Waters Alliance e2695 Manual

Waters Alliance e2695
Separations Module
Operator’s Guide
715003794/Revision B
Copyright © Waters Corporation 2013
All rights reserved
View More Resources at www.Chromatography.co

ii July 29, 2013, 715003794 Rev. B

July 29, 2013, 715003794 Rev. B iii
General Information
Copyright notice
© 2013 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, “THE SCIENCE OF WHAT’S POSSIBLE.”, and Alliance are
registered trademarks of Waters Corporation, and Empower, LAC/E,
PerformancePLUS, and SAT/IN are trademarks of Waters Corporation.
Phillips is a registered trademark of the Phillips Screw Company.
PEEK is a registered trademark of Victrex plc.
Sealtight is a trademark of Upchurch Scientific, Inc.
Other registered trademarks or trademarks are the sole property of their
owners.
Customer comments
Waters’ Technical Communications organization invites you to report any
errors that you encounter in this document or to suggest ideas for otherwise
improving it. Help us better understand what you expect from our
documentation so that we can continuously improve its accuracy and
usability.

iv July 29, 2013, 715003794 Rev. B
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.
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
standard operating procedures.
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
800 252-4752, 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

July 29, 2013, 715003794 Rev. B v
Considerations specific to the Waters Alliance e2695 Separations
Module
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.
Flammable solvents hazard
When using flammable solvents, ensure that a stream of nitrogen
continuously flushes the instrument’s source, and the nitrogen supply
pressure remains above 690 kPa (6.9 bar, 100 psi). You must also install a
gas-fail device that interrupts the solvent flowing from the LC system in the
event the supply of nitrogen fails.
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,determine whether
any solvents you use that are not listed are chemically
compatible with the composition of the O-rings.
Warning: To prevent ignition of flammable solvent vapors in the
enclosed space of a mass spectrometer’s ion source, ensure that nitrogen
flows continuously through the source. The nitrogen supply pressure
must not fall below 690 kPa (6.9 bar, 100 psi) during an analysis
requiring the use of flammable solvents. Also a gas-fail device must be
installed, to interrupt the flow of LC solvent should the nitrogen supply
fail.

vi July 29, 2013, 715003794 Rev. B
Hand crush hazard
High temperature hazard
FCC radiation emissions notice
Changes or modifications not expressly approved by the party responsible for
compliance, could void the users authority to operate the equipment. This
device complies with Part 15 of the FCC Rules. Operation is subject to the
following two conditions: (1) this device may not cause harmful interference,
and (2) this device must accept any interference received, including
interference that may cause undesired operation.
Canada spectrum management emissions notice
This class A digital product apparatus complies with Canadian ICES-001.
Cet appareil numérique de la classe A est conforme à la norme NMB-001.
Electrical power safety notice
Do not position the instrument so that it is difficult to operate the
disconnecting device.
Safety hazard symbol notice
Documentation needs to be consulted in all cases where the symbol is
used to find out the nature of the potential hazard and any actions which have
to be taken.
Warning: To avoid hazards associated with the reciprocating or rotating
parts in the source, keep clear of the regions marked with yellow and
gray labels.
Warning: To avoid burn injuries, avoid touching the source enclosure
when operating or servicing the instrument.

July 29, 2013, 715003794 Rev. B vii
Equipment misuse notice
If the equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired.
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 (QC)
procedures and the guidelines presented in this section.

viii July 29, 2013, 715003794 Rev. B
Applicable symbols
Audience and purpose
This guide is intended for use by individuals who need to install, operate,
maintain, or troubleshoot the Waters Alliance e2695 Separations Module.
This guide sets forth procedures for unpacking, installing, using, maintaining,
and troubleshooting the Waters Alliance e2695 Separations Module. It also
includes appendixes for specifications, spare parts, and solvent
considerations.
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
Electrical and electronic equipment with this
symbol may contain hazardous substances and
should not be disposed of as general waste.
For compliance with the Waste Electrical and
Electronic Equipment Directive (WEEE)
2012/19/EU, contact Waters Corporation for the
correct disposal and recycling instructions.

July 29, 2013, 715003794 Rev. B ix
Intended use of the Waters Alliance e2695 Separations Module
Waters designed the Alliance e2695 Separations Module, an integrated
solvent and sample management platform, to facilitate all critical separations
functions. The Waters Alliance e2695 Separations Module is for research use
only and is not intended for use in diagnostic applications.
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 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. If sample trays are the same or very
similar, vary the location of the QC samples in the trays. 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,

x July 29, 2013, 715003794 Rev. B
nonresidential) locations and can be directly connected to a low voltage,
power-supply network.
EC authorized representative
Waters Corporation (Micromass UK Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

July 29, 2013, 715003794 Rev. B xi
General Information .................................................................................... iii
Copyright notice .................................................................................................. iii
Trademarks ........................................................................................................... iii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iv
Safety considerations .......................................................................................... iv
Considerations specific to the Waters Alliance e2695 Separations Module..... v
FCC radiation emissions notice ......................................................................... vi
Canada spectrum management emissions notice ............................................. vi
Electrical power safety notice ............................................................................ vi
Safety hazard symbol notice............................................................................... vi
Equipment misuse notice ................................................................................. vii
Safety advisories............................................................................................... vii
Operating this instrument ................................................................................ vii
Applicable symbols .......................................................................................... viii
Audience and purpose...................................................................................... viii
Intended use of the Waters Alliance e2695 Separations Module..................... ix
Calibrating .......................................................................................................... ix
Quality control .................................................................................................... ix
ISM classification ................................................................................................. ix
ISM Classification: ISM Group 1 Class A ......................................................... ix
EC authorized representative ............................................................................ x
1 Getting started with the Alliance e2695 Separations Module ...... 21
Separations module overview ......................................................................... 21
HPLC system configurations ............................................................................ 22
Solvent bottle tray kits ...................................................................................... 23
Control of chromatographic functions .............................................................. 25
Table of Contents

xii July 29, 2013, 715003794 Rev. B
Spill protection................................................................................................... 26
Record-keeping functions .................................................................................. 26
Power supply...................................................................................................... 27
Solvent management system overview ......................................................... 27
Solvent blending ................................................................................................ 28
Prime/vent valve ................................................................................................ 28
Plunger seal-wash system................................................................................. 28
Loss of prime protection .................................................................................... 29
Preferred plunger stroke volume ...................................................................... 29
In-line vacuum degasser.................................................................................... 29
Sample management system overview ......................................................... 31
Flow path............................................................................................................ 31
Normal flow........................................................................................................ 32
Injection.............................................................................................................. 32
Carousel configuration ...................................................................................... 32
Vial presence ...................................................................................................... 33
Syringe assembly ............................................................................................... 33
Operating configurations ................................................................................. 34
System Controller mode .................................................................................... 35
No Interaction mode .......................................................................................... 37
Remote Control mode ........................................................................................ 37
Options and accessories ................................................................................... 39
Column heater ................................................................................................... 40
Column heater/cooler......................................................................................... 40
Sample heater/cooler ......................................................................................... 40
Syringes.............................................................................................................. 40
Sample loops ...................................................................................................... 40
Column selection valve...................................................................................... 41

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2 Install the e2695 Separations Module ................................................ 45
Installation overview ........................................................................................ 45
Site requirements .............................................................................................. 46
Firmware and software requirements .......................................................... 47
Unpack .................................................................................................................. 48
Connect to the electrical power supply ........................................................ 48
Connect tubing and attachments ................................................................... 50
Install B-series detector base and drip tray..................................................... 50
Install A and C series drip tray and support bracket...................................... 53
Install solvent supply tubing............................................................................. 58
Install the degasser vent tubing ....................................................................... 59
Make waste line connections............................................................................. 60
Install needle-wash and plunger seal-wash reservoirs.................................... 61
Connect the column ........................................................................................... 62
Connect the column selection valve.................................................................. 64
Connect the detector.......................................................................................... 68
Signal connections ............................................................................................. 69
I/O signal connections........................................................................................ 71
Digital signal connections ................................................................................. 75
Add hardware options ...................................................................................... 78
Install an optional sample loop ......................................................................... 78
Install the column heater and column heater/cooler ....................................... 81
Install a syringe ................................................................................................. 81
3 Prepare the e2695 Separations Module for Operation .................. 83
Power-on the separations module ................................................................. 83
Startup diagnostic tests..................................................................................... 83
The Main screen................................................................................................. 84
Operating overview ........................................................................................... 84
Screen display overview .................................................................................... 85
Use the keypad................................................................................................... 86

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Enter values in parameter fields ...................................................................... 88
Configure the separations module ................................................................ 91
Set configuration parameters............................................................................ 91
Configure the operating mode........................................................................... 98
Prepare the solvent management system .................................................. 103
Prepare solvent reservoirs............................................................................... 104
Degassing solvents........................................................................................... 105
Prime the plunger seal-wash pump................................................................ 106
Prime the solvent management system.......................................................... 107
Prepare the sample management system for operation ......................... 107
Purge the system ............................................................................................. 108
Prime the needle-wash pump.......................................................................... 109
Adjust the seal pack......................................................................................... 110
Load carousels.................................................................................................. 111
Procedures for preparing the separations module for operation ........ 112
Prepare a new or dry separations module for operation ............................... 112
Prepare an idle or powered-off separations module for operation ................ 113
Change from a buffered solvent to an organic solvent................................... 114
Power-off the separations module ............................................................... 114
Flush the flow path.......................................................................................... 115
Power-off the separations module................................................................... 115
4 Front Panel Control ............................................................................. 117
Routine startup ................................................................................................ 117
Reinitialize the system .................................................................................... 118
Load sample vials ............................................................................................. 118
Remove the carousel ........................................................................................ 118
Load vials ......................................................................................................... 118
Load the carousel............................................................................................. 119
Add new sample vials during a run................................................................ 119

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Monitor your HPLC system ........................................................................... 119
Perform direct functions ................................................................................ 123
Dry prime the system ...................................................................................... 126
Run System Prep ............................................................................................. 128
Wet prime the system...................................................................................... 129
Purge the 2410 and 410 reference cell............................................................ 132
Equilibrate the system .................................................................................... 132
Condition the column....................................................................................... 133
Inject samples .................................................................................................. 133
5 Automatic Runs ..................................................................................... 135
System Controller or No Interaction mode..................................................... 135
Controlled by Empower software.................................................................... 136
Controlled by MassLynx software .................................................................. 136
Perform automatic runs in a standalone mode ........................................ 136
Run a sample set.............................................................................................. 137
View sample sets.............................................................................................. 139
Perform a run from a sample template .......................................................... 140
Modify a sample set during a run................................................................... 141
Stop a run......................................................................................................... 142
Perform automatic runs under Empower software control .................. 142
Perform automatic runs under MassLynx control .................................. 144
Perform an automatic run using MassLynx software ................................... 144
6 Create Methods, Sample Sets, and Sample Templates ................. 145
Separation methods ......................................................................................... 145
Sample sets ...................................................................................................... 146
Sample templates ............................................................................................ 146
Create and edit separation methods ........................................................... 146
Create a separation method ............................................................................ 148
Edit a separation method ................................................................................ 149
Copy and edit a separation method ................................................................ 149
Lock and unlock a separation method............................................................ 150

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Set separation method parameters ............................................................. 150
Set Mobile Phase screen parameter values.................................................... 151
Set sample parameter values.......................................................................... 157
Set autosampler parameter values................................................................. 159
Set column parameter values.......................................................................... 161
Set I/O parameter values ................................................................................ 162
Set detector parameters .................................................................................. 166
Create and edit a sample set ......................................................................... 174
Link rows in a sample set................................................................................ 179
Create a sample template ............................................................................... 180
7 Maintenance ........................................................................................... 181
Maintenance considerations ......................................................................... 181
Safety and handling ........................................................................................ 181
Proper operating procedures ........................................................................... 182
Reinitialize the system .................................................................................... 182
Spare parts....................................................................................................... 182
Maintain the solvent management system ................................................ 183
Overview .......................................................................................................... 183
Remove the head, seal-wash assembly, and plunger .................................... 185
Notes on replacing the plunger seals ............................................................. 187
Replace the seal-wash assembly seals............................................................ 190
Clean and replace the plunger ....................................................................... 192
Replace an inlet check valve cartridge ........................................................... 194
Replace the in-line filter ................................................................................. 196
Maintain the sample management system ................................................. 197
Remove side panel of separations module...................................................... 201
Replace the lower needle-wash frit................................................................. 203
Replace the injector needle and seal pack...................................................... 209
Clean the sample compartment ...................................................................... 216
8 Diagnostic Testing and Troubleshooting ........................................ 219
Proper operation .............................................................................................. 219

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Safety and handling ........................................................................................ 219
Use the error log ............................................................................................. 220
Perform main diagnostic tests ...................................................................... 221
Exit the Diagnostics screens ........................................................................... 221
Prime the plunger seal-wash pump................................................................ 223
Perform the compression check ...................................................................... 224
Prime the needle-wash pump ......................................................................... 225
Adjust the seals................................................................................................ 226
Service utilities diagnostic tests ..................................................................... 228
Perform other diagnostic tests and functions .......................................... 228
Perform the motors and valves diagnostic test .............................................. 230
Sensors diagnostic function............................................................................. 233
Static leak test ................................................................................................ 234
Valve leak test.................................................................................................. 236
Head removal and replacement function ....................................................... 237
Inputs and outputs test ................................................................................... 237
Keypad test ..................................................................................................... 239
Display test ...................................................................................................... 239
Carousel test ................................................................................................... 239
Sample heater/cooler test ............................................................................... 239
Defrost sample heater/cooler function ........................................................... 240
Column heater or column heater/cooler test ................................................. 241
Rebuild injector valves function...................................................................... 242
Create a GPV Test Method ............................................................................. 242
Verify the firmware checksum ........................................................................ 243
Troubleshoot ..................................................................................................... 243
General troubleshooting hints ........................................................................ 243
When to call Waters Technical Service ......................................................... 245
Troubleshoot chromatography problems ....................................................... 245
Troubleshooting hardware problems ............................................................. 252
A Safety Advisories .................................................................................. 261
Warning symbols .............................................................................................. 262
Specific warnings ............................................................................................. 263

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Caution advisory .............................................................................................. 265
Warnings that apply to all Waters instruments and devices ................. 266
Warnings that address the replacing of fuses ........................................... 271
Electrical and handling symbols .................................................................. 273
Electrical symbols ............................................................................................ 273
Handling symbols ............................................................................................ 274
B Specifications ........................................................................................ 275
Physical specifications ................................................................................... 276
Environmental specifications ....................................................................... 276
Electrical specifications ................................................................................. 276
Solvent management specifications ............................................................ 279
Sample management specifications ............................................................ 281
Instrument control and communication specifications ......................... 282
C Spare Parts ............................................................................................ 283
Solvent management system spare parts ................................................... 284
Sample management system spare parts ................................................... 285
Separations module spare parts ................................................................... 286
Vials and low volume inserts ........................................................................ 286
D Solvent Considerations ....................................................................... 291
Introduction ...................................................................................................... 291
Clean solvents .................................................................................................. 291
Solvent quality ................................................................................................. 292
Solvent reservoirs ............................................................................................ 292
Preparation checklist....................................................................................... 292
Water ................................................................................................................ 293
Buffers .............................................................................................................. 293
Tetrahydrofuran (THF) ................................................................................... 293

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GPC solvents and seal choices ........................................................................ 293
Solvent compatibility ...................................................................................... 294
Solvents to avoid .............................................................................................. 295
Solvents to use ................................................................................................. 295
Solvent miscibility ........................................................................................... 297
How to use miscibility numbers (M-numbers) ............................................... 299
Buffered solvents ............................................................................................. 300
Head height ....................................................................................................... 300
Solvent viscosity ............................................................................................... 300
Mobile phase solvent degassing ................................................................... 301
Gas solubility ................................................................................................... 301
Vacuum degassing ........................................................................................... 302
Wavelength selection ...................................................................................... 302
UV cutoffs for common solvents...................................................................... 303
Mixed mobile phases........................................................................................ 304
Refractive indices of common solvents ........................................................... 305

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