Waters Quattro Premier XE Manual

Waters
Quattro Premier XE
Combined APPI and
APCI Source
Operator’s Guide
71500112702/Revision A
Copyright © Waters Corporation 2007
All rights reserved

ii
Copyright notice
© 2007 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND 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
Waters is registered trademark, and MassLynx and Quattro Premier are
trademarks of Waters Corporation.
Viton is a registered trademark of DuPont Dow Elastomers.
PEEK is a trademark of Victrex Corporation.
Other trademarks or registered trademarks are the sole property of their
respective owners.

iii
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].

iv
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.
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.
Waters contact information
Contacting medium Information
Internet The Waters Web site includes phone numbers
for Waters locations worldwide. Go to
www.waters.com, and click About Waters >
Worldwide Offices.
Telephone In the USA or Canada, phone [phone].
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

v
Considerations specific to the Quattro Premier XE Combined
APPI and APCI Source
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
“Materials of Construction and Compliant Solvents” on
page B-1), and determine whether any solvents you use that
are not listed are chemically compatible with the composition
of the O-rings.

vi
High temperature hazard
Mass spectrometer high temperature hazard
Warning: To avoid burn injuries, avoid touching the source enclosure
with your hand when operating or servicing the instrument.
Source enclosure assembly

vii
High voltage hazard
Mass spectrometer in APCI ionization mode
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.
Warning:
• To avoid electric shock, do not remove the mass spectrometer’s
protective panels. The components they cover are not
user-serviceable.
• 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.
Ion block and cone assembly
High voltage connector
Corona discharge pin

viii
Operating this instrument
When operating this instrument, follow standard quality control procedures
and the guidelines presented in this section.
Symbols
Intended use
Waters designed the Quattro Premier™ XE Combined APPI and APCI Source
option instrument to be used with a Quattro Premier XE Mass Spectrometer.
The instrument is intended for use as a research tool to deliver authenticated
mass measurement in both MS and MS/MS modes.
The Waters Quattro Premier XE Mass Spectrometer can be used for general
in vitro diagnostic applications. However, only professionally trained and
qualified laboratory personnel should use the instrument for those purposes.
Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards should include the entire range of quality-control samples, typical
specimens, and atypical specimens.
To calibrate mass spectrometers, consult the calibration section of the
operator’s guide for the instrument you are calibrating.
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
The Waters Quattro Premier XE Combined APPI and APCI
Source option is CE-marked according to the European Union In
Vitro Diagnostic Device Directive 98/79/EC.

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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, etc., 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.

x
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 Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

Table of Contents 1
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iv
Safety considerations .......................................................................................... iv
Considerations specific to the Quattro Premier XE Combined APPI
and APCI Source............................................................................................ v
Safety advisories............................................................................................... vii
Operating this instrument .............................................................................. viii
Symbols ............................................................................................................ viii
Intended use..................................................................................................... viii
Calibrating ....................................................................................................... viii
Quality control .................................................................................................... ix
IVD authorized representative information .................................................. x
IVD authorized representative ........................................................................... x
1 APPI, APCI, and Dual APPI/APCI Modes ......................................... 1-1
APPI mode .......................................................................................................... 1-2
APCI mode .......................................................................................................... 1-3
Dual APPI/APCI mode ..................................................................................... 1-4
2 The Combined APPI/APCI Source ..................................................... 2-1
Combined APPI/APCI Source ........................................................................ 2-2
APCI probe ....................................................................................................... 2-2
APPI lamp drive assembly .............................................................................. 2-2
Installing the Combined APPI/APCI Source .............................................. 2-5
Installing the Combined APPI/APCI Source software upgrade.................... 2-5
Installing the APPI lamp drive assembly and APCI probe........................... 2-5
Table of Contents

2 Table of Contents
Removing the Combined APPI/APCI Source ............................................. 2-8
Removing the APCI probe and APPI lamp drive assembly........................... 2-8
3 Operating in APPI, APCI, and Dual APPI/APCI Modes ................ 3-1
Operating in APPI mode ................................................................................. 3-2
Operating in APCI mode ............................................................................... 3-10
Operating in Dual APPI/APCI mode .......................................................... 3-13
4 Maintenance Procedures ..................................................................... 4-1
General ................................................................................................................ 4-2
Maintenance schedule ..................................................................................... 4-2
Safety and handling ......................................................................................... 4-3
Removing O-rings and seals ........................................................................... 4-3
Changing the UV lamp bulb ........................................................................... 4-4
Cleaning the lamp window ............................................................................. 4-7
Replacing the APPI lamp drive assembly O-rings .................................... 4-9
Removing the APPI lamp drive assembly O-rings......................................... 4-9
Fitting the new APPI lamp drive assembly O-rings.................................... 4-12
A Safety Advisories .................................................................................. A-1
Warning symbols ............................................................................................... A-2
Task-specific hazard warnings........................................................................ A-2
Warnings that apply to particular instruments, instrument components,
and sample types ....................................................................................... A-3
Caution symbol .................................................................................................. A-5
Warnings that apply to all Waters instruments ......................................... A-5
Electrical and handling symbols ................................................................. A-13
Electrical symbols .......................................................................................... A-13
Handling symbols .......................................................................................... A-14

Table of Contents 3
B Materials of Construction and Compliant Solvents ..................... B-1
Preventing contamination ............................................................................. B-2
Items exposed to solvent ................................................................................ B-2
Solvents used to prepare mobile phases .................................................... B-3
Index ..................................................................................................... Index-1

4 Table of Contents

1-1
1APPI, APCI, and Dual APPI/APCI
Modes
This chapter describes the Quattro Premier™ XE Combined APPI and
APCI Source operation modes.
Contents
Topic Page
APPI mode 1-2
APCI mode 1-3
Dual APPI/APCI mode 1-4

1-2 APPI, APCI, and Dual APPI/APCI Modes
APPI mode
In atmospheric pressure photoionization (APPI) mode, the source is fitted
with an APCI probe, and the APPI lamp drive assembly is advanced into the
source.
See also: “APCI probe” on page 2-2 and “APPI lamp drive assembly” on
page 2-2.
APPI mode
The APCI probe introduces vaporized sample into the source where photons
generated by an ultra-violet (UV) lamp (mounted in the APPI lamp drive
assembly) produce sample ions. Direct photoionization of a sample molecule
occurs when the photon energy exceeds the ionization potential of the sample
molecule.
A repeller electrode (mounted on the APPI lamp drive assembly) deflects and
focuses the sample ions towards the sample cone.
APCI probe
Sample molecules
APPI lamp drive assembly
Repeller electrodeUV lamp
Sample ions
Sample cone
Photons from
the UV lamp

APCI mode 1-3
APCI mode
Atmospheric Pressure Chemical Ionization (APCI) produces singly-charged
protonated or deprotonated molecules for a large range of nonvolatile
analytes.
In APCI mode, the source fitted with an APCI corona pin. The APPI lamp
drive assembly is not used, and is retracted from the source.
APCI mode
The APCI probe introduces vaporized sample into the source. The sample
passes between the sample cone and the corona pin, which typically operates
with a discharge current of 5 µA. The corona discharge generates ions that
react with the mobile phase molecules to produce stable reagent ions. Analyte
molecules in the mobile phase react with the reagent ions at atmospheric
pressure and become protonated (in the positive ion mode) or deprotonated (in
the negative ion mode). The sample and reagent ions pass through the sample
cone.
APCI probe
Retracted APPI lamp drive
assembly
Sample cone
APCI corona pin

1-4 APPI, APCI, and Dual APPI/APCI Modes
Dual APPI/APCI mode
Dual APPI/APCI mode enables rapid switching between ionization modes, and
allows high throughput (for example, for sample screening).
The standard corona pin is replaced with a specially-shaped dual APPI/APCI
corona pin, so that the APPI lamp holder can be advanced into the source for
dual APPI/APCI operation.
When the source is configured for dual operation in APCI mode, current is
applied to the corona pin, but the repeller electrode is inactive.
Dual operation in APCI mode
When the source is configured for dual operation in APPI mode, the corona pin
is inactive, and a voltage is applied to the repeller electrode.
Dual operation in APPI mode
Sample cone
APCI probe
Photons from the UV lamp
Repeller electrode inactive
Dual APCI/APPI corona pin with
current applied
Sample cone
APCI probe
Photons from the UV lamp
Repeller electrode with
voltage applied
Dual APCI/APPI corona
pin inactive

2-1
2The Combined APPI/APCI
Source
This chapter describes the Quattro Premier XE Combined APPI and
APCI Source components and how to install and remove the source.
Contents
Topic Page
Combined APPI/APCI Source 2-2
Installing the Combined APPI/APCI Source 2-5
Removing the Combined APPI/APCI Source 2-8

2-2 The Combined APPI/APCI Source
Combined APPI/APCI Source
The Combined APPI/APCI Source comprises an APCI probe and the APPI
lamp drive assembly.
APCI probe
The APCI probe is the standard probe used by the Quattro Premier XE for
APCI operation.
See also: The Waters Quattro Premier XE Mass Spectrometer Operator’s
Guide.
APPI lamp drive assembly
The APPI lamp drive assembly comprises:
•AUVlamp.
• A repeller electrode.
•Alampholder.
• A mounting shaft with indexing scales.
• An aluminum enclosure, housing drive electronics.
• An APPI source enclosure side plate.
See also: Figure “APPI lamp drive assembly and side plate” on page 2-3 and
Figure “APPI lamp drive assembly showing the UV lamp and repeller
electrode” on page 2-4.
The APPI lamp drive assembly mounts onto the APPI source enclosure side
plate, which in turn mounts onto the side of the instrument’s source enclosure.
See also: Figure “APPI lamp drive assembly fitted to the source enclosure” on
page 2-4.