Waters 2707 Manual

Waters 2707
Autosampler
Operator’s Guide
71500168202 / Revision A
Copyright © Waters Corporation 2008
All rights reserved

ii
Copyright notice
© 2008 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 a registered trademark and Empower and THE SCIENCE OF
WHAT’S POSSIBLE are trademarks of Waters Corporation.
Windows is a registered trademark of Microsoft Corporation.
PEEK is a trademark of Victrex®Corporation.
Teflon, Viton, and Tefzel are registered trademarks of E.I. duPont de
Nemours and Company.
Silco is a registered trademark of Silco Incorporated.
Phillips is a registered trademark of the Phillips Screw Company.
Valco is a registered trademark of Valco Instruments Inc.
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 [e-mail].

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.
Decontamination information
For an explanation about how to decontaminate Waters liquid
chromatography/mass spectrometry (LC/MS) products, see the Waters
publication Controlling Contamination in LC/MS Systems (part number
715001307).
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
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.
Operating this instrument
When operating this instrument, follow standard quality control procedures
and the guidelines in this section.
Intended use
Waters designed the 2707 Autosampler as a sample handler with a reliable,
precise fluid path versatile enough foruse in varied methods and applications.
The optional heating/cooling module accommodates a wide range of samples,
from heat labile biological samples to viscous polymer samples.
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 can be invalid. Do not report these data until you are certain that the
instrument performs satisfactorily.

vi

Table of Contents vii
1 Understanding Operating Principles ................................................ 1-1
Describing the autosampler ........................................................................... 1-2
Listing component parts.................................................................................. 1-3
Identifying options ........................................................................................... 1-5
Exploring injection principles ....................................................................... 1-6
Defining pressure-assisted sample aspiration............................................... 1-6
Understanding syringe and buffer tubing...................................................... 1-7
Full loop injections........................................................................................... 1-8
Partial loop needle overfill injections ........................................................... 1-13
Partial loop injections.................................................................................... 1-18
Using well plates and vial trays .................................................................. 1-24
2 Preparing the Autosampler ................................................................. 2-1
Preparing for installation ............................................................................... 2-2
Setting up the instrument ............................................................................... 2-2
Plumbing the instrument ................................................................................ 2-3
Identifying instrument tubing ........................................................................ 2-7
Routing and connecting the tubing................................................................. 2-8
Working with waste tubing........................................................................... 2-10
Accommodating the wash solvent and syringe rinse................................... 2-10
Making Ethernet connections ...................................................................... 2-11
Controlling I/O connections ......................................................................... 2-12
Defining TTL inputs...................................................................................... 2-12
Explaining contact closure output ................................................................ 2-12
Table of Contents

viii Table of Contents
Connecting to the electricity source .......................................................... 2-13
Installing the prep kit .................................................................................... 2-14
Installing the biocompatibility kit .............................................................. 2-14
3 Maintaining the Autosampler ............................................................. 3-1
Outlining maintenance basics ....................................................................... 3-2
Contacting Waters Technical Service .......................................................... 3-2
Heeding maintenance considerations ......................................................... 3-3
Safety and handling......................................................................................... 3-3
Proper operating procedures........................................................................... 3-4
Cleaning the autosampler ............................................................................... 3-4
Removing or replacing the injection valve rotor seal .............................. 3-5
Installing a sample loop .................................................................................. 3-6
Replacing the sample needle .......................................................................... 3-6
Adjusting needle position ............................................................................... 3-8
Maintaining air needles .................................................................................. 3-8
Replacing air needles..................................................................................... 3-12

Table of Contents ix
Replacing a syringe ........................................................................................ 3-14
Replacing syringe plungers and plunger tips .......................................... 3-15
Replacing the syringe dispenser valve ...................................................... 3-16
Replacing fuses ................................................................................................ 3-19
4 Troubleshooting ..................................................................................... 4-1
Addressing instrument errors ....................................................................... 4-2
Running diagnostic tests ................................................................................. 4-2
Displaying the statuses of signal connections ........................................... 4-2
Changing the rear-panel interface connections ........................................ 4-3
Understanding power surges ......................................................................... 4-4
Understanding the status LED....................................................................... 4-4
Conducting analytical troubleshooting ....................................................... 4-4
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

x Table of Contents
B Materials of Construction and Compliant Solvents ..................... B-1
Preventing contamination ............................................................................. B-2
Naming solvents for mobile phase preparation ....................................... B-2
C Specifications ........................................................................................ C-1
Outlining general specifications .................................................................. C-2
Outlining prep version specifications ........................................................ C-6

1-1
1Understanding Operating
Principles
Contents
Topic Page
Describing the autosampler 1-2
Identifying options 1-5
Exploring injection principles 1-6
Using well plates and vial trays 1-24

1-2 Understanding Operating Principles
Describing the autosampler
The Waters 2707 Autosampler is a comprehensive, high-throughput
instrument that offers the following features:
• Service-friendly design that requires little bench space
• High-resolution syringe control for high-precision injections
• Interchangeable fixed-volume sample loops
• Variable-volume partial-loop injection capability
• Optional sample cooling for consistent results (see the “Identifying
options” section on page 1-5)
• Pressure-assisted sample aspiration injection capability (see the
“Defining pressure-assisted sample aspiration” section on page 1-6)

Describing the autosampler 1-3
Listing component parts
The autosampler’s sampling compartment includes the following parts:
These parts are fitted as standard equipment:
• 100-µL sample loop
• 15-µL injection needle
• 500-µL syringe
• 1000-µL buffer tubing
The instrument uses standard high or low well plates or vial trays. The
sampling compartment can house two well plates in any combination.
Exception: The sampling compartment cannot accommodate 384 short
on the left and 96 tall on the right (see the “Using well plates and vial
trays” section on page 1-24).
Syringe
Needle arm Injection valve
Valve leak bin
Sample
compartment
Needle wash
position
Wash bottle

1-4 Understanding Operating Principles
These items appear on the instrument’s rear panel:
ETHERNET I/O
RJ-45 Ethernet
connection
9-pin male connector
(I/O connections)
Warning label
On/off switch
Fuse drawer
Power connector
Sample
compartment
cooler with fan
(optional)
Serial number
label

Identifying options 1-5
Identifying options
With the factory-installed sample cooling option, the instrument has a cooling
fan at its back (see the preceding figure) and a cooling cover in its sampling
compartment (see the following figure). It also includes the following parts:
These are the user-installable options:
• Biocompatible sample flow path and valve – Inert sample needle (Silco®
steel) and biocompatible valve (PEEK®)
• Prep kit for large-volume sampling – 2500 µL syringe, prep valve,
10000-µL sample loop, large sample volume (LSV) needle, and sample
tray for 10-mL vials
• Air needles – Six types, each for a different type of well/vial plate, for
pressurizing sample vials of varied heights during aspiration
Tubing guide
Wash/waste Condensed water/leakage
Cooling cover
(with cooler
option)

1-6 Understanding Operating Principles
Exploring injection principles
The autosampler has three injection modes:
• Full loop– For maximum injection volume precision
• Partial loop needle overfill – For maximum flexibility
• Partial loop – For zero sample loss
Defining pressure-assisted sample aspiration
For all injection modes, the instrument method can enable loop injection with
pressure-assisted sample aspiration. This option pairs an on-board
compressor with intelligent valve switching and highly accurate syringe
control, resulting in these benefits:
• Helps aspirate viscous samples
• Reduces the risk of bubbles in the sample line
• Prevents unwanted sample movement in the needle
Pressurizing vial
Buffer tubing
HPLC pump
Sample loop
HPLC column
Air pressure
Syringe

Exploring injection principles 1-7
The syringe aspirates the sample from a vial into the sample loop. Buffer
tubing between the syringe and the injection valve prevents syringe
contamination. Wash solvent serves to:
• Remove sample from the buffer tubing and sample needle
• Rinse the buffer tubing and sample needle
Understanding syringe and buffer tubing
The instrument has two syringe sizes:
• 500 µL (standard)
• 2500 µL (included in the prep kit)
With standard 1000-µL buffer tubing and the standard 100-µL sample loop,
injection volume ranges are as follows:
• Full loop – 100 µL
• Partial loop needle overfill – 0 to 50 µL
• Partial loop – 0 to 27 µL
Maximum injection volumes are calculated as follows:
• Full loop – Loop volume
• Partial loop needle overfill – Half the loop volume
• Partial loop – (Loop volume - [3 × needle volume])/2

1-8 Understanding Operating Principles
Full loop injections
In the standard configuration, full loop injections yield maximum possible
reproducibility < 0.3% RSD but not necessarily maximum accuracy, because
loop volume is typically specified with an accuracy of ± 10%. Typical sample
usage is 330 µL (3 × loop overfill + 30 µL flush volume for the needle). The
minimum flush volume of 30 µL is recommended; you can program smaller
flush volumes, but they decrease performance.
This is the full loop injection sequence:
1. The injection valve moves to the Inject position, and the sample needle
and air needle enter the well or vial. When the instrument method
enables sample pressurization, the air needle applies headspace
pressure to prevent air or vapor bubbles from forming during sample
aspiration.
Sample
Buffer tubing
Syringe
Needle
Sample loop
INJECT Column
Pump

Exploring injection principles 1-9
2. The syringe dispenser aspirates the flush volume (30 µL default) from
the sample well or vial to fill the sample line with sample and remove
wash solvent.
Sample
Buffer tubing
Syringe
Needle
Sample loop
INJECT Column
Pump
Air gap
(optional)

1-10 Understanding Operating Principles
3. The injection valve switches to the Load position, placing a sample plug
at the sample loop inlet.
TP03046
Sample
Syringe
Needle
Sample loop
LOAD Column
Pump
Buffer tubing
Air gap
(optional)