPLC
Console, you can also manually submit a Connections Insight request to
Waters customer support.
Consult these sources for more information about Connections Insight:
• http://www.waters.com.
• Your sales representative.
• Your local Waters subsidiary.
• Waters Customer Support, at 800 252-4752 (when phoning from the
USA or Canada).

Spare parts 4-5

 To submit a Connections Insight request
1. Select Troubleshoot > Submit Connections Insight request.

Connections Insight Request dialog box

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, allowing 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 ACQUITY UPLC Console can require up to
150 MB of file space.

4-6 Maintenance Procedures

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

Warning: The instrument components can be contaminated with

biologically hazardous materials. Always wear
chemical-resistant, powder-free gloves while handling the
components.

Warning: To prevent injury, always observe Good Laboratory Practices

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: The probe and source can be hot. To avoid burn injuries, take
great care while working with these components.

Caution: When performing maintenance inside the source enclosure,

ensure that the following criteria are met:
• Instrument is in Standby mode.
• LC flow is diverted to waste or set to off.
• Desolvation gas is turned off.

See Appendix A for safety advisory information.

Safety and handling 4-7

Preparing the instrument for work performed 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, operating the source isolation valve, and when
maintaining the source).

To prepare the instrument

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

b. Click Control .
c. Select Waste as the flow state.
2. In the Instrument Console, click Standby , and confirm that the
Operate indicator is not illuminated.
3. Wait 3 minutes to allow the desolvation gas flow to cool the probe and
source.
4. In the Instrument Console, click API to stop the desolvation gas
flow.

4-8 Maintenance Procedures

Operating the source isolation valve
You must close the source isolation valve to isolate the source from the
instrument vacuum system for certain maintenance procedures.
Required material: Chemical-resistant, powder-free gloves

To close the source isolation valve before starting a maintenance procedure

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

suitably prepared before commencing this procedure.

1. Prepare the instrument for working on the source (see “Preparing the
instrument for work performed on the source” on page 4-8).

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

Warning: To avoid puncture wounds, take great care while

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

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.

Operating the source isolation valve 4-9

 4. Close the source isolation valve by moving its handle counterclockwise,
to the vertical position.

Isolation valve handle in closed position

RP00005

To open the source isolation valve after completing a maintenance

procedure

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

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

Caution: Do not apply any downward force to the source enclosure door
while the door is open.

1. Open the source isolation valve by moving its handle clockwise to the
horizontal position.
2. Close the source enclosure door, and secure it with both spring-clips.
3. Close the instrument’s access door.

4-10 Maintenance Procedures

Removing O-rings and seals
When performing certain maintenance procedures, you must remove O-rings
or seals from instrument components. An O-ring removal kit is provided with
the instrument. You must dispose of all used O-rings and seals; do not re-use
old O-rings or seals on the instrument.

O-ring removal kit

Tool 1

Tool 2

To remove an O-ring

Caution: When removing an O-ring or seal from a component, be

careful not to scratch the component with either removal tool.

1. Use the forked end of tool 1 to impale the O-ring or seal.

2. Pull the O-ring or seal from its groove; if necessary, use tool 2 as an aid.

Warning: The O-ring or seal can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

regulations.

Removing O-rings and seals 4-11

Cleaning the instrument’s exterior
Caution: Do not use abrasives or solvents to clean the instrument’s
case.

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

Emptying the exhaust trap bottle

Check the exhaust trap bottle in the instrument exhaust line daily and empty
it before it is completely full.

Instrument exhaust trap bottle

To laboratory
exhaust port
From instrument (10-mm OD)
exhaust connection
(12-mm OD)

Required materials:
• Chemical-resistant, powder-free gloves
®
• snoop (or equivalent) leak detector liquid

4-12 Maintenance Procedures

To empty the exhaust trap bottle
1. In the ACQUITY UPLC Console, click Stop Flow to stop the LC
flow.

2. In the ACQUITY UPLC Console, click API to stop the desolvation

gas flow.

Warning: The waste liquid in the exhaust trap bottle

comprises ACQUITY UPLC solvents and analytes. Always
wear chemical-resistant, powder-free gloves while handling
the exhaust trap bottle.

3. Unscrew and remove the exhaust trap bottle cap.

Warning: The waste liquid can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

regulations.
5. Fit and tighten the exhaust trap bottle cap.
6. Ensure that the exhaust trap bottle is secured in the upright position.

7. In the ACQUITY UPLC Console, click API to start the desolvation

gas flow.
8. In the ACQUITY UPLC Console, click Start Flow to start the LC
flow.

Warning: To confirm the integrity of the source exhaust

system, the following leak test must be performed.

Caution: To avoid damage to the instrument, snoop (or

equivalent) leak detector liquid must be used only for the
purpose described in the following step; it must not be used on
any other part of the instrument.

9. Use snoop (or equivalent) leak detector liquid to ensure that there are no
leaks at the exhaust trap bottle cap.

Emptying the exhaust trap bottle 4-13

Emptying the roughing pump exhaust liquid trap bottle
Check the liquid trap bottle in the roughing pump exhaust line daily and
empty it before it is completely full.

Roughing pump exhaust liquid trap bottle for an oil-filled roughing pump

TP02800

Roughing pump exhaust liquid trap bottle for an oil-free roughing pump

TP02997

TP02800

TP02996

4-14 Maintenance Procedures

Required materials:
• Chemical-resistant, powder-free gloves
• snoop (or equivalent) leak detector liquid

To empty the exhaust liquid trap bottle

1. Close the source isolation valve (see “Operating the source isolation
valve” on page 4-9).

Warning: The liquid in the roughing pump liquid trap

bottle can be contaminated with analyte accumulated
during normal operation. Always wear chemical-resistant,
powder-free gloves while handling the bottle.

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

near the roughing pump: it can be hot.

2. Unscrew and remove the roughing pump liquid trap bottle cap.

Warning: The waste liquid can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

regulations.
4. Fit and tighten the roughing pump liquid trap bottle cap.
5. Ensure that the roughing pump liquid trap bottle is secured in the
upright position.
6. Open the source isolation valve (see “Operating the source isolation
valve” on page 4-9).

Caution: To avoid damage to the instrument, snoop (or

equivalent) leak detector liquid must be used only for the
purpose described in the following step; it must not be used on
any other part of the instrument.

7. Use snoop (or equivalent) leak detector liquid to ensure that there are no
leaks at the liquid trap bottle cap.

Emptying the roughing pump exhaust liquid trap bottle 4-15

Gas ballasting the roughing pump
Note: This procedure is not required for an Alcatel oil-free roughing pump.

Roughing pump

Exhaust port flange

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

Gas ballast valve

Caution: Failure to routinely gas ballast the roughing pump shortens

oil life and, consequently, pump life.

The roughing pump draws large quantities of solvent vapors. The vapors tend
to condense in the pump oil, diminishing pumping efficiency. Gas ballasting
purges condensed contaminants from the oil.
Gas ballast the roughing pump when these conditions apply:
• With ESI operation, once a week.
• With frequent APCI operation, once a day.
• When the roughing pump oil appears cloudy.
• When the vacuum pressure is higher than normal.
• When condensate forms in the roughing pump exhaust line.
• When you change the roughing pump oil.

4-16 Maintenance Procedures

 Your roughing pump can be fitted with either of the following:
• A screwdriver-operated gas ballast valve. See “Gas ballasting a pump
fitted with a screwdriver-operated gas ballast valve” on page 4-17.
• A handle-operated gas ballast valve. See “Gas ballasting a pump fitted
with a handle-operated gas ballast valve” on page 4-18.

Gas ballasting a pump fitted with a screwdriver-operated gas

ballast valve
Required material: Flat-blade screwdriver

To gas ballast the roughing pump

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

Caution: To avoid damage,

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

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

TP02654

Gas ballasting the roughing pump 4-17

 2. Run the pump for 30 to 60 minutes.
Tip: It is normal for the roughing pump temperature to increase during
ballasting. To maintain an ambient temperature of 40 °C (104 °F)
where the pump is located, ensure there is adequate ventilation.
3. Use the flat-blade screwdriver to turn the gas ballast valve to the closed,

, position.

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

valve
To gas ballast the roughing pump

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

Caution: To avoid damage,

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

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

TP02654

4-18 Maintenance Procedures

 2. Run the pump for 30 to 60 minutes.
Tip: It is normal for the roughing pump temperature to increase during
ballasting. To maintain an ambient temperature of 40 °C (104 °F)
where the pump is located, ensure there is adequate ventilation.
3. Move the gas ballast valve handle on the pump clockwise from the
vertical position to the horizontal position.

Checking the roughing pump oil level

Caution: To ensure correct operation of the roughing pump, do not
operate the pump with the oil level at less than 30% of the MAX level.

Note: This procedure is not required for an Alcatel oil-free roughing pump.
Requirement: You must check the oil level while the roughing pump is
running.
The roughing pump oil level appears in the roughing pump’s oil level sight
glass. Check the oil level at weekly intervals; you must maintain the oil level
so that it is at or near the MAX level when the pump is not operating.
Tip: The oil level in the sight glass is lower when the roughing pump is
running than when it is stopped. When the pump is running, the oil level is
typically at 30% to 60% of the MAX level. For further information, see the
figure “Roughing pump” on page 4-16 and “Adding oil to the roughing pump”
on page 4-19.

Adding oil to the roughing pump

If you check the roughing pump oil level and it is found to be low, you must
add oil to the roughing pump. See “Checking the roughing pump oil level” on
page 4-19.
Required materials:
• Chemical-resistant, powder-free gloves
• 8-mm Allen wrench
• Container to catch used oil
• Funnel
• Anderol vacuum oil, type GS 495

Checking the roughing pump oil level 4-19

 To add oil to the roughing pump
1. Vent and shut-down the instrument (see the mass spectrometer’s online
Help for details).

Warning: The pump oil can be contaminated with analyte

accumulated during normal operation. Always wear
chemical-resistant, powder-free gloves when adding or
replacing oil.

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

with the roughing pump: it can be hot.

2. Use the 8-mm Allen wrench to unscrew and remove the roughing pump’s
oil filler plug (see the figure “Roughing pump” on page 4-16).

Caution: To maintain pump performance, use only Anderol

vacuum oil, type GS 495.

3. Using the funnel, add Anderol vacuum oil, type GS 495, into the oil filler
aperture until the oil reaches the oil level sight glass MAX level.
4. Ensure that the O-ring on the oil filler plug is clean and properly seated.

Caution: To avoid oil leakage, when fitting the oil filler plug to
the roughing pump,
• ensure that the plug is not cross-threaded.
• ensure that the O-ring is not pinched.
• do not over-tighten the plug.

5. Use the 8-mm Allen wrench to fit and tighten the roughing pump’s oil
filler plug.
Tip: When the oil filler plug is tightened, the plug seals with an O-ring.
Compression is controlled by the O-ring groove depth in the plug.
Increased torque does not improve the plug seal; it only makes the plug
difficult to remove later.
6. Start the instrument (see “Starting the instrument” on page 2-2).
Tips: After you add oil to the pump, the following situations can occur:
• The oil level drops slightly during the first month of operation.
• The oil changes color (darkens) over time.

4-20 Maintenance Procedures

 • After running the pump for 12 to 48 hours, it is common to see a few
drops of oil near the filler plug. Excess oil around the lip of the filler
plug will run down and drip off the pump once the pump reaches
operating temperature.
• When the pump begins to run at normal operating temperature,
spilled oil smells slightly.

Cleaning the source components

Clean the sample cone and gas cone when these conditions apply:
• The sample cone and gas cone are visibly fouled.
• LC and sample-related causes for decreased signal intensity have been
dismissed.
See “Cleaning the sample cone and gas cone” on page 4-21.
If cleaning the sample cone and gas cones fails to increase signal sensitivity,
also clean the ion block, isolation valve, and extraction cone (see “Cleaning the
ion block, isolation valve, and extraction cone” on page 4-31).
If cleaning the ion block, isolation valve, and extraction cone fails to increase
signal sensitivity, also clean the source hexapole assembly (see “Cleaning the
source hexapole assembly” on page 4-47).

Cleaning the sample cone and gas cone

The cone gas assembly (comprising the sample cone, O-ring, and gas cone) can
be removed for cleaning without venting the instrument.

Removing the cone gas assembly from the source

Required material: Chemical-resistant, powder-free gloves

Cleaning the source components 4-21

 To remove the cone gas assembly from the source

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

Standby mode before commencing this procedure.

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

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

Warning: The source can be hot. To avoid burn injuries, take great care
while working with the instrument’s access door open.

Caution: Do not apply any downward force to the source enclosure door
while the door is open.

1. Close the source isolation valve (see “Operating the source isolation
valve” on page 4-9).
2. Disconnect the PTFE tube from the cone gas assembly connection tube.

Cone gas assembly

Connection tube

PTFE tube
RP00006

4-22 Maintenance Procedures

3. Grasp the cone gas assembly connection tube, and use it as a lever to
rotate the cone gas assembly 90 degrees, moving the connection tube
from the vertical to the horizontal position.

Cone gas assembly

rotated 90 degrees
RP00007

Caution: Do not open the isolation valve at any time when the
cone gas assembly has been removed from the ion block
assembly.

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

Ion block assembly

RP00008

Cleaning the sample cone and gas cone 4-23

Disassembling the cone gas assembly
Required material: Chemical-resistant, powder-free gloves

To disassemble the cone gas assembly

Warning: The cone gas assembly can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Caution: Do not apply excessive force to the source enclosure door

when using the extraction tool on the source door.

1. Position the cone gas assembly inlet over the extraction tool on the
source enclosure door.
Alternative: Use the hand-held extraction tool supplied with the
instrument. This tool is used in a similar manner to that fitted to the
source enclosure door.

Cone gas assembly

Extraction tool

Source enclosure
door

RP00020

4-24 Maintenance Procedures

 Caution: The sample cone is fragile. Never place it on its tip;
always place it on its flanged base.

2. Carefully push down on the gas cone to separate the gas cone, sample
cone, and O-ring.
O-ring
Sample cone
Gas cone

RP00021

Warning: The O-ring can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

regulations.

Cleaning the sample cone and gas cone

Required materials:
• Chemical-resistant, powder-free gloves.
• Appropriately sized glass vessels in which to completely immerse
components when cleaning. Use only glassware not previously cleaned
with surfactants.
• HPLC-grade, or better, methanol.
• HPLC-grade, or better, water.

Cleaning the sample cone and gas cone 4-25

 • Formic acid.
• Ultrasonic bath.
• Source of oil-free, inert gas (nitrogen or helium) for drying (air-drying
optional).
• Wash-bottle containing HPLC-grade, or better, 1:1 methanol/water.
• Large beaker.

To clean the sample cone and gas cone

Warning: The sample cone and gas cone can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: Use extreme care when working with formic acid. Work in a
fume hood, and use suitable protective equipment.

Caution: The sample cone is fragile. Never place it on its tip; always
place it on its flanged base.

1. If the sample cone contains debris, place a drop of formic acid on its
orifice.
2. Immerse the sample cone and gas cone separately in glass vessels
containing 1:1 methanol/water.
Tip: If the components are obviously contaminated, use 45:45:10
methanol/water/formic acid.
3. Place the vessels in the ultrasonic bath for 30 minutes.
4. If you used formic acid in the cleaning solution, do as follows:
a. Rinse the components by immersing them separately in glass
vessels containing water and then placing the vessels in the
ultrasonic bath for 20 minutes.
b. Displace the water by immersing the components in separate glass
vessels containing methanol and then placing the vessels in the
ultrasonic bath for 10 minutes.

4-26 Maintenance Procedures

 Caution: To avoid recontaminating the components, wear clean,
chemical-resistant, powder-free gloves for the rest of this
procedure.

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

Cleaning the sample cone and gas cone 4-27

Assembling the cone gas assembly
Required material: Chemical-resistant, powder-free gloves

To assemble the cone gas assembly

Caution:
• To avoid recontaminating the cone gas assembly, wear clean
chemical-resistant, powder-free gloves during this procedure.
• The sample cone is fragile. Never place it on its tip; always place it
on its flanged base.

1. Carefully fit the sample cone into the gas cone.

O-ring

Sample cone

Gas cone

TP02663

2. Fit a new O-ring into the groove created between the sample cone and
gas cone.

4-28 Maintenance Procedures

Fitting the cone gas assembly to the source
Required material: Chemical-resistant, powder-free gloves

To fit the cone gas assembly to the source

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

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

Caution: To avoid damage,

• do not apply any downward force to the source enclosure door while
the door is open.
• do not open the source isolation valve before fitting the cone gas
assembly to the ion block assembly.

Cleaning the sample cone and gas cone 4-29

 1. Ensure that the source isolation valve is in the closed position (see
“Operating the source isolation valve” on page 4-9).
2. Hold the cone gas assembly so that the connection tube is horizontal and
at the top, then slide the cone gas assembly into the ion block assembly.

Ion block
assembly
Cone gas
assembly
RP00009

3. Grasp the cone gas assembly connection tube and use it as a handle to
rotate the cone gas assembly 90 degrees, moving the connection tube
from the horizontal to the vertical position.
4. Connect the PTFE tube to the cone gas assembly connection tube.
5. Open the source isolation valve.
6. Close the source enclosure door, and secure it with both spring-clips.
7. Close the instrument’s access door.

4-30 Maintenance Procedures

Cleaning the ion block, isolation valve, and extraction
cone
The ion block and extraction cone must be cleaned if cleaning the sample cone
and gas cone fails to increase signal sensitivity.

Removing the ion block assembly from the source assembly

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

To remove the ion block assembly

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

Warning: The source can be hot. To avoid burn injuries, allow it

to cool for at least 30 minutes before proceeding.

2. Open the instrument’s access door.

Warning: To avoid puncture wounds, take great care while

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

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.

Cleaning the ion block, isolation valve, and extraction cone 4-31
 4. Close the source isolation valve (see “Operating the source isolation
valve” on page 4-9).
5. Disconnect the PTFE tube from the cone gas assembly connection tube.
6. Use the 6-mm Allen wrench to unscrew and remove the 2 ion block
assembly securing screws and associated washers.

Washers

Ion block securing screws

RP000010

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

Ion block assembly

RP00011

4-32 Maintenance Procedures

Disassembling the source ion block assembly
Required materials:
• Chemical-resistant, powder-free gloves
• 2.5-mm and 6-mm Allen wrenches
• O-ring removal kit
• Needle-nose pliers

To disassemble the ion block assembly

Warning: The ion block assembly can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Ensure that the isolation valve is closed.

Isolation valve handle

in closed position

Gas cone position

blocks

TP02650

2. Grasp the cone gas assembly connection tube and use it as a lever to
rotate the cone gas assembly 90 degrees.

Cleaning the ion block, isolation valve, and extraction cone 4-33
 Caution: To ensure correct operation of the ion block assembly after
reassembly,
• the gas cone position block must not be removed
• the screws holding the gas cone position blocks in place must not be
adjusted.

3. Slide the cone gas assembly out of the ion block assembly.
4. Use the 2.5-mm Allen wrench to loosen the 4 ion block cover plate
captive securing screws.

Ion block cover plate securing screw

Ion block cover plate

TP02649

5. Remove the ion block cover plate.

4-34 Maintenance Procedures

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

Isolation valve

O-ring

7. Use the O-ring removal kit to carefully remove the isolation valve O-ring
(see “Removing O-rings and seals” on page 4-11).

Warning: The isolation valve O-ring can be contaminated

with biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

8. Dispose of the isolation valve O-ring in accordance with local

environmental regulations.

Cleaning the ion block, isolation valve, and extraction cone 4-35
 9. Use the 2.5-mm Allen wrench to loosen the captive PEEK terminal block
securing screw.
PEEK terminal block securing screw

TP02616

Caution: To avoid damaging the heater cartridge assembly

wires, do not bend or twist them either side of the heater
cartridge assembly heat-shrink tubing when removing the
assembly from the ion block.

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

4-36 Maintenance Procedures

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

Heater cartridge assembly

TP02618

12. Use the O-ring removal kit to carefully remove the cover seal from the
ion block (see also “Removing O-rings and seals” on page 4-11).

Cover seal

TP02619

Cleaning the ion block, isolation valve, and extraction cone 4-37
 Warning: The cover seal can be contaminated with
biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

13. Dispose of the cover seal in accordance with local environmental

regulations.
14. Use the 6-mm Allen wrench to remove the ion block blanking plug and
associated seal.
Blanking plug

Seal

TP02648

Warning: The blanking plug seal can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

15. Dispose of the blanking plug seal in accordance with local environmental
regulations.

4-38 Maintenance Procedures

16. Use the 2.5-mm Allen wrench to loosen the captive extraction cone
retainer securing screw.

Securing
screw

Extraction
cone

TP02612

Caution:
• Take great care not to damage the extraction cone aperture
when removing the extraction cone from the ion block.
• The extraction cone is fragile. Never place it on its tip; always
place it on its flanged base.

17. Remove the extraction cone retainer and extraction cone from the ion
block.
Extraction cone retainer Extraction cone aperture

TP02613

Cleaning the ion block, isolation valve, and extraction cone 4-39
 18. Remove the extraction cone retainer from the extraction cone.
19. Remove the extraction cone seal from the ion block.

Extraction cone seal

TP02614

Cleaning the ion block, isolation valve, and extraction cone

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

4-40 Maintenance Procedures

To clean the ion block components

Warning: The ion block components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: Use extreme care when working with formic acid. Use a
fume hood and appropriate protective equipment.

Caution: The extraction cone is fragile. Never place it on its tip; always
place it on its flanged base.

1. Immerse the ion block, isolation valve, and extraction cone separately in
glass vessels containing 1:1 methanol/water.

Caution: To avoid damage, do not clean non-metal parts (for example,

the heater cartridge assembly) in this way.

Tip: If the components are obviously contaminated, use 45:45:10

methanol/water/formic acid.
2. Place the vessels in the ultrasonic bath for 30 minutes.
3. If you used formic acid in the cleaning solution, do as follows:
a. Rinse the components by immersing them separately in glass
vessels containing water and then placing the vessels in the
ultrasonic bath for 20 minutes.
b. Displace the water by immersing the components separately in
glass vessels containing methanol and then placing the vessels in
the ultrasonic bath for 10 minutes.

Caution: To avoid recontaminating the components, wear clean,

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

4. Carefully remove the components from the vessels, and blow-dry them
using inert, oil-free gas.

Cleaning the ion block, isolation valve, and extraction cone 4-41
 5. Inspect each component for persisting contamination. If contamination
is present, do as follows:
a. Use the wash-bottle containing 1:1 methanol/water to rinse the
component over the large beaker.
b. Blow-dry the component with inert, oil-free gas.
6. Inspect each component for persisting contamination. If contamination
is present, dispose of the component, and obtain a new one before
reassembling the ion block assembly.

Assembling the source ion block assembly

Required materials:
• Chemical-resistant, powder-free gloves
• 1.5-mm, 2.5-mm, and 6-mm Allen wrenches
• Needle-nose pliers
• Isopropyl alcohol in small container

To assemble the ion block assembly

Caution:
• To avoid recontaminating the ion block assembly, wear clean
chemical-resistant, powder-free gloves during this procedure.
• The sample cone is fragile. Never place it on its tip; always place it
on its flanged base.

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

2. Fit the extraction cone retainer to the extraction cone.

Caution: Take great care not to damage the extraction cone

aperture when fitting the extraction cone to the ion block.

3. Fit the extraction cone retainer and extraction cone to the ion block.
4. Use the 2.5-mm Allen wrench to tighten the captive screw securing the
extraction cone retainer.
5. Fit a new blanking plug seal to the ion block blanking plug.

4-42 Maintenance Procedures

6. Use the 6-mm Allen wrench to fit and tighten the blanking plug to the
ion block.

Caution: To avoid damaging the heater cartridge assembly

wires, do not bend or twist them either side of the heater
cartridge assembly heat-shrink tubing when fitting the assembly
to the ion block.

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

the heater cartridge assembly, slide the assembly and the PEEK
terminal block into the ion block.
8. Use the 2.5-mm Allen wrench to tighten the captive PEEK terminal
block securing screw.
9. Ensure that the grooves for the cover seal and extraction cone seal are
free from dirt and debris.
Tip: If contamination is present, use 1:1 methanol/water, applied to a
lint-free cloth, to carefully clean the grooves.
10. Fit a new cover seal to the ion block, ensuring that it is correctly seated.
11. Soak a new isolation valve O-ring in isopropyl alcohol for a few minutes.
Rationale: Doing so lubricates the O-ring and aids your fitting the
O-ring to the isolation valve.
12. Fit the new O-ring to the isolation valve.
13. Fit the isolation valve to the ion block assembly.

Cleaning the ion block, isolation valve, and extraction cone 4-43
 14. If an ion block assembly set screw is fitted, use the 1.5 mm Allen wrench
to loosen the set screw. If an ion block assembly set screw is not fitted go
to step 18.

Ion block assembly set

screw

TP02651

15. To tighten the ion block assembly set screw, hold the ion block in
position against the PEEK ion block support on the instrument.

Caution: To avoid damage to the thermocouple, do not

overtighten the set screw.

16. Carefully tighten the set screw until it makes contact with the
thermocouple.
17. Remove the ion block from the PEEK ion block support on the
instrument.
18. Fit the ion block cover plate to the ion block assembly, and then use the
2.5-mm Allen wrench to tighten the 4 ion block cover plate captive
securing screws.
19. Holding the cone gas assembly so that the connection tube is horizontal
and at the top, slide the cone gas assembly into the ion block assembly.
20. Grasp the cone gas assembly connection tube, and use it as a handle to
rotate the cone gas assembly 90 degrees, moving the connection tube
from the horizontal to the vertical position.

4-44 Maintenance Procedures

Fitting the ion block assembly to the source assembly
Required materials:
• Chemical-resistant, powder-free gloves
• 6-mm Allen wrench

To fit the ion block assembly

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

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

Caution: To avoid recontaminating the ion block assembly, wear clean

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

1. Unscrew and remove the 3 thumbscrews that secure the right-hand side
flange to the source enclosure.

Thumbscrew

Spring-clip

Source enclosure side flange

RP00024

2. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.
3. Remove the side flange from the source enclosure.
Rationale: This step allows you to see the ion block assembly as you fit it
to the PEEK ion block support.

Cleaning the ion block, isolation valve, and extraction cone 4-45
 Caution: Do not apply any downward force to the source
enclosure door while the door is open.

4. Fit the ion block assembly to the PEEK ion block support.
5. Use the 6-mm Allen wrench to fit and then slowly and evenly tighten the
2 ion block assembly securing screws and their associated washers.
6. Look through the hole in the side of the source enclosure and view the
area where the ion block assembly meets the PEEK ion block support. If
you see a gap, the extraction cone has slipped out of position during
installation. If this is the case, remove the ion block assembly, refit the
extraction cone, and reinstall the ion block assembly on the PEEK ion
block support.
7. When you are satisfied with the installation of the ion block assembly,
fit the side flange to the source enclosure.
8. Fit and tighten the 3 thumbscrews that secure the right-hand side
flange to the source enclosure.
9. Connect the PTFE tube to the cone gas assembly connection tube.
10. Open the source isolation valve (see “Operating the source isolation
valve” on page 4-9).
11. Close the source enclosure door, and secure it with both spring-clips.

4-46 Maintenance Procedures

Cleaning the source hexapole assembly
The source hexapole assembly must be cleaned if cleaning the ion block,
isolation valve, and extraction cone fails to increase signal sensitivity.

Removing the ion block assembly, ion block support, and

hexapole from the source assembly
Required materials:
• Chemical-resistant, powder-free gloves
• 3-mm Allen wrench
• O-ring removal kit

To remove the ion block assembly, ion block support, and hexapole

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear chemical-
resistant, powder-free gloves while performing this procedure.

1. Remove the ion block assembly from the PEEK ion block support (see
“Removing the ion block assembly from the source assembly” on
page 4-31).
2. Use the 3-mm Allen wrench to unscrew and remove the 3 screws
securing the PEEK ion block support to the adaptor housing.

Adaptor housing

PEEK ion block

support
Hexapole
assembly
Securing screws

Cleaning the source hexapole assembly 4-47

 3. Remove the PEEK ion block support from the adaptor housing.
4. Use the O-ring removal kit to carefully remove all the O-rings from the
PEEK ion block support (see “Removing O-rings and seals” on
page 4-11).

Warning: The O-rings can be contaminated with

biohazardous and/or toxic materials. Ensure that they are
correctly disposed of according to local environmental
regulations.

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

regulations.

Caution: To avoid damage, when removing the hexapole

assembly from the adaptor housing, observe these precautions:
• Avoid scratching the internal surfaces of the adaptor block.
• Do not compress the hexapole rods.

6. Carefully grasp the source hexapole assembly and remove it from the
adaptor housing.

4-48 Maintenance Procedures

Cleaning the hexapole assembly
Required materials:
• Chemical-resistant, powder-free gloves.
• 500-mL measuring cylinder or appropriately sized glass vessel in which
to completely immerse the hexapole when cleaning. Use only glassware
not previously cleaned with surfactants.
• Length of small diameter stainless steel tube.
• HPLC-grade, or better, methanol.
• Ultrasonic bath.
• Source of oil-free, inert gas (nitrogen or helium) for drying (air-drying
optional).
• HPLC-grade, or better, 1:1 methanol/water.
• Wash-bottle containing HPLC-grade, or better, 1:1 methanol/water.
• Large beaker.
• Small, flat-blade screwdriver.

To clean the source hexapole assembly

Warning: The source hexapole assembly can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Bend the stainless steel tube into a hook shape.

2. Insert one end of the hook into one of the holes on the hexapole
assembly’s rear support ring.

Cleaning the source hexapole assembly 4-49

 Caution: To avoid vibration damage to the hexapole assembly,
ensure that the bottom of the assembly is not in contact with the
bottom of the glass vessel.

3. Use the hook to carefully suspend the hexapole assembly into the glass
vessel with the bottom of the assembly clear of the bottom of the vessel.

Hook

Rear support ring

TP02658

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

Caution: To avoid recontaminating the hexapole assembly, wear

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

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

4-50 Maintenance Procedures

7. Inspect the hexapole assembly for persisting contamination, If
contamination is present, do as follows:
a. Use the wash-bottle containing methanol to rinse the source
hexapole assembly over the large beaker.
b. Blow-dry the hexapole assembly with inert, oil-free gas.
8. Use the small flat-blade screwdriver to ensure that the hexapole
assembly screws are tight.

Cleaning the source hexapole assembly 4-51

Fitting the hexapole assembly, PEEK ion block support, and ion
block assembly to the source assembly
Required materials:
• Chemical-resistant, powder-free gloves
• 3-mm Allen wrench
• Lint-free cloth
• HPLC-grade, or better, 1:1 methanol/water

To fit the hexapole assembly and PEEK ion block support to the source

Caution: To avoid recontaminating the source, wear clean,

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

Caution: To avoid damage, when fitting the hexapole assembly into the
adaptor housing, observe these precautions:
• Avoid scratching the internal surfaces of the adaptor block.
• Do not compress the hexapole rods.

1. Carefully fit the source hexapole assembly into the adaptor housing,
aligning the notches in the differential aperture at its rear with the two
bottom support rails on the analyzer assembly. Then carefully slide the
assembly fully into place.
2. Ensure that the grooves for the PEEK ion block support O-rings are free
from dirt and debris.
Tip: If contamination is present, use 1:1 methanol/water, applied to a
lint-free cloth, to carefully clean the grooves.
3. Fit new O-rings to the PEEK ion block support.
Tip: To fit an O-ring in its groove, start fitting the O-ring at the notch in
the groove and then progressively work the ring into the groove in either
direction from the notch.
4. Fit the PEEK ion block support to the instrument’s housing.

Caution: To ensure correct operation of the instrument, neither

hexapole spring must touch a hexapole rod.

4-52 Maintenance Procedures

5. Use the 3-mm Allen wrench to fit and tighten the 3 PEEK ion block
support securing screws.
Tip: Look through the PEEK ion block support as you tighten the
securing screws. Ensure that neither hexapole spring buckles and
touches a hexapole rod.

Hexapole spring

Hexapole rod

TP02659

6. Fit the ion block assembly to the PEEK ion block support (see “Fitting
the ion block assembly to the source assembly” on page 4-45).

Cleaning the source hexapole assembly 4-53

Replacing the ESI probe tip
Replace the ESI probe tip if a blockage occurs in the internal metal sheathing
through which the stainless steel capillary passes or if the probe tip threads
are damaged.
Required materials:
• Chemical-resistant, powder-free gloves
• 6-mm (¼-inch) wrench

To replace the ESI probe tip

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: The probe and source can be hot. To avoid burn injuries, take
great care while performing this procedure.

Warning: The ESI probe tip is sharp. To avoid puncture wounds,

handle the probe with care.

1. Remove the probe from the source (see also “Removing the ESI probe” on
page 3-9).
2. Use the 6-mm (¼-inch) wrench to unscrew and remove the probe tip.

Warning: The probe tip can be contaminated with

biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

regulations.
4. Use the 6-mm (¼-inch) wrench to fit and tighten the new probe tip to the
probe.

4-54 Maintenance Procedures

 5. Adjust the probe tip so that the fully extended capillary (when the probe
nebulizer adjuster knob is fully screwed down) protrudes by
approximately 1 to 1.5 mm.
6. Fit the probe to the source (see also “Installing the ESI probe” on
page 3-2).

Replacing the ESI probe sample capillary

The stainless steel sample capillary in the ESI probe must be replaced if it
becomes blocked and cannot be cleared, or if it becomes contaminated or
damaged.
Required materials:
• Chemical-resistant, powder-free gloves
• 1.5-mm Allen wrench
• 6-mm (¼-inch) wrench
• 5/16-inch wrench
• 7/16-inch wrench
• Flat-blade screwdriver
• Needle-nose pliers
• LC pump
• HPLC-grade, or better, 1:1 acetonitrile/water

Replacing the ESI probe sample capillary 4-55

 To replace the capillary

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: The probe and source can be hot. To avoid burn injuries, take
great care while performing this procedure.

Warning: The ESI probe tip is sharp. To avoid puncture wounds,

handle the probe with care.

1. Remove the probe from the source (see “Installing the corona pin” on
page 3-5).
2. Use the screwdriver to remove the 2 probe end-cover retaining screws.

Retaining screws

TP03004

4-56 Maintenance Procedures

3. Use the 1.5-mm wrench to loosen the set screw on the LC PEEK union.

Setscrew

TP03005

4. Remove the end-cover.

End-cover

TP03006

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

Probe tip

TP03007

Replacing the ESI probe sample capillary 4-57

 6. Use the 5/16-inch and 7/16-inch wrenches to unscrew the coupling.

Coupling

LC union

TP03009

7. Withdraw the LC union, coupling and capillary from the probe.

8. Remove the LC union, capillary and seal from the coupling.

Seal

TP03011
GVF16 Ferrule Capillary Coupling

LC union PTFE liner

Warning: The capillary, PTFE liner, ferrule assembly, and

seal can be contaminated with biohazardous and/or toxic
materials. Ensure that they are correctly disposed of
according to local environmental regulations.

9. Dispose of the capillary, PTFE liner, ferrule assembly, and seal in

accordance with local environmental regulations.

4-58 Maintenance Procedures

10. Use the needle-nose pliers to remove the conductive sleeve from the
inner bore of the probe assembly fitting.

Conductive sleeve

TP03012

11. Slide a new GVF16 ferrule onto the PTFE liner tube.
12. Fit a new seal into the groove facing the short end of the coupling.

Seal

Coupling

TP03013

13. Slide the coupling—short end first—onto the capillary, followed by the
new PTFE liner tube and ferrule and screw the coupling into the LC
union.

Replacing the ESI probe sample capillary 4-59

 14. Slide a compression screw and ferrule onto a piece of 1/16 × 0.0025 bore
(5M) PEEK tubing and connect the tubing to the opposite side of the LC
union.

TP03014

PEEK tubing LC union Capillary

Compression Coupling
screw

15. Push the capillary into the union until it seats.

16. Tighten the adaptor nut on the LC union so that it is snug but not tight.
17. Gently tug the capillary to make sure it remains secure.
18. Remove the PEEK tubing from the union.
19. Check for leaks in the assembly by attaching the free end of the PEEK
tubing to an LC pump and pumping 1:1 acetonitrile/water through it at
1 mL/min.
20. If leakage occurs, disassemble and remake the connection, and then
repeat the leak test.
21. When performing the leak test, check the backpressure on the LC pump,
which will be relatively high if the capillary is blocked. If this is the case,
replace the capillary.
22. When the leak test is performed successfully, disconnect the PEEK
tubing from the LC pump.
23. Slide the conductive sleeve onto the capillary, and then feed the
capillary through the probe.

TP03015

Conductive sleeve

4-60 Maintenance Procedures

24. Attach the coupling nut to the probe, and gently tighten it with the
7/16-inch wrench.

Coupling

LC union

TP03009

25. Replace the probe tip, and then screw down until the capillary protrudes
approximately 0.5 mm from the end of the tip.
Capillary protrudes 0.5 mm
from the end of the probe tip

26. Fit the probe end-cover.

27. Fit and tighten the two probe end-cover retaining screws.
28. Tighten the set screw to clamp the LC union in place.
29. Attach the nebulizer gas connection to the probe.
30. Fit the probe to the instrument.

Replacing the ESI probe sample capillary 4-61

Cleaning the IonSABRE APCI probe tip
Clean the APCI probe tip when a buffer buildup is detected on the probe tip or
when the signal intensity weakens.

To clean the APCI probe tip

1. Stop the liquid flow.
2. In the Tune window, click Gas to start the desolvation gas flow.
3. In the Source tab, set Desolvation to 650 L/hr.
4. Set APcI Probe Temp to 650 °C.

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

Replacing the IonSABRE APCI probe sample capillary

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

Removing the existing capillary

Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• 7-mm wrench
• 2.5-mm Allen wrench

4-62 Maintenance Procedures

To remove the existing capillary

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: The probe and source can be hot. To avoid burn injuries, take
great care while performing this procedure.

1. Remove the probe from the source (see “Removing the IonSABRE APCI
probe” on page 5-6).
2. Use the 2.5-mm Allen wrench to remove the 2 probe end-cover retaining
screws.
End-cover retaining screws

TP02676

Replacing the IonSABRE APCI probe sample capillary 4-63

 3. Remove the end-cover.
End-cover

TP02677

4. Unscrew and remove the nebulizer adjuster knob to reveal a PEEK

union/UNF coupling assembly and the capillary.

Capillary

TP02674
Nebulizer adjuster knob

5. Remove the nebulizer adjuster knob, PEEK union/UNF coupling

assembly, and capillary from the probe.

4-64 Maintenance Procedures

6. Remove the PEEK union/UNF coupling assembly and capillary from the
nebulizer adjuster knob.
PEEK union/UNF assembly

TP02675

7. Use the 7-mm wrench to loosen the locknut securing the PEEK union
and UNF coupling.
PEEK union 7-mm wrench

TP02672

Locknut UNF coupling

Replacing the IonSABRE APCI probe sample capillary 4-65

 8. Unscrew the PEEK union from the UNF coupling. This connection is
finger-tight only.

TP02679

9. Remove the ferrule from the capillary.

Ferrule

TP02667

10. Remove the capillary from the UNF coupling.

Installing the new capillary

Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• 7-mm wrench
• 2.5-mm Allen wrench
• Length of red PEEK tubing
• LC pump
• HPLC-grade, or better, 1:1 acetonitrile/water

4-66 Maintenance Procedures

To install the new capillary

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Insert a square-cut length of red PEEK tubing in the probe inlet

connector, and screw the connector, finger-tight, into the PEEK union.
This step ensures a minimum dead volume when fitting the capillary.
Probe inlet connector

TP02671
PEEK tubing

2. Fit the UNF coupling to the new capillary.

3. Use the needle-nose pliers to slide a new ferrule onto the capillary.
4. Insert the capillary in the PEEK union, and ensure that it is fully
seated.
5. Screw the UNF coupling into the PEEK union, finger-tight only.
6. Pull on the capillary gently, testing to ensure that it stays in place.
7. Use the 7-mm wrench to tighten the locknut against the PEEK union.
8. Check for leaks in the assembly by attaching the free end of the PEEK
tubing to an LC pump and pumping 1:1 acetonitrile/water at 1 mL/min.

Replacing the IonSABRE APCI probe sample capillary 4-67

 9. If leakage occurs, disassemble and remake the connection, and repeat
the leak test.
10. When performing the leak test, check the backpressure on the LC pump,
which will be high if the capillary is blocked. If this is the case, replace
the capillary.
11. When the leak test has been performed successfully, disconnect the
PEEK tubing from the LC pump.
12. Remove the probe inlet connector and PEEK tubing from the PEEK
union.
13. Remove the probe heater (see “Replacing the APCI probe heater” on
page 4-71, step 2 through step 4).
14. Fit the PEEK union/UNF coupling assembly to the nebulizer adjuster
knob.
15. Carefully thread the capillary through the probe assembly.
16. Depress the PEEK union so that the locating pin on the UNF coupling is
fully engaged in the locating slot at the head of the probe assembly.
When the union is fully depressed, tighten the nebulizer adjuster knob.
Do not tighten the knob fully.
Locating pin Locating slot

TP02668

17. Fit the probe end-cover to the probe assembly.

4-68 Maintenance Procedures

18. Use the 2.5-mm Allen wrench to fit and tighten the 2 end-cover securing
screws.

Caution:
• When handling the probe heater, take great care to grip the
heater so as not to damage its electrical wiring.
• Take great care not to damage the probe heater’s electrical
connections, capillary sleeve, or capillary when fitting the
heater over the capillary sleeve.

19. Fit the probe heater (see “Replacing the APCI probe heater” on
page 4-71, step 5 through step 8).
20. Fit the probe to the instrument (see “Installing the IonSABRE APCI
probe” on page 5-3).
21. In the ACQUITY UPLC Console, click API to start the desolvation
gas flow.
22. Use the probe adjuster knob to adjust the capillary so that the capillary
protrudes approximately 0.5 mm from the end of the probe.

Replacing the IonSABRE APCI probe sample capillary 4-69

Cleaning or replacing the corona pin
Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• HPLC-grade, or better, methanol
• Lint-free tissue

To clean or replace the corona pin

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Warning: The probe and source can be hot. To avoid burn injuries, take
great care while performing this procedure.

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

Standby mode before commencing this procedure.

Warning: The corona pin tip is sharp. To avoid puncture wounds,

handle the corona pin with care.

Caution: Do not apply any downward force to the source enclosure door
while the door is open.

1. Remove the corona pin from the source (see “Removing the corona pin”
on page 3-7).
2. Replace the pin if it is deformed or otherwise damaged.
Requirement: Otherwise clean the tip of the pin with the lapping film,
and then wipe it clean with a methanol-saturated tissue.
3. Install the corona pin in the source (see “Installing the corona pin” on
page 3-5).

4-70 Maintenance Procedures

Replacing the APCI probe heater
Replace the APCI probe heater if it fails to heat.
Required materials:
• Chemical-resistant, powder-free gloves
• Flat-blade jeweler’s screwdriver

To replace the APCI probe heater

Warning: The probe and source components can be contaminated

with biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Remove the probe from the source (see “Removing the IonSABRE APCI
probe” on page 5-6).
2. Use the jeweler’s screwdriver to loosen the 2 set screws securing the
probe heater cover to the probe.

Set screw Probe heater cover

TP02673

Replacing the APCI probe heater 4-71

 Caution: Take great care not to damage the probe heater’s
electrical wiring when removing the probe heater cover or while
the probe heater is exposed.

3. Carefully pull the probe heater cover off the probe, revealing the probe
heater.
Probe heater electrical wiring

TP02680

Caution:
• When handling the probe heater, take great care to grip the
heater so as not to damage its electrical wiring.
• To avoid damaging the probe heater’s electrical connections,
do not twist the heater when removing it from the probe
assembly.

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

TP02678

4-72 Maintenance Procedures

 Caution:
• When handling the probe heater, take great care to grip the
heater so as not to damage its electrical wiring.
• Take great care not to damage the probe heater’s electrical
connections, capillary sleeve, or capillary when fitting the
heater over the capillary sleeve.

5. Carefully slide the probe heater over the capillary sleeve on the probe
assembly.
Probe heater connections

TP02670
Capillary Capillary sleeve

Caution: To avoid damaging the probe heater’s electrical

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

6. Fit the probe heater to the probe assembly, ensuring that the heater is
fully seated on the probe assembly.

TP02669

Replacing the APCI probe heater 4-73

 7. Fit the probe heater cover to the probe assembly.
8. Use the jeweler’s screwdriver to tighten the 2 set screws securing the
probe heater cover to the probe.
9. Fit the probe to the instrument (see “Installing the IonSABRE APCI
probe” on page 5-3).
10. In the ACQUITY UPLC Console, click API to start the desolvation
gas flow.
11. Use the probe adjuster knob to adjust the capillary so that the capillary
protrudes approximately 0.5 mm from the end of the probe.

4-74 Maintenance Procedures

Replacing the ion block source heater
Replace the ion block source heater if it fails to heat when the instrument is
pumped down (evacuated).
Required materials:
• Chemical-resistant, powder-free gloves
• Needle-nose pliers
• 1.5-mm and 2.5-mm Allen wrenches

To replace the ion block source heater

Warning: The ion block assembly can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Remove the ion block assembly from the instrument (see “Removing the
ion block assembly from the source assembly” on page 4-31).
2. Ensure that the isolation valve is closed.

Isolation valve handle

in closed position

TP02650

Replacing the ion block source heater 4-75

 3. Use the 2.5-mm Allen wrench to loosen the 4 captive screws securing the
ion block cover plate.

Ion block cover plate captive

securing screw

Ion block cover plate

TP02649

4. Remove the ion block cover plate.

5. Use the 1.5-mm Allen wrench to remove the 2 screws securing the
heater wires to the PEEK terminal block.

Heater cartridge wire

securing screws

TP02616

PEEK terminal block

4-76 Maintenance Procedures

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

TP02617

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

Heater cartridge assembly

TP02618

Replacing the ion block source heater 4-77

 8. Dispose of the heater cartridge assembly.

Caution: To avoid damaging the heater cartridge assembly

wires, do not bend or twist them either side of the heater
cartridge assembly heat-shrink tubing when fitting the assembly
to the ion block.

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

Caution: To avoid a short circuit to the ion block cover, ensure

that the two heater cartridge ring tags are pushed fully down on
the PEEK block terminals.

10. Use the needle-nose pliers to position the 2 heater wire ring tags fully
down on the PEEK block terminals.
11. Use the 1.5-mm Allen wrench to fit and tighten the 2 screws securing
the heater wires to the PEEK terminal block.
12. Fit the ion block cover plate to the ion block assembly, and then use the
2.5-mm Allen wrench to tighten the 4 captive screws securing ion block
cover plate.
13. Fit the ion block assembly to the instrument (see “Fitting the ion block
assembly to the source assembly” on page 4-45).

4-78 Maintenance Procedures

Replacing the source assembly seals
Warning: To avoid possible excessive leakage of solvent vapor
into the laboratory atmosphere, the seals listed below must be
renewed, at intervals of no greater than 1 year, exactly as
described in this section.

To avoid possible excessive leakage of solvent vapor into the laboratory

atmosphere, the following seals must be renewed at intervals of no greater
than 1 year:
• Source enclosure door seal
• Source enclosure door glass seal
• Source enclosure housing seal
• Source enclosure side flange seal
• Probe adjuster assembly probe seal
• Probe adjuster assembly flange seal
To complete this procedure, you must pressure test the source, as described in
the Waters Micromass Source Pressure Test Unit Operator’s Guide.

Removing the source enclosure from the instrument

Required materials:
• Chemical-resistant, powder-free gloves
• 5-mm Allen wrench

Replacing the source assembly seals 4-79

 To remove the source enclosure

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

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

Warning: The source can be hot. To avoid burn injuries, allow it

to cool for at least 30 minutes before proceeding.

2. Remove the probe from the source.

• If you are removing an ESI probe, see “Removing the ESI probe” on
page 3-9.
• If you are removing an IonSABRE APCI probe, see “Removing the
IonSABRE APCI probe” on page 5-6.

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.

Warning: The corona pin tip is sharp. To avoid puncture wounds,

handle the corona pin with care.

4. If using ESCi mode or an IonSABRE APCI probe, carefully remove the

corona pin (see “Removing the corona pin” on page 3-7).
5. Disconnect the probe’s electrical connection at the instrument’s front
panel.
6. Disconnect the PTFE tubing at the desolvation gas connection on the
front panel.
7. Disconnect the 2-pin connector at the rear of the source enclosure.

4-80 Maintenance Procedures

8. Use the 5-mm Allen wrench to loosen the 3 captive source enclosure
securing screws.

Source enclosure
Source enclosure securing screw
securing screws

RP00027
RP000 27
Caution: Do not apply any downward force to the source
enclosure door when removing the source enclosure from the
instrument’s housing.

9. Remove the source enclosure from the instrument.

Replacing the source assembly seals 4-81

Disassembling the source enclosure and probe adjuster
assembly
Required materials:
• Chemical-resistant, powder-free gloves
• 4-mm Allen wrench

To dismantle the source enclosure and probe adjuster assembly

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Use the 4-mm Allen wrench to remove the 4 screws securing the probe
adjuster assembly to the source enclosure.

Probe adjuster
assembly
Probe adjuster assembly
securing screw
Thumbscrew

Source enclosure
side flange

RP00024

2. Remove the probe adjuster assembly from the source enclosure.

3. Unscrew and remove the 3 thumbscrews and door spring-clip that
secure the source enclosure side flange to the source enclosure.
4. Remove the source enclosure side flange from the source enclosure.

4-82 Maintenance Procedures

Removing the seals from the source enclosure and probe
adjuster assembly
Required materials:
• Chemical-resistant, powder-free gloves
• Flat-blade screwdriver
• O-ring removal kit

To remove the seals from the source enclosure and probe adjuster
assembly

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Use the O-ring removal kit to carefully remove the probe adjuster
assembly probe seal from the probe adjuster assembly (see “Removing
O-rings and seals” on page 4-11).
Probe adjuster assembly probe seal

TP02632

Replacing the source assembly seals 4-83

 2. Use the O-ring removal kit to carefully remove the following seals from
the source enclosure:
• Source enclosure housing seal
• Source enclosure side flange seal
• Probe adjuster assembly flange seal

Probe adjuster
assembly flange seal

Source enclosure
housing seal
Source side
flange seal

RP00025

Caution: Do not apply any downward force to the source

enclosure door while the door is open.

3. Open the source enclosure door by releasing both spring-clips and

lowering the door towards you.

4-84 Maintenance Procedures

 4. Use the O-ring removal kit to carefully remove the seal from the source
enclosure door.

Door glass retaining

screw
Source enclosure
glass seal

Source enclosure
door seal

RP00019

5. Use the screwdriver to remove the 4 screws securing the glass-retaining

plate to the source enclosure door.
6. Remove the plate from the source enclosure door.
7. Remove the glass from the source enclosure door.
8. Use the O-ring removal kit to carefully remove the door glass seal from
the source enclosure door.

Warning: The seals can be contaminated with biohazardous

and/or toxic materials. Ensure that they are correctly
disposed of according to local environmental regulations.

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

regulations.

Replacing the source assembly seals 4-85

Fitting the new source enclosure and probe adjuster assembly
seals
Required materials:
• Chemical-resistant, powder-free gloves
• Wash bottle containing HPLC-grade, or better, 1:1 methanol/water

To fit the new source enclosure and probe seals

Warning: The source components can be contaminated with

biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

Caution: Do not apply any downward force to the source enclosure door
while the door is open.

1. Ensure that all the grooves for seals are free from dirt and debris.
Tip: If contamination is present, use 1:1 methanol/water, applied to a
lint-free cloth, to carefully clean the grooves.
2. Fit the new door glass seal to the source enclosure door.
3. Fit the glass to the source enclosure door.
4. Fit the glass retaining plate to the source enclosure door.

Caution: The 4 screws securing the glass retaining plate must be

sequentially and incrementally tightened until they are all fully
tight.

5. Fit and tighten the 4 screws securing the glass retaining clips to the
source enclosure door.

Caution: Ensure that the tails of the source enclosure door seals
are correctly located in the groove when fitting them to the
source enclosure door.

6. Fit the new source enclosure door seal to the source enclosure door.
7. Close the source enclosure door, and secure it with both spring-clips.

4-86 Maintenance Procedures

 8. Fit the following new seals to the source enclosure:
• Source enclosure housing seal
• Source enclosure side flange seal
• Probe adjuster assembly flange seal
9. Fit the new probe adjuster assembly probe seal to the probe adjuster
assembly.

Assembling the probe adjuster assembly and source enclosure

Required materials:
• Chemical-resistant, powder-free gloves
• 4-mm Allen wrench

To assemble the probe adjuster assembly and source enclosure

1. Fit the source enclosure side flange to the source enclosure.

Caution: The source enclosure side flange securing thumbscrews

must each be sequentially and incrementally tightened until
they are all fully tight.

2. Fit and tighten the 3 thumbscrews that secure the source enclosure side
flange to the source enclosure.
3. Fit the probe adjuster assembly to the source enclosure.

Caution: The probe adjuster assembly securing screws must each

be sequentially and incrementally tightened until they are all
fully tight.

4. Use the 4-mm Allen wrench to fit and tighten the 4 screws securing the
probe adjuster assembly to the source enclosure.

Replacing the source assembly seals 4-87

Fitting the source enclosure to the instrument
Required materials:
• Chemical-resistant, powder-free gloves
• 5-mm Allen wrench

To fit the source enclosure to the instrument

Warning: To confirm the integrity of the source exhaust system,

perform the procedure exactly as described in this section.

Caution:
• To avoid recontaminating the source, wear clean,
chemical-resistant, powder-free gloves during this procedure.
• Do not apply any downward force to the source enclosure door when
fitting the source enclosure to the instrument’s housing.

1. Ensuring that the wires to the microswitch do not become trapped

between the source enclosure and the instrument’s housing, fit the
source enclosure to the housing.

Caution: The source enclosure securing screws must each be

sequentially and incrementally tightened until they are all fully
tight.

2. Use the 5-mm Allen wrench to tighten the 3 captive screws securing the
source enclosure.
3. Connect the 2-pin connector at the rear of the source enclosure.
4. Connect the PTFE tubing to the desolvation gas connection at the
instrument’s front panel
5. Connect the probe’s electrical connection at the instrument’s front panel.

Warning: The corona pin tip is sharp. To avoid puncture wounds,

handle the corona pin with care.

6. If using ESCi mode or an IonSABRE APCI probe, carefully fit the corona
pin (see “Installing the corona pin” on page 3-5).
7. Close the source enclosure door, and secure it with both spring-clips.

4-88 Maintenance Procedures

8. Fit the probe to the source.
• If you are fitting an ESI probe, see “Installing the ESI probe” on
page 3-2.
• If you are fitting an IonSABRE APCI probe, see “Installing the
IonSABRE APCI probe” on page 5-3.
9. Start the instrument (see “Starting the instrument” on page 2-2).

Warning: To confirm the integrity of the source exhaust

system, a source pressure test must be performed, as
described in the Waters Micromass Source Pressure Test
Unit Operator’s Guide.

10. Perform a source pressure test, as described in the Waters Micromass

Source Pressure Test Unit Operator’s Guide.

Replacing the source assembly seals 4-89

Maintaining the instrument air filters

Cleaning the air filter inside the instrument’s lower bezel

Required materials:
• T10 TORX driver
• Vacuum cleaner

To clean the air filter inside the instrument’s lower bezel

1. Use the T10 TORX driver to remove the 5 screws that secure the lower
bezel in place.

Instrument’s lower bezel

Screws

TP02636

Screws

2. Use a vacuum cleaner to clean the air filter located inside the
instrument’s lower bezel.

4-90 Maintenance Procedures

 Air filter inside the instrument’s lower bezel

Air filter

Frame

TP02638

3. Reinstall the lower bezel.

Replacing the air filter inside the lower bezel

If you cannot clean the air filter by vacuuming, replace it with a new filter.
Required materials:
• T10 TORX driver
• SQ Detector lower bezel air filter

To replace the air filter inside the lower bezel

1. Remove the 5 screws that secure the lower bezel in place (see the figure
“Instrument’s lower bezel” on page 4-90).
2. Use the T10 TORX driver to remove the 4 screws that secure the air
filter frame and air filter to the inside of the lower bezel.

Maintaining the instrument air filters 4-91

 Air filter inside the lower bezel

Screws

Air filter

Frame

TP02638

Screws

3. Remove the air filter from the air filter frame and dispose of it.
4. Align the new air filter within the air filter frame.
5. Use the T10 TORX driver to fit and tighten the 4 screws securing the air
filter and frame to the inside of the lower bezel.
6. Reinstall the lower bezel.

Cleaning the air filter behind the source probe

Required material: Vacuum cleaner

To clean the air filter behind the source probe

1. Remove the probe from the source.
• If you are removing an ESI probe, see “Removing the ESI probe” on
page 3-9.
• If you are removing an IonSABRE APCI probe, see “Removing the
IonSABRE APCI probe” on page 5-6.
2. Grasp the air filter tab, and remove the air filter frame by lifting it
toward you.

4-92 Maintenance Procedures

 Air filter tab

Air filter tab

RP00023

3. Use a vacuum cleaner to clean the air filter.

Air filter removed from behind the source probe

Air filter

Frame

TP02637

4. Reinstall the air filter.

5. Fit the probe to the source.

Maintaining the instrument air filters 4-93

 • If you are fitting an ESI probe, see “Installing the ESI probe” on
page 3-2.
• If you are fitting an IonSABRE APCI probe, see “Installing the
IonSABRE APCI probe” on page 5-3.

Replacing the air filter behind the source probe

To replace the air filter behind the source probe
1. Remove the probe from the source.
• If you are removing an ESI probe, see “Removing the ESI probe” on
page 3-9.
• If you are removing an IonSABRE APCI probe, see “Removing the
IonSABRE APCI probe” on page 5-6.
2. Grasp the air filter tab and remove the air filter frame by lifting it
toward you (see the figure “Air filter tab” on page 4-93).
3. Remove the air filter from the air filter frame and dispose of it.

Removing air filter from frame

Frame

Air filter

TP02640

4. Insert the new air filter in the air filter frame.

5. Reinstall the air filter.
6. Fit the probe to the source.

4-94 Maintenance Procedures

 • If you are fitting an ESI probe, see “Installing the ESI probe” on
page 3-2.
• If you are fitting an IonSABRE APCI probe, see “Installing the
IonSABRE APCI probe” on page 5-3.

Replacing the roughing pump oil

Change the roughing pump oil annually.
Note: This procedure is not required for an Alcatel oil-free roughing pump.
Required materials:
• Chemical-resistant, powder-free gloves
• 8-mm Allen wrench
• Flat-blade screwdriver
• Container to catch used oil
• Funnel
• 1-L container of Anderol vacuum oil, type GS 495

To replace the roughing pump oil

1. Gas ballast the roughing pump for 1 hour to reduce the oil viscosity (see
“Gas ballasting the roughing pump” on page 4-16).
Rationale: Gas ballasting helps to circulate and mix the oil through the
pump before draining.
2. Vent and shut-down the instrument (see the mass spectrometer’s online
Help for details).
3. Allow the roughing pump to cool.

Warning: The roughing pump oil can be contaminated with

analyte accumulated during normal operation. Always
wear chemical-resistant, powder-free gloves when adding
or replacing oil.

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

with the roughing pump: it can be hot.

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

Replacing the roughing pump oil 4-95

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

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

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

Warning: The roughing pump oil can be contaminated with

biohazardous and/or toxic materials. Ensure that they are
correctly disposed of according to local environmental
regulations.

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

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

Caution: Observe these precautions to avoid oil leakage when

fitting the oil drain plug to the roughing pump:
• Ensure that the plug is not cross-threaded.
• Ensure that the O-ring is not pinched.
• Do not overtighten the plug.

4-96 Maintenance Procedures

10. Use the 8-mm Allen wrench to fit and tighten the roughing pump’s oil
drain plug.
Tip: When the oil drain plug is tightened, the plug seals with an O-ring.
Compression is controlled by the O-ring groove depth in the plug.
Increased torque does not improve the plug seal; it only makes the plug
difficult to remove later.

Caution: To maintain pump performance, use Anderol vacuum

oil, type GS 495.

11. Using the funnel, pour all the oil from the 1-L container into the oil filler
aperture.
12. Wait a few minutes, and then recheck the oil level.
13. Ensure that the O-ring on the oil filler plug is clean and properly seated.

Caution: Observe these precautions to avoid oil leakage when

fitting the oil filler plug to the roughing pump:
• Ensure that the plug is not cross-threaded.
• Ensure that the O-ring is not pinched.
• Do not over tighten the plug.

14. Use the 8-mm Allen wrench to refit the oil filler plug.
15. Start the instrument (see “Starting the instrument” on page 2-2).
16. Gas-ballast the roughing pump (see “Gas ballasting the roughing pump”
on page 4-16).
Tips: After you add oil to the pump, the following situations can occur:
• The oil level drops slightly during the first month of operation.
• The oil changes color (darkens) over time.
• After running the pump for 12 to 48 hours, it is common to see a few
drops of oil near the filler plug. Excess oil around the lip of the filler
plug will run down and drip off the pump once the pump reaches
operating temperature.
• When the pump begins to run at normal operating temperature,
spilled oil smells slightly.

Replacing the roughing pump oil 4-97

Replacing the roughing pump’s oil demister element
Replace the roughing pump’s oil demister element annually.
Note: This procedure is not required for an Alcatel oil-free roughing pump.
Required materials:
• Chemical-resistant, powder-free gloves
• 6-mm Allen wrench
• 10-mm wrench

To remove the roughing pump oil demister element

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

Warning: The pump oil can be contaminated with analyte

accumulated during normal operation. Always wear
chemical-resistant, powder-free gloves when replacing the
oil demister element.

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

with the roughing pump: it can be hot.

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

Securing bolt

Exhaust flange

TP02694

4-98 Maintenance Procedures

4. Using both hands, carefully remove the exhaust flange and oil demister
element from the roughing pump.
Oil demister element

TP02693

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

TP02686

Replacing the roughing pump’s oil demister element 4-99

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

TP02692

7. Remove the spring from the oil demister element.

Warning: The oil demister element can be contaminated

with biohazardous and/or toxic materials. Ensure that it is
correctly disposed of according to local environmental
regulations.

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

environmental regulations.

4-100 Maintenance Procedures

To fit the new oil demister element

Warning: The pump oil can be contaminated with analyte

accumulated during normal operation. Always wear
chemical-resistant, powder-free gloves when replacing the oil
demister element.

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

TP02682

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

Caution: The nut that secures the oil demister element to the
exhaust flange must not be overtightened; ensure that only
approximately 1 mm of thread is exposed beyond the nut when it
is tightened.

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

1 mm exposed thread
after tightening

TP02686

Replacing the roughing pump’s oil demister element 4-101

 4. Ensure that the inscription “TOP” is at the top of the oil demister
element, and, using both hands, carefully fit the oil demister element
and exhaust flange to the roughing pump.

Caution: The bolts securing the source exhaust flange to the

roughing pump must each be sequentially and incrementally
tightened until they are all fully tight.

5. Use the 6-mm Allen wrench to fit the 4 bolts securing the exhaust flange
to the roughing pump.
6. Start the instrument (see “Starting the instrument” on page 2-2).

4-102 Maintenance Procedures

5 Optional APCI Mode of
Operation
This chapter describes the optional atmospheric pressure chemical
ionization (APCI) mode of operation, which uses the IonSABRE APCI
source.
Contents

Topic Page
Atmospheric pressure chemical ionization 5-2
IonSABRE APCI probe 5-2
Installing the IonSABRE APCI probe 5-3
Installing the corona pin 5-5
Removing the corona pin 5-5
Removing the IonSABRE APCI probe 5-6

5-1
Atmospheric pressure chemical ionization
APCI, an option for the instrument, produces singly charged protonated or
deprotonated molecules for a broad range of nonvolatile analytes.
The APCI interface consists of the standard source fitted with a corona pin
and a heated IonSABRE APCI probe. Mobile phase from the ACQUITY UPLC
column enters the probe, where it is pneumatically converted to an aerosol,
rapidly heated, and vaporized or gasified at the probe tip.

APCI mode

IonSABRE APCI probe

Sample cone

Corona pin

Hot gas from the IonSABRE APCI probe passes between the sample cone and
the corona pin, which is typically operated with a discharge current of 5 µA.
Mobile phase molecules rapidly react with ions generated by the corona
discharge to produce stable reagent ions. Analyte molecules introduced into
the mobile phase react with the reagent ions at atmospheric pressure and
typically become protonated (in the positive ion mode) or deprotonated (in the
negative ion mode). The sample and reagent ions then pass through the
sample cone and into the mass spectrometer.

IonSABRE APCI probe

In the IonSABRE APCI probe, the nebulized gas plume expands in a directly
heated region with a larger internal diameter. The increased aerosol
expansion gives more efficient droplet evaporation than the standard ESI
probe. The nebulizer support gas controls the droplet residence times and
positively sweeps the sample from the probe, giving optimized probe
performance. The gas flow must be maintained at all times.

5-2 Optional APCI Mode of Operation

Installing the IonSABRE APCI probe
Required material: Chemical-resistant, powder-free gloves

To install the IonSABRE APCI probe

Warning: The ACQUITY UPLC system connections, IonSABRE

APCI probe, and source can be contaminated with biohazardous
and/or toxic materials. Always wear chemical-resistant,
powder-free gloves while performing this procedure.

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

suitably prepared before commencing this procedure.

1. Prepare the instrument for working on the source (see “Preparing the
instrument for work performed on the source” on page 4-8).

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

3. Ensure that the contacts on the IonSABRE APCI probe align with the
probe adjuster assembly contacts, and carefully slide the IonSABRE
APCI probe into the hole in the probe adjuster assembly.

Probe adjuster assembly IonSABRE APCI

probe

Probe adjuster
assembly contacts

TP02632

Installing the IonSABRE APCI probe 5-3

 4. Secure the IonSABRE APCI probe by tightening the 2 thumbscrews
shown in the following figure.

IonSABRE APCI probe mounted on the source enclosure, showing the

connections to the front panel
Vernier probe adjuster Thumbscrew

Nebulizer gas connection

Desolvation gas
connection
PO W ER O PER ATE

DESOLVATION NEBULIZER

HV
APCI probe APPI

electrical lead
PROBE

Probe adjuster
assembly electrical
lead (not connected
when using the
IonSABRE APCI
probe) RP00022

Probe adjuster assembly IonSABRE APCI probe

5. Connect the IonSABRE APCI probe’s PTFE tube to the nebulizer gas
connection.
6. At the instrument’s front panel, disconnect the probe adjuster
assembly’s electrical lead from the probe connection.
7. Connect the IonSABRE APCI probe’s electrical lead to the instrument’s
probe connection.

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

tubing to connect the diverter valve to the IonSABRE APCI
probe; use the PEEK™ tubing supplied with the instrument.

8. Using tubing of the appropriate internal diameter (ID), connect the

fluidics system’s diverter valve to the IonSABRE APCI probe.

5-4 Optional APCI Mode of Operation

 Tip: Two tubes of differing ID are supplied with the instrument.
Requirement: If you are replacing the tubing supplied with the
instrument, minimize the length of the tube connecting the diverter
valve to the IonSABRE APCI probe. Doing so minimizes delays and
dispersion.
9. Close the instrument’s access door.

Installing the corona pin

To install the corona pin

Refer to “Installing the corona pin” on page 3-5.

Removing the corona pin

To remove the corona pin

Refer to “Removing the corona pin” on page 3-7.

Installing the corona pin 5-5

Removing the IonSABRE APCI probe
Required material: Chemical-resistant, powder-free gloves

To remove the IonSABRE APCI probe

Warning: The ACQUITY UPLC system connections, IonSABRE

APCI probe, and source can be contaminated with biohazardous
and/or toxic materials. Always wear chemical-resistant,
powder-free gloves while performing this procedure.

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

suitably prepared before commencing this procedure.

1. Prepare the instrument for working on the source (see “Preparing the
instrument for work performed on the source” on page 4-8).

Warning: The source can be hot. To avoid burn injuries, take

great care while working with the instrument’s access door open.

2. Open the instrument’s access door.

3. Disconnect the diverter valve tubing from the IonSABRE APCI probe.
4. Disconnect the IonSABRE APCI probe’s electrical lead from the
instrument’s probe connection.
5. Disconnect the IonSABRE APCI probe’s PTFE tube from the nebulizer
gas connection.
6. Undo the 2 thumbscrews securing the probe to the probe adjuster
assembly.
7. Carefully remove the probe from the probe adjuster assembly.
8. Close the instrument’s access door.

5-6 Optional APCI Mode of Operation

A Safety Advisories

Waters instruments display hazard symbols designed to alert you to the

hidden dangers of operating and maintaining the instruments. Their
corresponding user guides also include the hazard symbols, with
accompanying text statements describing the hazards and telling you
how to avoid them. This appendix presents all the safety symbols and
statements that apply to the entire line of Waters products.

Contents

Topic Page
Warning symbols A-2
Caution symbol A-5
Warnings that apply to all Waters instruments A-5
Electrical and handling symbols A-11

A-1
Warning symbols
Warning symbols alert you to the risk of death, injury, or seriously adverse
physiological reactions associated with an instrument’s use or misuse. Heed
all warnings when you install, repair, and operate Waters instruments.
Waters assumes no liability for the failure of those who install, repair, or
operate its instruments to comply with any safety precaution.

Task-specific hazard warnings

The following warning symbols alert you to risks that can arise when you
operate or maintain an instrument or instrument component. Such risks
include burn injuries, electric shocks, ultraviolet radiation exposures, and
others.
When the following symbols appear in a manual’s narratives or procedures,
their accompanying text identifies the specific risk and explains how to avoid
it.

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

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

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

Warning: (Risk of electric shock.)

Warning: (Risk of fire.)

Warning: (Risk of needle puncture.)

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

Warning: (Risk of exposure to ultraviolet radiation.)

Warning: (Risk of contacting corrosive substances.)

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

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

A-2 Safety Advisories

 Warning: (Risk of exposure to biological agents that can pose a serious
health threat.)

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

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

Warning: Pressurized nonmetallic, or polymer, tubing can burst.

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

Mass spectrometer flammable solvents warning

This warning applies to instruments operated with flammable solvents.

Warning: Where significant quantities of flammable solvents are

involved, a continuous flow of nitrogen into the ion source is required
to prevent possible ignition in that enclosed space.
Ensure that the nitrogen supply pressure never falls below 690 kPa
(6.9 bar, 100 psi) during an analysis in which flammable solvents are
used. Also ensure a gas-fail connection is connected to the LC system
so that the LC solvent flow stops if the nitrogen supply fails.

Warning symbols A-3

 Mass spectrometer shock hazard
This warning applies to all Waters mass spectrometers.

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

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

This warning applies to certain instruments when they are in Operate mode.

Warning: High voltages can be present at certain external surfaces of

the mass spectrometer when the instrument is in Operate mode. To
avoid non-lethal electric shock, make sure the instrument is in
Standby mode before touching areas marked with this high voltage
warning symbol.

Biohazard warning
This warning applies to Waters instruments that can be used to process
material that might contain biohazards: substances that contain biological
agents capable of producing harmful effects in humans.

Warning: Waters's instruments and software can be used to analyze or

process potentially infectious human-sourced products, inactivated
microorganisms, and other biological materials. To avoid infection with
these agents, assume that all biological fluids are infectious, observe
Good Laboratory Practices and, consult your organization’s biohazard
safety representative regarding their proper use and handling. Specific
precautions appear in the latest edition of the US National Institutes
of Health (NIH) publication, Biosafety in Microbiological and
Biomedical Laboratories (BMBL).

A-4 Safety Advisories

 Chemical hazard warning
This warning applies to Waters instruments that can process corrosive, toxic,
flammable, or other types of hazardous material.

Warning: Waters instruments can be used to analyze or

process potentially hazardous substances. To avoid injury
with any of these materials, familiarize yourself with the
materials and their hazards, observe Good Laboratory
Practices (GLP), and consult your organization’s safety
representative regarding proper use and handling.
Guidelines are provided in the latest edition of the National
Research Council's publication, Prudent Practices in the
Laboratory: Handling and Disposal of Chemicals.

Caution symbol
The caution symbol signifies that an instrument’s use or misuse can damage
the instrument or compromise a sample’s integrity. The following symbol and
its associated statement are typical of the kind that alert you to the risk of
damaging the instrument or sample.

Caution: To avoid damage, do not use abrasives or solvents to clean the

instrument’s case.

Warnings that apply to all Waters instruments

When operating this device, follow standard quality control procedures and
the equipment guidelines in this section.

Caution symbol A-5

 Attention: Changes or modifications to this unit not expressly approved by the
party responsible for compliance could void the user’s authority to operate the
equipment.

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

Achtung: Jedwede Änderungen oder Modifikationen an dem Gerät ohne die

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

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

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

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

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

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

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

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

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

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

A-6 Safety Advisories

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

Warnings that apply to all Waters instruments A-7

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

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

A-8 Safety Advisories

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

경고: 가압 폴리머 튜브로 작업할 경우에는 주의하십시오.

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

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

Warnings that apply to all Waters instruments A-9

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

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

Vorsicht: Der Benutzer wird darauf aufmerksam gemacht, dass bei

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

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

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

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

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

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

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

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

제대로 작동하지 않을 수 있다는 점을 사용자에게 반드시 인식시켜야 합니다.

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

A-10 Safety Advisories

Electrical and handling symbols

Electrical symbols
These can appear in instrument user manuals and on the instrument’s front
or rear panels.

Electrical power on

Electrical power off

Standby

Direct current

Alternating current

Protective conductor terminal

Frame, or chassis, terminal

Fuse

Recycle symbol: Do not dispose in municipal waste.

Electrical and handling symbols A-11

Handling symbols
These handling symbols and their associated text can appear on labels affixed
to the outer packaging of Waters instrument and component shipments.

Keep upright!

Keep dry!

Fragile!

Use no hooks!

A-12 Safety Advisories

B External Connections

This appendix describes the instrument’s external connections.

Warning: The instrument is heavy. To avoid injury, Waters

recommends that the instrument be lifted using suitable
machinery and the supplied harness.

Caution:
• Contact Waters Technical Service before moving the
instrument.
• If you must transport the instrument, or remove it from
service, contact Waters Technical Service for recommended
cleaning, flushing, and packaging procedures.
See “Troubleshooting with Connections Insight” on page 4-5.

Contents

Topic Page
External wiring and vacuum connections B-2
Connecting the oil-filled roughing pump B-3
Connecting the oil-free roughing pump B-10
Connecting to the nitrogen gas supply B-18
Connecting the nitrogen exhaust line B-20
Connecting the liquid waste line B-23
Connecting the workstation B-25
Connecting Ethernet cables B-26
I/O signal connectors B-26
Connecting to the electricity source B-31

B-1
External wiring and vacuum connections
Rear panel connections appear in the figure below.

Rear panel

!
Event inputs
and outputs
RS 232

1 1
Analog O ut InjectS tart In
2 2
3 G round 3 G round
4 4
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9

Shielded
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

Power cord V ~ 200 - 240 !

Hz 50 - 60
VA 900 Ethernet
PUMP
API Gas
6.9 Bar Maximum
Roughing pump
Nitrogen inlet relay switch
VACUUM
SOURCE VENT

Source vent
VACUUM

Turbo vacuum 01757 U.S.A.

Source
vacuum

RP00001

B-2 External Connections

Connecting the oil-filled roughing pump
Note: To connect the alternative dry roughing pump, see “Connecting the
oil-free roughing pump” on page B-10.

Exhaust port flange

Oil filler plug

Oil-level sight glass

TP02689
Drain plug

Gas ballast valve

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

Connecting the oil-filled roughing pump B-3

 To connect the roughing pump

Warning: The pump and its connections can be

contaminated with biohazardous and/or toxic materials.
Always wear chemical-resistant, powder-free gloves when
performing this procedure.

Caution:
• To ensure correct operation of the roughing pump, the pump
must be installed within 1 degree of horizontal.
• The area where the roughing pump is located must have an
ambient temperature of 15 to 40 ºC (59 to 104 ºF).
• To ensure proper ventilation, the pump must be installed with
the following minimum clearances:

Left side minimum clearance Back side minimum clearance

is 15.24 cm (6 inches) is 15.24 cm (6 inches)

TP02689

Front side minimum clearance Right side minimum clearance

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

Requirement: The pump must be oriented in a way that allows easy

daily access to the gas ballast valve and oil-level sight glass.
1. Place the PTFE drip tray on the floor, within 5 feet of the instrument.

Warning: The roughing pump is heavy. To avoid injury, at least

two people must lift the pump.

2. Place the pump on the PTFE drip tray.

B-4 External Connections

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

1-inch ID
vacuum hose

Clamps

Flange

NW25 tee

Pump inlet

TP02625

4. Attach the flanged end of a length of 1-inch ID vacuum hose to each open
port on the NW25 tee. Use the NW25 center rings and clamps provided
in the startup kit. Use the 7-mm nut driver to install the clamps.
5. Connect the opposite ends of the two lengths of vacuum hose in step 4 to
the two, 1-inch OD, straight, vacuum ports on the instrument’s rear
panel. Secure the hose ends with clamps supplied in the startup kit;
install 2 clamps on each hose end.

Connecting the oil-filled roughing pump B-5

 Caution:
• To prevent condensation from forming in the exhaust tubing
between the roughing pump and the exhaust trap bottle, you
must minimize the length of the tube.
• To avoid gas leaks, use the sharp knife to cut the PVC exhaust
tubing squarely (that is, perpendicular to its horizontal axis).

6. Connect an approximately 36.4-cm (2.5-inch) length of 12.7-mm clear

PVC exhaust tubing to the roughing pump exhaust port NW25 nozzle
fitting. Secure the tubing with a hose clamp.

Caution: To prevent condensation from draining backward and

damaging the pump, the exhaust tubing must be installed with
an exhaust trap bottle; the bottle must be positioned at or below
the roughing pump exhaust port.

7. Connect an elbow to the other end of the PVC exhaust tubing, and
connect the elbow to one of the fittings on the exhaust trap bottle
(included in the startup kit).

Exhaust port

Elbow

Exhaust trap bottle

TP02800

B-6 External Connections

 Caution: To avoid gas leaks, use the sharp knife to cut the PVC
exhaust tubing squarely (that is, perpendicular to its horizontal
axis).

8. Connect a length of 12.7-mm clear PVC exhaust tubing to an elbow and

connect the elbow to the other fitting on the exhaust trap bottle. The exit
line of the exhaust trap bottle can be at any elevation.
9. Secure the exhaust trap bottle in a conspicuous location.

Caution: The instrument requires two separate exhaust systems:

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

10. Route the open end of the exhaust tubing to a suitable exhaust vent.
11. Check the oil level in the pump.

Caution: To ensure correct operation of the roughing pump, do

not operate the pump with the oil level at less than 30% of the
MAX level.

See “Checking the roughing pump oil level” on page 4-19, and, if needed,
“Adding oil to the roughing pump” on page 4-19.
12. Make the electrical connections to the roughing pump.
• If your roughing pump has an external relay box, see “Making the
electrical connections for a roughing pump with an external relay
box” on page B-8.
• If your roughing pump does not have an external relay box, see
“Making the electrical connections for a roughing pump without an
external relay box” on page B-9.

Connecting the oil-filled roughing pump B-7

Making the electrical connections for a roughing pump with an
external relay box
Roughing pump connections with an external relay box

Instrument rear panel

RS 232

Roughing pump main 1

2
3
Analog

G round
O ut
1
2
3
InjectS tart

G round
In

4 4

power connector
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

!
IVD
V ~ 200 - 240
Hz 50 - 60
VA 900

PUMP
API Gas
6.9 Bar Maximum

VACUUM
SOURCE VENT

VACUUM

01757 U.S.A.

Relay box
RP00013

To power source

B-8 External Connections

 To make the electrical connections for a roughing pump with an external
relay box
1. Connect the power cable from the roughing pump relay box connector to
the relay box.
2. Connect the relay cable from the relay box to the pump connector on the
instrument’s rear panel.
3. Connect the relay box power connector to the main power source.

Making the electrical connections for a roughing pump without an

external relay box
Roughing pump connections without an external relay box

Instrument rear panel

Roughing pump d.c. connector

!

RS 232

Roughing pump main 1

2
3
Analog

G round
O ut
1
2
3
InjectS tart

G round
In

power connector
4 4
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

!
IVD
V ~ 200 - 240
Hz 50 - 60
VA 900

PUMP
API Gas
6.9 Bar Maximum

VACUUM
SOURCE VENT

VACUUM

01757 U.S.A.
RP00015

To power
source

Connecting the oil-filled roughing pump B-9

 To make the electrical connections for a roughing pump without an external
relay box
1. Connect the roughing pump power cord to the main power source.
2. Connect the relay cable from the roughing pump d.c. connector to the
pump connector on the instrument’s rear panel.

Connecting the oil-free roughing pump

The oil-free roughing pump is an optional alternative to the standard oil-filled
roughing pump. To connect the oil-filled roughing pump, see “Connecting the
oil-filled roughing pump” on page B-3.
The noise reduction cover must be installed over the pump to minimize
operating noise, unless the pump is installed in a cabinet that includes sound
dampening and ventilation.

Exhaust port
Noise reduction
flange
cover
Inlet flange

TP02995

Required materials:
• Chemical-resistant, powder-free gloves
• 7-mm nut driver
• 8-mm Allen wrench

B-10 External Connections

 • Sharp knife
• 1-L exhaust trap bottle (included in the startup kit)
• Elbows (included in the Waters Rough Pump Connect Kit)
• NW25 tee (included in the startup kit)
• NW25 center rings (included in the startup kit)
• NW25 clamps (included in the startup kit)
• NW25 full nipple (included in the Alcatel pump kit)
• DN25 reducing nipple (included in the Alcatel pump kit)
• NW40 center rings (included in the Alcatel pump kit)
• NW40 clamps (included in the Alcatel pump kit)
• DN40 full nipple flange (included in the Alcatel pump kit)
• PVC exhaust tubing (included in the Waters Rough Pump Connect Kit)
• PVC hose clamps (included in the Waters Rough Pump Connect Kit)
• 1-inch ID vacuum hose (included in the Waters Rough Pump Connect
Kit)
• Isolation valve (included in the Alcatel pump kit)
• External silencer (included in the Alcatel pump kit)
• Noise reduction cover (included in the Alcatel pump kit)

To install the noise reduction cover

1. Remove the clamp and blank flange from the pump inlet.
2. Attach the DN40 nipple to the top of the inlet filter and o-ring assembly
and then secure the connection with a clamp.
3. Attach the DN25 nipple to the outlet fitting and secure the connection
with a clamp.
4. Connect the gray pump control cable to the rear of the pump.

Connecting the oil-free roughing pump B-11

 5. Connect the power cord to the rear of the pump.
6. Install the noise reduction cover.

DN 25 nipple

DN 40 nipple

Clamps

TP02996

B-12 External Connections

To connect the oil-free roughing pump

Warning: The pump and its connections can be

contaminated with biohazardous and/or toxic materials.
Always wear chemical-resistant, powder-free gloves when
performing this procedure.

Caution:
• To ensure correct operation of the roughing pump, the pump
must be installed within 1 degree of horizontal.
• The area where the roughing pump is located must have an
ambient temperature of 15 to 40 ºC (59 to 104 ºF).
• To ensure proper ventilation, the pump must be installed with
the following minimum clearances:

Left side minimum clearance Back side minimum clearance

is 15.24 cm (6 inches) is 15.24 cm (6 inches)

TP02995

Front side minimum clearance Right side minimum clearance

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

Warning: The roughing pump is heavy. To avoid injury, at least

two people must lift the pump.

Connecting the oil-free roughing pump B-13

 1. Place the pump on the floor, within 1.5 m (5 feet) of the instrument.
2. Attach the isolation valve, NW25 tee, and elbows to the DN40 nipple on
the pump inlet, and then secure these connections with clamps, as
shown in the figure below.

NW25 tee

Elbow
1-inch ID
vacuum hose
Isolation valve

DN40 nipple
on pump inlet

TP02997

3. Attach the flanged end of a length of 1-inch ID vacuum hose to each open
port on the NW25 tee.
Tip: Use the NW25 center rings and clamps provided in the startup kit.
Use the 7-mm nut driver to install the clamps.
4. Connect the opposite ends of the two lengths of vacuum hose in step 3 to
the two, 1-inch OD, straight, vacuum ports on the instrument’s rear

B-14 External Connections

 panel. Secure the hose ends by installing 2 clamps supplied in the
startup kit on each hose end.

Caution:
• To prevent condensation from forming in the exhaust tubing
between the roughing pump and the exhaust trap bottle, you
must minimize the length of the tube.
• To avoid gas leaks, use the sharp knife to cut the PVC exhaust
tubing squarely (that is, perpendicular to its horizontal axis).

5. Attach the DN25 elbow to the DN25 nipple on the pump exhaust outlet
and secure the connection with a clamp.
6. Install the external silencer, with the arrow pointing toward the pump,
to the open port of the DN25 elbow, and then secure the connection with
a clamp.
7. Attach the DN25 reducing nipple to the outlet of the external silencer
and secure the connection with a clamp.
8. Connect an approximately 300 mm (12 inch) length of 12.7-mm clear
PVC exhaust tubing to the DN25 reducing nipple, securing the tubing
with a hose clamp.

Caution: To prevent condensation from draining backward and

damaging the pump, the exhaust tubing must be installed with
an exhaust trap bottle; the bottle must be positioned at or below
the roughing pump exhaust port.

9. Connect an elbow to the other end of the PVC exhaust tubing, and
connect the elbow to one of the fittings on the exhaust trap bottle
(included in the startup kit).

Connecting the oil-free roughing pump B-15

 External silencer

Exhaust port

TP02997
Elbow

Exhaust trap bottle

TP02800

TP02996

Caution: To avoid gas leaks, use the sharp knife to cut the PVC
exhaust tubing squarely (that is, perpendicular to its horizontal
axis).

10. Connect a length of 12.7-mm clear PVC exhaust tubing to an elbow and
connect the elbow to the other fitting on the exhaust trap bottle. The exit
line of the exhaust trap bottle can be at any elevation.
11. Secure the exhaust trap bottle in a conspicuous location.
12. Route the open end of the exhaust tubing to a suitable exhaust vent.
13. Make the electrical connections to the roughing pump.

B-16 External Connections

Making the electrical connections for an oil-free roughing pump
Roughing pump connections

Instrument rear panel

RS 232

1 1
Analog O ut InjectS tart In
2 2
3 G round 3 G round
4 4
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

!
IVD
V ~ 200 - 240
Hz 50 - 60
VA 900

Roughing pump PUMP

control cable API Gas

6.9 Bar Maximum

VACUUM
SOURCE VENT

VACUUM

01757 U.S.A.

To power source
RP00014

To make the electrical connections for a oil-free roughing pump

1. Route the cables through the opening in the rear of the noise reduction
cover.
2. Connect the gray pump control cable to the pump connector on the
instrument’s rear panel.
3. Connect the power cable and power-on the instrument.

Connecting the oil-free roughing pump B-17

Connecting to the nitrogen gas supply
Required materials:
• Chemical-resistant, powder-free gloves
• Sharp knife
• Wrench
• 6-mm PTFE tubing (included in the Waters Rough Pump Connect Kit)

To connect the nitrogen gas supply

Caution: To avoid gas leaks, use the sharp knife to cut the PTFE
tubing squarely (that is, perpendicular to its horizontal axis).

1. Use the sharp knife to cut a 3.8 to 5.0-cm (1.5 to 2-inch) length of 6-mm
PTFE tubing.
2. Connect this piece of tubing to one end of the nitrogen supply in-line
filter.
3. Connect the remaining length of the 6-mm PTFE tubing to the other end
of the filter.
4. Connect the free end of the short piece of 6-mm PTFE tubing to the
nitrogen inlet port on the rear of the instrument.

B-18 External Connections

 Gas and exhaust connections

RS 232

1 1
Analog O ut InjectS tart In
2 2
3 G round 3 G round
4 4
N otused Event In
5
6
Stop Flow O ut
5
6
Sw itch 3 O ut
ETHERNET
7 7
ACN 065444751 8 G round 8 G round
9 9
Sw itch 2 O ut Sw itch 4 O ut
10 10
Serial Number

V ~ 200 - 240
Hz 50 - 60
!
VA 900

PUMP
API Gas
6.9 Bar Maximum

Nitrogen inlet
VACUUM
SOURCE VENT

Source vent
VACUUM

Turbo vacuum 01757 U.S.A.

Source
vacuum

RP00001

5. Attach a nitrogen regulator (not provided) to the nitrogen supply.

6. Install the 6-mm stud into the regulator outlet.

7. Connect the free end of the long piece of 6-mm PTFE tubing to the 6-mm
stud.

Connecting to the nitrogen gas supply B-19

Connecting the nitrogen exhaust line
Required materials:
• Chemical-resistant, powder-free gloves
• Sharp knife
• 10-mm and 12-mm PTFE tubing (included in the Waters Rough Pump
Connect Kit)
• snoop® (or equivalent) leak detector liquid

To connect the nitrogen exhaust line

Warning:
• LC solvents and analytes can be carried in the nitrogen
exhaust, which must be vented via the nitrogen exhaust trap
bottle and laboratory exhaust system. The laboratory exhaust
system must provide a minimum vacuum of 0.20 kPa (2 mbar,
0.03 psi) below atmospheric pressure (negative pressure).
• The exhaust connections can be contaminated with
biohazardous and/or toxic materials. Always wear
chemical-resistant, powder-free gloves when performing this
procedure.
• To avoid the buildup of hazardous gases, do not place the
nitrogen exhaust trap bottle in an enclosed cabinet.

Caution: The instrument requires two separate exhaust systems: one

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

1. Locate the exhaust trap bottle in an accessible area below the

instrument. See the figure “Exhaust trap bottle” on page B-22.

Caution: To avoid gas leaks, use the sharp knife to cut the PTFE
tubing squarely (that is, perpendicular to its horizontal axis).

2. Cut a length of 12-mm tubing long enough to connect the instrument to

the exhaust trap bottle.

B-20 External Connections

3. Connect one end of the tubing to the exhaust port on the rear panel.
Connect the other end to one of two ports on the exhaust trap bottle.

Caution: To avoid gas leaks, use the sharp knife to cut the PTFE
tubing squarely (that is, perpendicular to its horizontal axis).

4. Cut a second length of 10-mm tubing long enough to connect the exhaust
trap bottle to the exhaust vent.
5. Insert one end of the tubing into the remaining port on the exhaust trap
bottle. Route the other end to the exhaust vent.

Warning: To confirm the integrity of the source exhaust

system, the following leak test must be performed.

Caution: To avoid damage to the instrument, snoop (or its

equivalent) leak detector liquid must be used only for the
purpose described in the following step. It must not be used on
any other part of the instrument.

6. Use snoop (or equivalent) leak detector liquid to ensure that there are no
leaks at the instrument exhaust and laboratory exhaust system line
connections.

Connecting the nitrogen exhaust line B-21

 Exhaust trap bottle

To laboratory
exhaust port
From instrument (10-mm OD)
exhaust connection
(12-mm OD)

B-22 External Connections

Connecting the liquid waste line
Required material: Chemical-resistant, powder-free gloves

To connect the liquid waste line

Warning: The waste line and connection can be contaminated

with biologically hazardous materials. Always wear
chemical-resistant, powder-free gloves while performing this
procedure.

1. Place a suitable waste container below the instrument.

Caution: To avoid distorting the drip tray or causing the drain

cup to leak, restrain the drain cup when attaching or removing
the waste line.

2. Slide a drain line over the barbed fitting of the drain (located at the
bottom of the instrument).

Drain cup

Barbed fitting

TP02684

Drain line

Connecting the liquid waste line B-23

 Warning: To prevent leakage of biologically hazardous
materials, ensure that the
• drain line does not crimp or bend. A crimp or bend can
impede flow to the waste container.
• waste container is emptied before the lower end of the
drain tube is covered by waste solvent.

3. Route the waste line to the waste container. If necessary, shorten the
waste tube so that its end is above the surface of the waste solvent.

Positioning of drain tube

Correct Incorrect
TP01807

B-24 External Connections

Connecting the workstation
Before connecting the workstation to the instrument, set up the workstation
according to its accompanying instructions. Locate the workstation within
5 meters (16 feet) of the instrument.
Requirement: Shielded network cables must be used with the instrument to
ensure compliance with FCC, and other, limits.

To connect the workstation

1. Connect the monitor to the PC.
2. Connect one end of the shielded network cable to the appropriate port on
the rear panel of the instrument.
3. Connect the other end of the shielded network cable to the port labeled
instrument LAN on the workstation rear panel.

To connect the instrument to the power source

Caution: Do not connect the instrument’s power supply cord until you
complete the installation procedures in the previous sections.

1. Select the correct power cord for your location.

2. Connect the female end of the power cord to the power port on the rear
panel of the instrument.

Connecting the workstation B-25

Connecting Ethernet cables
Requirement: Shielded Ethernet cables must be used with the instrument to
ensure compliance with FCC, and other, limits.

To make Ethernet connections

1. Connect one end of one shielded Ethernet cable to the network switch,
and then connect the other end to the Ethernet card on the
preconfigured ACQUITY™ workstation.
Tip: On preconfigured systems, the Ethernet card is identified as the
Instrument LAN card.
2. Connect one end of the other shielded Ethernet cable to the back of the
instrument, and then connect the other end to the network switch.

I/O signal connectors

Warning: To avoid electric shock, all electrical connections to the rear
panel must be separated from hazardous voltages by double or
reinforced insulation. Circuits of this type are classified as safety extra
low voltage (SELV). Examples of circuits that are typically SELV
include contact closure inputs and outputs for auto-samplers, and UV,
RI, and fluorescence detector signal outputs for LC/MS systems. The
electrical connections on the rear panel of this mass spectrometer are
all SELV.
To avoid electric shock and damage to the instrument, do not apply
more than
• ±30 V d.c. to the Analog (Out) connection.
• 30 V d.c. to the Stop Flow (Out), Inject Start (In), Switch 2 (Out),
Switch 3 (Out), and Switch 4 (Out) connections.

The instrument’s rear panel includes two removable connectors that hold the
screw terminals for I/O signals. These connectors are keyed so that they can
receive a signal cable inserted only one way.

B-26 External Connections

I/O signal connectors

Connector I Connector II

1  Analog (Out) 1  Inject Start (In)

2  Analog (Out) 2  Inject Start (In)
3 Ground 3 Ground
4 Not Used 4  Event (In)
5 Not Used 5  Event (In)
6 Stop Flow (Out) 6  Switch 3 (Out)
7 Stop Flow (Out) 7  Switch 3 (Out)
8 Ground 8 Ground
9 Switch 2 (Out) 9  Switch 4 (Out)
10 Switch 2 (Out) 10  Switch 4 (Out)

I/O signal connectors B-27

Signal connections
Instrument analog-out/event-in connections

Signal connections Description

Analog (Out) Used for analog chart output functionality. The
output voltage range is 0 to 2 V. The resolution of
the voltage output is 12 bits.
Stop Flow (Out) Used to stop the solvent flow if the nitrogen gas
supply fails. Maximum 30 V, 0.5 A, 10 W.
Inject Start (In) Signals the start of an injection. Maximum 30 V.
Event (In) Allows an external device to start data acquisition.
Maximum 30 V.
Switch 2 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.
Switch 3 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.
Switch 4 (Out) Used to send time-based contact closure signals to
external devices. Maximum 30 V, 0.5 A, 10 W.

Requirement: To meet the regulatory requirements of immunity from

external electrical disturbances, you must install connection covers over the
signal connectors.

B-28 External Connections

To make signal connections
1. Reference the signal connection location from the silk-screened label for
inject start or any other input/output connection you plan to use from
Connector I or II on the rear panel of each instrument.
2. To make the signal connections, attach the positive and negative leads of
the signal cable to the connector.

Connector

Signal cable

TP02585

3. Slide the clamp (with the bend facing down) into the protective shield.
4. Insert the clamp and shield (with the bend facing down) into the
connection cover, and loosely tighten with one self-tapping screw.

Clamp

Shield

Connection cover
TP02586

I/O signal connectors B-29

 5. Insert the connector with the signal cable into the connection cover, and
position the clamp over the cable leads. Tighten the clamp into place
with the second self-tapping screw.

Cable leads

Clamp

TP02587

6. Place the second connection cover over the first cover, and snap it into
place.

Signal connector

Connection cover

TP02588

B-30 External Connections

Connecting to the electricity source
The instrument requires a separate, grounded electricity source. The ground
connection in the electrical outlet must be common and connected near the
system.

To connect to the electricity source

Recommendation: Use a line conditioner or an uninterruptible power supply
(UPS) for optimum long-term input voltage stability.

Warning: To avoid electrical shock, use the SVT-type power cord in the
United States and HAR-type (or better) in Europe. For information
regarding what cord to use in other countries, contact your local
Waters distributor.

1. Connect the female end of the power cord to the receptacle on the rear
panel of the instrument.
2. Connect the male end of the instrument power cord to a suitable 200 to
240 V AC wall outlet.
3. Connect the power cord from the roughing pump relay box to a 200 to
240 V AC wall outlet.
The system software controls electrical power to the pump.

Connecting to the electricity source B-31

B-32 External Connections
C Materials of Construction and
Compliant Solvents

Warning: To confirm the integrity of the source exhaust

system, you must address any safety issues raised by the
contents of this Appendix.

Contents

Topic Page
Preventing contamination C-2
Items exposed to solvent C-2
Solvents used to prepare mobile phases C-3

C-1
Preventing contamination
For information on preventing contamination, refer to Controlling
Contamination in LC/MS Systems (part number 715001307). You can find
this document on http://www.waters.com; click Services and Support and then
Support Center.

Items exposed to solvent

The items that appear in the following table can be exposed to solvent. You
must evaluate the safety issues if the solvents used in your application differ
from the solvents normally used with these items. See “Solvents used to
prepare mobile phases” on page C-3 for details about the most common
ingredients used to prepare mobile phases.

Items exposed to solvent

Item Material
Autotune reservoirs High-density polyethylene
Corona discharge pin mounting PEEK™
contact
Gas exhaust port Aluminium
Gas tubes Fluorinated ethylene propylene
Ion block Stainless steel
Ion block support PEEK
Isolation valve Gold-plated aluminium/bronze
O-rings ®
Viton or PTFE-encapsulated Viton
Probe adjuster bellows PTFE/Viton
Probe adjuster assembly Anodized aluminium, glass filled
acetal, and stainless steel
Probe shaft PEEK
Push-in gas fittings Nickel/brass
Solvent waste/leak management Tygon tubing
Source enclosure Alochromed aluminium
Source enclosure view port Toughened plate glass

C-2 Materials of Construction and Compliant Solvents

 Items exposed to solvent

Item Material
Trap bottle Polypropylene
Trap bottle push-in fittings Nitrile butadiene rubber, stainless
steel, polybutylene terephthalate,
and polyoxymethylene

Solvents used to prepare mobile phases

These solvents are the most common ingredients used to prepare mobile
phases for reverse-phase LC/MS (API):
• Water
• Methanol
• Acetonitrile
• Formic acid (<0.1%)
• Acetic acid (<0.1%)
• Trifluoroacetic acid (<0.1%)
• Ammonium acetate (<10 mM)
• Ammonium formate (<10 mM)
These solvents are not expected to cause any problems with the materials
identified in “Items exposed to solvent” on page C-2.

Solvents used to prepare mobile phases C-3

C-4 Materials of Construction and Compliant Solvents
D Preparing Samples for LC/MS
System Check with Empower
software
This appendix describes the procedure for preparing a sulfadimethoxine
standard for use with the LC/MS System Check projects supplied for
Empower software.
Contents:

Topic Page
Assembling required materials D-2
Preparing the sulfadimethoxine standard D-2
Storing the solutions D-3
Using the solution in an LC/MS System Check run D-3

D-1
Assembling required materials
You must assemble the following materials before starting to prepare your
sample:
• Solution kit containing 1 mg/mL sulfadimethoxine stock in methanol.
This solution kit is provided with your instrument.
• 1 L of solvent made up of 90:10 water/acetonitrile plus 0.1% formic acid
(v/v).
• Clean class A volumetric flasks: 100-mL (2), 10-mL.
• Clean class A pipettes (TD), 1-mL (3).
• PTFE-sealed screw-top amber sample bottles (glass or Nalgene™):
125-mL (2), 15-mL (2).
• Sample vial, 2-mL.

Preparing the sulfadimethoxine standard

The target mass of sulfadimethoxine on the ACQUITY UPLC column is
100 pg. Because the supplied LC/MS System Check methods specify an
injection volume of 5 µL, you must prepare a 20 pg/µL sulfadimethoxine
solution.

To dilute the stock solutions to the final standard concentration:

1. Pour 1 mL of the stock solution into one of the 100-mL volumetric flasks.
2. Dilute to the 100 mL mark with solvent.
Result: The flask contains a 10 ng/µL sulfadimethoxine solution.
3. Into a second 100-mL volumetric flask, pour 1 mL of the solution created
in step 2.
4. Dilute to the 100 mL mark with solvent.
Result: The flask contains a 100 pg/µL sulfadimethoxine solution.

D-2 Preparing Samples for LC/MS System Check with Empower software
 5. Into the 10-mL volumetric flask, pour 2 mL of the solution created in
step 4.
6. Dilute to the 10 mL mark with solvent.
Result: The flask contains the 20 pg/µL sulfadimethoxine standard
solution.

Storing the solutions

Store each of the solutions in an appropriate container. Waters recommends
using the following sample bottles:
• For the stock solution, a 15-mL sample bottle.
• For the 10 ng/µL solution, a 125-mL sample bottle.
• For the 100 pg/µL solution, a 125-mL sample bottle.
• For the final sulfadimethoxine standard solution, a 15-mL sample
bottle.

Using the solution in an LC/MS System Check run

The final sulfadimethoxine standard solution is ready for use in an LC/MS
System Check run with the Empower software.

To use the solution in an LC/MS System Check run:

1. Pour 1 mL of the sulfadimethoxine standard solution into the 2-mL
sample vial.
2. Place the vial in position 2:A,7 in the ACQUITY Sample Manager.
3. Run LC/MS System Check, as described in the instrument’s online Help.

Storing the solutions D-3

D-4 Preparing Samples for LC/MS System Check with Empower software
Index
A chemical hazard warning A-5
ACQUITY SQD UPLC/MS system 1-4 cleaning
ACQUITY UPLC air filter
Console 1-6 behind source probe 4-92
system components 1-4 inside lower bezel 4-90
air filter APCI probe tip 4-3, 4-62
cleaning corona pin 4-4, 4-70
behind source probe 4-92 ESI probe tip 4-3, 4-54
inside lower bezel 4-90 extraction cone 4-31
replacing gas cone 4-21, 4-25
behind source probe 4-94 hexapole assembly 4-47, 4-49
inside lower bezel 4-91 instrument case 4-3, 4-12
analog signal connection B-28 ion block 4-31
APCI 1-8, 5-2 isolation valve 4-31
APCI probe sample cone 4-21, 4-25
cleaning tip 4-3, 4-62 source components 4-3, 4-21
installing 5-2 source hexapole assembly 4-49
replacing capillary 4-4, 4-62 clearances, roughing pump B-4, B-13
replacing heater 4-4, 4-71 closing source isolation valve 4-9
APPI 1-8 combined position, of fluidics system
assembling diverter valve 2-10
cone gas assembly 4-28 comments iii
probe adjuster 4-87 compliant solvents C-1
source enclosure 4-87 cone gas assembly
source ion block assembly 4-42 assembling 4-28
disassembling 4-24
B handling guidelines 4-28
biohazard warning A-4 connecting
burst warning A-3 electricity source B-31
Ethernet B-26
C
exhaust trap bottle B-7, B-16
cables, network B-25
liquid waste line B-23
calibrating 2-4
nitrogen exhaust B-20
calibration, guidelines ix
nitrogen supply B-18
caution symbol A-5
NW25 tee B-5, B-14
checking, roughing pump oil level 4-3,
relay box B-9
4-19, 4-97

Index-1
 roughing pump B-3, B-10 vacuum connections B-2
signal connections B-29 verifying state of 2-4
vacuum B-2 disassembling
workstation B-25 cone gas assembly 4-24
Connections Insight, troubleshooting ion block assembly 4-33
with 4-5 probe adjuster 4-82
console, Waters Instrument 1-6 source enclosure 4-82
construction materials C-1 diverter valve positions 2-8
contamination, preventing C-2 door glass, tightening guidelines 4-86
corona pin drain tube positioning B-24
cleaning 4-4, 4-70 drip tray, installing 2-6
installing 3-6
mounting contact blanking plug E
installing 3-9 electrical symbols A-11
removing 3-5 electricity source, connecting B-31
removing 3-7 electrospray ionization 1-7
replacing 4-4, 4-70 emergency shutdown 2-12
covers, for signal connectors B-28 emptying
customer comments iii exhaust trap bottle 4-3, 4-12
liquid trap bottle 4-3, 4-14
D equipment guidelines viii, 5
demister element, replacing 4-4, 4-98 error messages, viewing 2-4
detector ESCi 1-7
calibrating 2-4 ESI
compliant solvents C-1 optimizing probe for ESCi 3-7
external wiring B-2 ESI probe
flow rates 2-5 capillary, replacing 4-3, 4-55
I/O signal connectors B-26 installing 3-2
materials of construction C-1 removing 3-9
operate LED 2-5 tip
power LED 2-5 cleaning 4-3, 4-54
preparing for working on the source replacing 4-54
4-8 Ethernet, connecting B-26
rear panel B-2 event signal connection B-28
rebooting 2-11 exhaust system
signal connectors B-26 checking for leaks 4-13, B-21
specifications 1-2 requirements B-20
starting 2-2 exhaust systems, separation of B-7,
tuning 2-4 B-20

Index-2
exhaust trap bottle B-22 handling symbols A-12
connecting B-7, B-16 hazards
emptying 4-3, 4-12 flammable solvents v
external connections B-1 high temperature vi I
extraction cone high voltage vii
cleaning 4-31 solvent leakage v
handling guidelines 4-39 heater cartridge assembly
extraction tool, cone gas assembly 4-24 replacing 4-75
hexapole assembly
F cleaning 4-47, 4-49
flammable solvents v, A-3 handling 4-48, 4-52
flow path diagrams 2-8 high temperature hazard vi
flow rates 2-5 high voltage hazard vii
fluidics system home position, of fluidics system
diverter valve positions diverter valve 2-8
combined 2-10
home 2-8 I
infusion 2-9 I/O signal connectors B-26
LC 2-9 in vitro diagnostic applications ix
waste 2-10 infusion position, of fluidics system
diverter valve 2-9
G inject start signal connection B-28
gas ballasting, roughing pump 4-3, inlet, overview 1-10
4-16 installing
gas cone, cleaning 4-21, 4-25 APCI probe 5-2
guidelines APCI probe sample capillary 4-66
calibration ix corona pin 3-6
demister element nut tightening corona pin mounting contact
4-101 blanking plug 3-9
door glass tightening 4-86 drip tray, solvent manifold 2-6
probe adjuster screw tightening ESI probe 3-2
4-87 low-volume vials 2-7
quality control ix reservoir bottles 2-7
thumbscrew tightening 4-87 solvent manifold drip tray 2-6
H instrument
handling case, cleaning 4-3, 4-12
extraction cone 4-39 LAN card B-26
hexapole assembly 4-48, 4-52 leaving ready for operation 2-12
waste liquid 4-13 integral reservoirs 1-3, 1-12

Index-3
IntelliStart cleaning 4-90
configuring 2-4 replacing 4-91
operating 1-13 low-volume vials, installing 2-7
overview 1-3, 1-12
intended use viii M
ion block maintenance
cleaning 4-31 safety 4-7
disassembling 4-33 schedule 4-3
grub screw 4-44 mass spectrometer
heater cartridge assembly, leaving ready for operation 2-12
replacing 4-75 mass spectrometer shock hazard A-4
removing 4-31 MassLynx software 1-5
ion optics 1-9 materials of construction C-1
ionization modes 3-2 mobile phases, solvents used in
APCI 1-8, 5-1 preparation of C-3
APPI 1-8 mode
ESI 1-7 scanning 1-10
IonSABRE APCI probe 5-2 selected ion recording 1-10
IP addresses 2-2 monitoring, system instrument LEDs
isolating source from instrument 4-9 2-5
isolation valve, cleaning 4-31 MS operating modes 1-10
IVD authorized representative x multi-mode ESCi source 1-2

L N
LAN card B-26 network cables B-25
LC, position of fluidics system diverter nitrogen
valve 2-9 exhaust, connecting B-20
LC/MS System Check D-1 supply
Leak sensors 1-10 connecting B-18
leaks, checking for 4-13, 4-60, 4-67, pressure requirements v, 2-2
B-21 NW25 tee, connecting B-5, B-14
LED O
monitoring 2-5 oil, roughing pump
operate 2-5 adding 4-20
power 2-3, 2-5 changing 4-4
status 2-3 checking level 4-3, 4-19, 4-97
liquid trap bottle, emptying 4-3, 4-14 replacing 4-95
liquid waste line, connecting B-23 opening source isolation valve 4-10
lower bezel air filter operate LED 2-5

Index-4
operating modes, MS 1-10 replacing
operating source isolation valve 4-9 air filter
O-ring removal kit 4-11 behind source probe 4-94
O-rings, removing 4-11 inside lower bezel 4-91 I
overview 1-2 APCI probe heater 4-4, 4-71
corona pin 4-4, 4-70
P demister element 4-4, 4-98
PEEK terminal block, removing 4-36, ESI probe capillary 4-3, 4-55
4-76 ESI probe tip 4-54
photomultiplier detection system 1-9 ion block heater cartridge assembly
power LED 2-3, 2-5 4-75
power supply, connecting to B-25 sample capillary 4-62
powering-on 2-2 source assembly seals 4-4, 4-79
pressure test, performing 4-79, 4-89 requirements
preventing contamination C-2 exhaust system B-20
probe adjuster nitrogen supply pressure v, 2-2
assembling 4-87 reservoir bottles, installing 2-7
disassembling 4-82 reservoirs, integral 1-3, 1-12
probe capillary reset button 2-11
replacing 4-4 roughing pump 1-10
pump, gas ballasting 4-3 clearances B-4, B-13
Q connecting B-3, B-10
quality control guidelines ix gas ballasting 4-3, 4-16
oil
R adding 4-20
rear panel B-2 checking level 4-3, 4-19, 4-97
rebooting detector 2-11 replacing 4-95
relay box, connecting B-9 replacing demister element 4-4,
removing 4-98
APCI probe sample capillary 4-62 setting up B-4, B-13
corona pin 3-7 site requirements B-4, B-13
corona pin mounting contact
blanking plug 3-5 S
ESI probe 3-9 safety advisories A-1
ion block assembly 4-31 safety procedures, maintenance 4-7
O-rings 4-11 sample 4-62
PEEK terminal block 4-36, 4-76 sample bottles D-3
seals 4-11 sample capillary, replacing 4-62
replacement parts 4-5 sample cone, cleaning 4-21, 4-25

Index-5
sample inlet, overview 1-10 replacing 4-94
scan speed 1-2 spare parts 4-5
scanning mode 1-10 specifications 1-2
seals, removing 4-11 SQ detector
selected ion recording (SIR) mode 1-10 overview 1-2
shutdown starting, detector 2-2
emergency 2-12 status LED 2-3
signal connections, connecting B-29 stop flow signal connection B-28
site requirements, roughing pump B-4, sulfadimethoxine standard D-1
B-13 switch signal connection B-28
solvent leakage hazard v symbols
solvent manifold drip tray, installing caution A-5
2-6 electrical A-11
solvent vapor leakage, avoiding 4-79 handling A-12
solvents warning A-2
compliant C-1
exposure of detector components to T
C-2 thumbscrews, tightening 4-87
use in mobile phases C-3 tightening
source demister element nut 4-101
cleaning 4-3, 4-21 thumbscrews 4-87
enclosure trademarks ii
assembling 4-87 trap bottle
disassembling 4-82 connecting B-22
seals, replacing 4-79 emptying 4-12
hexapole assembly troubleshooting 4-5
cleaning 4-49 tuning 2-4
ion block assembly, assembling turbomolecular pump 1-10
4-42 V
isolation valve vacuum
closing 4-9 connections B-2
opening 4-10 system 1-10
operating 4-9 valve
preparing for work on 4-8 diverter 2-8
pressure test 4-89 source isolation 4-9
replacing assembly seals 4-4
types 1-2 W
source probe air filter warning symbols A-2, A-5
cleaning 4-92 waste

Index-6
 bottle, emptying 4-14
line, connecting B-23
liquid, handling 4-13
waste position, of fluidics system I
diverter valve 2-10
Waters Instrument, console 1-6
wiring, external B-2
workstation, connecting B-25
Z
ZSpray source 1-2

Index-7
Index-8