Waters APGC Owner's manual

Atmospheric Pressure
GC
Operator’s Guide Supplement
Revision F
Copyright © Waters Corporation 2010–2012
All rights reserved

ii
Copyright notice
© 2010–2012 WATERS CORPORATION. PRINTED IN THE UNITED
STATES OF AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS
DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY
FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use. For the
most recent revision of this document, consult the Waters Web site
(waters.com).
Trademarks
Waters and Xevo are registered trademarks of Waters Corporation, and
MassLynx, NanoLockSpray, “THE SCIENCE OF WHAT’S POSSIBLE.”, and
SYNAPT are trademarks of Waters Corporation.
Other registered trademarks or trademarks are the sole property of their
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].
Contacting Waters
Contact Waters®with enhancement requests or technical questions regarding
the use, transportation, removal, or disposal of any Waters product. You can
reach us via the Internet, telephone, or conventional mail.
Waters contact information
Contacting medium Information
Internet The Waters Web site includes contact
information for Waters locations worldwide.
Visit www.waters.com.
Telephone and fax From the USA or Canada, phone 800
252-HPLC, or fax [phone].
For other locations worldwide, phone and fax
numbers appear in the Waters Web site.
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

iv
Safety considerations
Some reagents and samples used with Waters instruments and devices can
pose chemical, biological, or radiological hazards (or any combination thereof).
You must know the potentially hazardous effects of all substances you work
with. Always follow Good Laboratory Practice, and consult your organization’s
safety representative for guidance.
Considerations specific to the Atmospheric Pressure GC
High temperature hazard
See also: The relevant Agilent 7890 GC user documentation.
Carrier-gas fire hazard
Warning: To avoid burn injuries, avoid touching the heated transfer
line, ion chamber, or heated vial carrier when operating or servicing the
instrument.
Warning: To avoid fire, do not use hydrogen (H2) or other flammable
gases as a carrier gas for the APGC.

v
Hazards associated with removing an instrument from service
When you remove the instrument from use to repair or dispose of it, you must
decontaminate all of the areas that have been in contact with samples. These
are the areas in which you can expect to encounter the highest levels of
contamination:
• Source interior
• APGC ion chamber
•GCcomponents
Do not dispose of the instrument or return it to Waters for repair until the
authority responsible for approving its removal from the premises specifies
the extent of decontamination required, and the level of residual
contamination permissible. That authority must also prescribe the method of
decontamination to be used, and the appropriate protection for personnel
undertaking the decontamination process.
You must handle items such as syringes, fused silica lines, and borosilicate
tips used to carry sample into the source area in accordance with laboratory
procedures for contaminated vessels and sharps.
See also: The relevant Agilent 7890 GC user documentation.
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.
Warning: To avoid personal contamination with biologically
hazardous, toxic, or corrosive materials, and to avoid
spreading contamination to uncontaminated surfaces, wear
clean, chemical-resistant, powder-free gloves during all
phases of instrument decontamination.
Warning: To avoid puncture injuries, handle syringes, fused
silica lines, and borosilicate tips with care.

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Operating this device
When operating this device, follow standard quality-control (QC) procedures
and the guidelines presented in this section.
Applicable symbols
Audience and purpose
This guide presents user installation, setup, and safety information for the
Waters Atmospheric Pressure Gas Chromatograph (APGC) used with
compatible mass spectrometers.
Intended use of the APGC
The APGC allows coupling of a GC (gas chromatography) instrument to the
atmospheric pressure ionization (API) source on compatible LCMS
instruments. The APGC is for research use only. It is not intended for use in
diagnostic applications. It is intended for use only by qualified laboratory
personnel, installation engineers, and field service engineers.
Symbol Definition
Manufacturer
Authorized representative of the European
Community
Confirms that a manufactured product complies
with all applicable European Community
directives
Australia C-Tick EMC compliant
Confirms that a manufactured product complies
with all applicable United States and Canadian
safety requirements
Consult instructions for use

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Calibrating
To calibrate GC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards should include the entire range of QC samples, typical specimens,
and atypical specimens.
When calibrating mass spectrometers, consult the calibration section of the
operator’s guide for the instrument you are calibrating. In cases where an
overview and maintenance guide, not operator’s guide, accompanies the
instrument, consult the instrument’s online Help system for calibration
instructions.
Quality control
Routinely run three QC samples that represent subnormal, normal, and
above-normal levels of a compound. Ensure that QC sample results fall within
an acceptable range, and evaluate precision from day to day and run to run.
Data collected when QC samples are out of range might not be valid. Do not
report these data until you are certain that the instrument performs
satisfactorily.
ISM classification
ISM Classification: ISM Group 1 Class A
This classification has been assigned in accordance with IEC 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.

viii
EC authorized representative
Waters Corporation (Micromass UK Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

Table of Contents ix
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iv
Considerations specific to the Atmospheric Pressure GC ................................ iv
Safety advisories.................................................................................................. v
Operating this device .......................................................................................... vi
Applicable symbols ............................................................................................. vi
Audience and purpose......................................................................................... vi
Intended use of the APGC.................................................................................. vi
Calibrating ........................................................................................................ vii
Quality control .................................................................................................. vii
ISM classification ................................................................................................ vii
ISM Classification: ISM Group 1 Class A ....................................................... vii
EC authorized representative ........................................................................ viii
1 Instrument Description ........................................................................ 1-1
Waters APGC ...................................................................................................... 1-2
APGC components ............................................................................................ 1-4
APGC trolley (SYNAPT G2 only).................................................................... 1-5
Heated transfer line......................................................................................... 1-8
APGC source enclosure.................................................................................... 1-9
Heated and unheated vial carriers ............................................................... 1-10
APGC ion chamber ........................................................................................ 1-11
Table of Contents

x Table of Contents
2 Setting up the APGC ............................................................................. 2-1
Preparing the mass spectrometer for operation with the APGC .......... 2-2
Preparing the instrument for work performed on its source......................... 2-2
Removing the LC source enclosure from the mass spectrometer.................. 2-3
Preparing the source ion block for GC operation........................................... 2-5
Installing the APGC ion chamber on the mass spectrometer’s ion block..... 2-9
Installing the APGC source enclosure in the mass spectrometer............... 2-12
Installing the APGC vial carriers in the mass spectrometer’s source ........ 2-13
Installing vials in the vial carriers ............................................................. 2-14
Connecting the APGC to the mass spectrometer .................................... 2-16
Disconnecting the APGC from the mass spectrometer .......................... 2-17
Removing vials from the vial carriers ....................................................... 2-18
Preparing the mass spectrometer for LC operation .............................. 2-19
Removing the APGC vial carriers from the mass spectrometer’s source ... 2-19
Removing the APGC source enclosure from the mass spectrometer .......... 2-20
Removing the APGC ion chamber from the mass spectrometer’s ion block 2-21
Preparing the source ion block for LC operation ......................................... 2-22
Installing the LC source enclosure on the instrument ................................ 2-24
3 Maintenance Procedures ..................................................................... 3-1
Maintenance schedule ..................................................................................... 3-2
Spare parts ......................................................................................................... 3-2
Safety and handling ......................................................................................... 3-3
Cleaning the mass spectrometer sample cone ........................................... 3-4
Cleaning or replacing the corona pin .......................................................... 3-4
Cleaning the APGC ion chamber .................................................................. 3-7
A Safety Advisories .................................................................................. A-1
Warning symbols ............................................................................................... A-2
Task-specific hazard warnings........................................................................ A-2

Table of Contents xi
Specific warnings ............................................................................................. A-3
Caution advisory ............................................................................................... A-5
Warnings that apply to all Waters instruments ......................................... A-6
Electrical and handling symbols ................................................................. A-11
Electrical symbols .......................................................................................... A-11
Handling symbols .......................................................................................... A-12
B Installing the GC Column ................................................................... B-1
C Preparing Sample Vials ...................................................................... C-1
Preparing vials ................................................................................................. C-2
Preparing closed vials...................................................................................... C-2
Preparing open vials........................................................................................ C-3

xii Table of Contents

1-1
1Instrument Description
The Waters®Atmospheric Pressure GC (APGC) couples an Agilent GC
with a compatible Waters LCMS instrument. Doing so makes possible
performing LC and GC analyses in the same system, without
compromising performance. It also avoids the need for separate,
dedicated GCMS and LCMS instrumentation.
Contents:
Topic Page
Waters APGC 1-2
APGC components 1-4

1-2 Instrument Description
Waters APGC
The APGC provides complementary information to the LCMS instrument,
enabling analysis of compounds of low molecular weight or low-to-
intermediate polarity.
The APGC is compatible with these Waters LCMS instruments:
•Xevo
® TQ MS
• Xevo TQ-S
• Xevo TQD
•Xevo
QTof MS
• Xevo G2 QTof
• Xevo G2 Tof
• SYNAPT™ G2 MS
• SYNAPT G2 HDMS
•SQDetector2
See also: The relevant instrument’s operator’s overview and maintenance
guide.For correct operation and maintenance of the GC oven and capillary
column, refer to the relevant manufacturer’s user documentation.

Waters APGC 1-3
Agilent GC and autosampler mounted on the APGC platform:
APGC platform
Agilent 7890 GC
Autosampler

1-4 Instrument Description
APGC components
The APGC comprises a sliding platform mounted on a supporting plinth,
which can hold an accessory storage drawer, depending on the
mass-spectrometer model. The platform carries the heated transfer line and
the GC instrument, which the mass spectrometer connects to via the APGC
source enclosure and ion chamber. A locking handle locks the sliding platform,
preventing its unintentional movement when you disconnect the locking ring
from the APGC source enclosure. The stability frame, which a Waters
engineer installs, mechanically locks the APGC to the mass spectrometer.
APGC main components:
When you operate the mass spectrometer in GCMS mode, the APGC source
enclosure and APGC ion chamber serve in place of the standard
mass-spectrometer source enclosure and cone gas nozzle.
You can quickly interchange the mass spectrometer and APGC source
enclosures, to adapt the mass spectrometer to LCMS or GCMS configuration.
Warning: To avoid injury from being struck by toppling equipment,
• do not overbalance the equipment by placing in the
accessory-storage drawer (where fitted) a load exceeding
10 kg;
• do not tamper with the stability frame.
APGC source enclosure
Locking handle
Plinth
Heated transfer line
Accessory storage drawer
(no drawer for Xevo TQD and SQ Detector 2)
Sliding platform
GC retaining bar
Locking ring
APGC ion chamber
Stability frame
(shorter for Xevo TQD and SQ Detector 2)

APGC components 1-5
APGC trolley (SYNAPT G2 only)
The optional APGC trolley allows you to use the APGC with SYNAPT G2
instruments. Note that the stability frame is not required with this version of
the APGC.
APGC trolley:
The APGC trolley is a mobile steel cabinet on top of which the APGC is fixed
in place. A locking lever and locking plate engage or disengage the trolley and
mass spectrometer.
Trolley cabinet
Locking plate
Locking lever
Stabilizers

1-6 Instrument Description
Engaging the APGC trolley:
To engage the APGC trolley:
1. Slide the locking plate forward so that the two indentations meet the
supporting pillars under the instrument.
2. Push the trolley toward the locking plate so that the two indentations
meet the supporting pillars under the trolley.
3. Lift the locking lever.
4. Push the locking tab toward the locking plate as far as it will go.
5. Release the locking lever, ensuring that the inner notch engages firmly
with the locking tab.
6. Adjust the stabilizers until the trolley is entirely stable, level, and at a
suitable height for the heated transfer line to engage with the
instrument source.
Tip: Use a spirit level to ensure that the trolley is level.
1
2
4
3
5
Supporting pillars
(trolley)
Locking plate
Locking lever Locking tab
Supporting pillars
(instrument)

APGC components 1-7
Disengaging the APGC trolley:
To disengage the APGC trolley:
Requirement: Before performing this procedure, ensure that you have first
loosened the stabilizers under the trolley.
1. Lift the locking lever.
2. Pull the locking tab outward as far as it will go.
3. Drop the locking lever so that the outermost notch engages with the
locking tab.
4. Carefully slide the trolley away from the locking plate.
5. Pull the locking plate away from the instrument.
1
2
4
3
5
Supporting pillars
(trolley)
Locking plate
Locking lever Locking tab
Supporting pillars
(instrument)

1-8 Instrument Description
Heated transfer line
To ensure the equipment’s proper operation, a Waters service engineer
establishes the optimum position of the heated transfer line within the mass
spectrometer’s source.
Important: Once the position of the heated transfer line is set, you must not
change it.
Heated transfer line assembly:
Warning: To avoid burn injuries, take great care when working with the
heated transfer line. The line heats during normal use, and hot gas can
escape from the capillary column’s tip. Use the APGC protection cap to
cover the tip when you withdraw the tube from the source enclosure for
extended periods.
Warning: To avoid burn injuries, the locking ring of the heated transfer
line must be replaced by a Waters field engineer when the line is
defective.
Caution: To avoid damaging the capillary column, do not operate the
heated transfer line at temperatures greater than those recommended
by the capillary column manufacturer.
Capillary column tip
APGC protection cap
Locking ring
Connection for GC
capillary column
Make-up gas connection
Mounting flange
Heated transfer line