Thermo Scientific thermoscientific Vanquish Pumps C User manual

thermoscientific
Vanquish
Pumps C, Pumps F
VC-Pxx, VF-Pxx
Operating Manual
4820.4405-EN Revision 4.0 •December 2019

Copyright © 2019 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Manual
The hardware descriptions in this manual revision refer to devices VC-P10-A-01, VC-P20-A-01,
VC-P21-A-01, VC-P32-A-01, VC-P33-A-01, VC-P40-A-01, VF-P10-A-01, VF-P20-A, VF-P32-A-01.
Trademarks
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MP35N is a trademark of SPS Technologies.
PharMed is a trademark of Saint-Gobain Performance Plastics.
Torx is a trademark of Acument Intellectual Properties, LLC.
All other trademarks are property of Thermo Fisher Scientific and its subsidiaries.
Disclaimer
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to
use in the product operation. The document is copyright protected; any reproduction of the
whole or any part of this document is strictly prohibited, except with the written authorization
of Thermo Fisher Scientific Inc.
This manual is provided "as is." The contents of this manual are subject to being changed,
without notice, in future revisions.
Thermo Fisher Scientific Inc. makes no representations that this document is complete,
accurate, or error-free. Thermo Fisher Scientific Inc. assumes no responsibility and will not be
liable for any errors, omissions, damage, or loss that might result from any use of this document,
even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a
purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale.
The Terms and Conditions of Sale shall govern all conflicting information between the two
documents.
Printed manual version only
Printed in Germany on 100% chlorine-free bleached, high-white paper that is produced in an
environmentally friendly process, leading to a paper profile of zero CO2 emissions.
Manufacturer's address
Dionex Softron GmbH, Part of Thermo Fisher Scientific, Dornierstrasse 4, D-82110 Germering

Contacting Us
There are several ways to contact us:
Ordering Information
For ordering information or sales support for HPLC products, contact
your local Thermo Fisher Scientific sales organization. For contact
information, go to Contact Us on http://www.thermofisher.com.
Technical Assistance
For technical support for HPLC products, contact your local Thermo
Fisher Scientific support organization. For contact information, go to
Contact Us on http://www.thermofisher.com.
Contacting Us
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 3

Contacting Us
Page 4 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual

Contents
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 5
Contents
1 Using this Manual ...................................................................... 11
1.1 About this Manual ................................................................................................12
1.2 Conventions..........................................................................................................13
1.2.1 Safety Messages....................................................................................... 13
1.2.2 Special Notices and Informational Notes ................................................. 13
1.2.3 Typographical Conventions ...................................................................... 14
1.3 Reference Documentation ...................................................................................15
2 Safety......................................................................................... 17
2.1 Safety Symbols and Signal Words.........................................................................18
2.1.1 Safety Symbols and Signal Words in This Manual .................................... 18
2.1.2 Observing this Manual ............................................................................. 18
2.1.3 Safety Symbols on the Device .................................................................. 19
2.1.4 Rating Plate .............................................................................................. 19
2.2 Intended Use ........................................................................................................20
2.3 Safety Precautions................................................................................................21
2.3.1 General Safety Information...................................................................... 21
2.3.2 Qualification of the Personnel ................................................................. 22
2.3.3 Personal Protective Equipment................................................................ 22
2.3.4 Electrical Safety Precautions .................................................................... 23
2.3.5 General Residual Hazards......................................................................... 24
2.3.6 In Case of Emergency ............................................................................... 25
2.4 Solvent and Additive Information ........................................................................26
2.4.1 General Compatibility .............................................................................. 26
2.4.2 Allowed pH Ranges................................................................................... 27
2.4.3 Allowed Concentrations ........................................................................... 27
2.4.4 Further Information ................................................................................. 28
2.5 Compliance Information.......................................................................................29
3 Device Overview ........................................................................ 31
3.1 Pump Features .....................................................................................................32
3.2 Operating Principle...............................................................................................33
3.3 Interior Components ............................................................................................34
3.4 Piston Seal Wash System......................................................................................35
3.5 Purge/Sensor Unit ................................................................................................36

Contents
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Operating Manual
3.6 Mixing System ......................................................................................................37
3.7 Leak Detection......................................................................................................38
3.8 Operation .............................................................................................................39
4 Unpacking .................................................................................. 41
4.1 Unpacking.............................................................................................................42
4.2 Scope of Delivery..................................................................................................44
5 Installation................................................................................. 45
5.1 Safety Guidelines for Installation .........................................................................46
5.2 Installing the Device .............................................................................................47
5.3 Site Requirements ................................................................................................49
5.3.1 Power Considerations .............................................................................. 49
5.3.2 Power Cord............................................................................................... 50
5.3.3 Condensation ........................................................................................... 50
5.4 Accessing the Interior Components .....................................................................51
5.5 Setting Up the Hardware......................................................................................52
5.5.1 System Arrangement................................................................................ 52
5.5.2 Connecting the Device ............................................................................. 53
5.5.3 Connecting the Power Cord ..................................................................... 55
5.6 Setting Up the Flow Connections .........................................................................56
5.6.1 General Information and Guidelines........................................................ 56
5.6.2 Guiding Capillaries and Tubing Through the System................................ 57
5.6.3 Connecting Fittings, Capillaries, and Tubing ............................................ 59
5.6.4 Guiding Liquids to Waste ......................................................................... 64
5.6.5 Connecting the Solvent Lines ................................................................... 64
5.6.6 Installing Solvent Shut Off Valves............................................................. 69
5.7 Seal Wash System.................................................................................................71
5.7.1 Choosing the Seal Wash Liquid ................................................................ 71
5.7.2 Setting Up the Seal Wash System ............................................................ 72
5.7.3 Flushing the Seal Wash System ................................................................ 78
5.8 Connecting the Pump and Autosampler ..............................................................80
5.9 Turning On the Device..........................................................................................81
5.10 Setting Up the Device in the Software .................................................................82

Contents
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 7
6 Operation................................................................................... 83
6.1 Introduction to this Chapter.................................................................................84
6.2 Safety Guidelines for Operation ...........................................................................85
6.3 Control Elements..................................................................................................86
6.3.1 Keypad...................................................................................................... 86
6.3.2 Status Indicators....................................................................................... 88
6.4 Power On/Off Control ..........................................................................................91
6.5 Use of Solvents and Additives ..............................................................................92
6.6 Preparing the Device for Operation .....................................................................95
6.7 Important Operating Parameters.........................................................................97
6.8 Purging the Pump .............................................................................................. 103
6.8.1 Automatic Purging.................................................................................. 104
6.8.2 Manual Purging ...................................................................................... 105
6.9 Optimizing the Performance of the Device ....................................................... 110
6.9.1 General Guidelines ................................................................................. 110
6.9.2 Installing Solvent Shut Off Valves........................................................... 110
6.10 Shutting Down the Device ................................................................................. 113
6.10.1 Short-Term Shutdown (Interruption of Operation) ............................... 113
6.10.2 Long-Term Shutdown............................................................................. 114
6.10.3 Restart after Long-Term Shutdown........................................................ 116
7 Maintenance and Service ......................................................... 117
7.1 Introduction to Maintenance and Service......................................................... 118
7.2 Safety Guidelines for Maintenance and Service................................................ 119
7.3 General Rules for Maintenance and Service ..................................................... 121
7.4 Routine and Preventive Maintenance............................................................... 122
7.4.1 Internal Maintenance............................................................................. 122
7.4.2 Maintenance Plan .................................................................................. 122
7.4.3 Flushing the Pump.................................................................................. 124
7.4.4 Cleaning or Decontaminating the Device............................................... 126
7.4.5 Predictive Performance.......................................................................... 127
7.5 Seal Wash System.............................................................................................. 129
7.5.1 Testing the Seal Wash System for Leakage ............................................ 130
7.5.2 Replacing the Seal Wash Lines ............................................................... 131
7.5.3 Replacing the Seal Wash Detector ......................................................... 134

Contents
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Operating Manual
7.6 Pump Head ........................................................................................................ 136
7.6.1 Overview of Pump Head Parts ............................................................... 137
7.6.2 Replacing the Pump Head ...................................................................... 138
7.6.3 Replacing the Pistons ............................................................................. 144
7.6.4 Cleaning the Piston................................................................................. 146
7.6.5 Replacing the Piston Seals or Support Ring............................................ 147
7.6.6 Recommendations for New Piston Seals................................................ 151
7.6.7 Replacing the Seal Wash Seals ............................................................... 154
7.6.8 Replacing the Pump Head Seals ............................................................. 157
7.6.9 Testing the Piston Seals for Leakage ...................................................... 159
7.7 Check Valves...................................................................................................... 162
7.7.1 Replacing the Inlet Check Valves............................................................ 162
7.7.2 Replacing the Outlet Check Valves......................................................... 164
7.7.3 Cleaning the Check Valves...................................................................... 167
7.8 Mixing System ................................................................................................... 168
7.8.1 Testing the Static Mixer for Permeability............................................... 168
7.8.2 Replacing the Static Mixer or Capillary Mixer ........................................ 169
7.9 Solvent Lines and Solvent Line Filters................................................................ 171
7.9.1 Emptying the Solvent Lines .................................................................... 171
7.9.2 Replacing Solvent Lines .......................................................................... 172
7.9.3 Replacing the Solvent Line Filter ............................................................ 175
7.10 Replacing the Purge Valve Knob........................................................................ 177
7.11 Testing the Pump for Leakage (General Test) ................................................... 179
7.12 Replacing the Main Power Fuses....................................................................... 182
7.13 Updating the Device Firmware.......................................................................... 184
7.14 Replacing the Doors........................................................................................... 186
7.15 Transporting or Shipping the Device ................................................................. 188
7.15.1 Preparing the Device for Transport........................................................ 188
7.15.2 Transporting the Device to a New Location ........................................... 189
7.15.3 Shipping the Device................................................................................ 190
7.16 Replacing the Slide-In Module........................................................................... 191
7.16.1 Removing the Slide-In Module ............................................................... 191
7.16.2 Returning the Slide-In Module ............................................................... 192
7.16.3 Installing the Slide-In Module ................................................................ 193
7.16.4 Setting Up the Slide-In Module .............................................................. 195

Contents
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 9
8 Troubleshooting....................................................................... 197
8.1 General Information about Troubleshooting .................................................... 198
8.2 Messages ........................................................................................................... 200
8.3 Testing the Pump for Leakage ........................................................................... 208
8.4 Resolving Liquid Leaks ....................................................................................... 209
8.5 Pressure Issues or Shifts in Retention Time....................................................... 210
8.5.1 Pressure Not Zero with Open Purge Valve............................................. 210
8.5.2 Checking the Compression Values ......................................................... 210
8.5.3 Testing the Static Mixer for Permeability............................................... 212
8.6 Removing Persistent Air Bubbles....................................................................... 213
9 Pump-Specific Information....................................................... 215
9.1 Introduction to this Chapter.............................................................................. 216
9.2 Quaternary Pump and Dual Pump..................................................................... 217
9.2.1 Interior Components .............................................................................. 218
9.2.2 Operating Principle................................................................................. 221
9.2.3 Dwell Volume of the Pump .................................................................... 222
9.2.4 Setting the Solvent Composition............................................................ 223
9.2.5 Synchronizing the Injection Time with the Pump Strokes...................... 224
9.2.6 Dual Pump Specifics ............................................................................... 225
9.3 Binary Pump ...................................................................................................... 228
9.3.1 Interior Components .............................................................................. 228
9.3.2 Operating Principle................................................................................. 230
9.3.3 Dwell Volume of the Pump .................................................................... 231
9.3.4 Setting the Solvent Composition............................................................ 232
9.4 Isocratic Pump ................................................................................................... 233
9.4.1 Interior Components .............................................................................. 233
9.4.2 Operating Principle................................................................................. 234
10 Modifying the Pump for Specific Applications .......................... 235
10.1 Gradient Delay Volume, Dwell Volume and Ripple ........................................... 236
10.1.1 Available Mixing Systems ....................................................................... 237
10.1.2 Exchanging the Mixing System............................................................... 239
10.2 Normal-Phase Compatible Solvents and Additives ........................................... 249
10.2.1 Modifying the Pump and Autosampler .................................................. 249
10.2.2 Considerations with Normal-Phase Compatible Solvents and Additives251

Contents
Page 10 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
11 Specifications ........................................................................... 253
11.1 Performance Specifications............................................................................... 254
11.1.1 Quaternary Pump and Dual Pump ......................................................... 254
11.1.2 Binary Pump ........................................................................................... 256
11.1.3 Isocratic Pump........................................................................................ 258
11.2 Physical Specifications....................................................................................... 260
12 Accessories, Consumables and Replacement Parts ................... 261
12.1 General Information.......................................................................................... 262
12.2 Ship Kit............................................................................................................... 263
12.2.1 Binary Pump ........................................................................................... 263
12.2.2 Dual Pump.............................................................................................. 265
12.2.3 Isocratic Pump........................................................................................ 266
12.2.4 Quaternary Pump................................................................................... 267
12.3 Optional Accessories ......................................................................................... 269
12.3.1 Optional Accessories (Miscellaneous).................................................... 269
12.3.2 Optional Mixing Systems and Inline Filters ............................................ 270
12.4 Consumables and Replacement Parts ............................................................... 273
12.4.1 Maintenance Kits ................................................................................... 273
12.4.2 Pump Heads and Components............................................................... 277
12.4.3 Solvents and Wash Systems ................................................................... 280
12.4.4 Mixing Systems....................................................................................... 282
12.4.5 Miscellaneous Parts ............................................................................... 282
12.4.6 Interface Cables and Power Cords ......................................................... 283
13 Appendix.................................................................................. 285
13.1 Compliance Information.................................................................................... 286
13.1.1 Declarations of Conformity .................................................................... 286
13.1.2 WEEE Compliance .................................................................................. 287
13.1.3 FCC Compliance...................................................................................... 287
13.1.4 Manual Release History.......................................................................... 287
13.2 Digital I/O .......................................................................................................... 288
Index........................................................................................ 291

1 • Using this Manual
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 11
1 Using this Manual
This chapter provides information about this manual, the conventions
used throughout the manual, and the reference documentation that is
available in addition to this manual.

1 • Using this Manual
Page 12 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
1.1 About this Manual
This manual describes the functional features and operating principle of
your Vanquish™ device and provides instructions for installation, set up,
start up, shut down, operation, maintenance and troubleshooting.
The layout of this manual is designed to provide quick reference to the
sections of interest to the user. To obtain a full understanding of your
device, read this manual thoroughly.
This manual also contains safety messages, precautionary statements,
and special notices that can prevent personal injury, damage to the
device, or loss of data when followed properly.
Note the following:
•The device configuration may vary; therefore, not all descriptions
necessarily apply to your particular device.
•If some detail applies to only one model or variant, the model or
variant is identified by name.
•Illustrations in this manual are provided for basic understanding.
They can vary from the actual model of the device or component.
However, this does not influence the descriptions. No claims can be
derived from the illustrations in this manual.
•The pump is referred to as device or pump in this manual. If some
detail applies to only one pump type or model, the type or model is
identified by name.
The descriptions in this manual assume that the device is installed in the
Vanquish system stack. If this is not the case, additional hardware is
required and must be ordered separately. The information in this
manual applies correspondingly.

1 • Using this Manual
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 13
1.2 Conventions
This section describes the conventions that are used throughout this
manual.
1.2.1 Safety Messages
The safety messages and precautionary statements in this manual
appear as follows:
•Safety messages or precautionary statements that apply to the
entire manual and all procedures in this manual are grouped in the
Safety chapter.
•Safety messages or precautionary statements that apply to an entire
section or to multiple procedures in a section appear at the
beginning of the section to which they apply.
•Safety messages that apply to only a particular section or procedure
appear in the section or procedure to which they apply. They appear
different from the main flow of text.
Safety messages are often preceded by an alert symbol and/or alert
word. The alert word appears in uppercase letters and in bold type.
Make sure that you understand and follow all safety messages
presented in this manual.
1.2.2 Special Notices and Informational Notes
Special notices and informational notes in this manual appear different
from the main flow of text. They appear in boxes and a note label
identifies them. The label text appears in uppercase letters and in bold
type.
NOTICE
Highlights information necessary to prevent damage to the device or
invalid test results.
TIP Highlights information of general interest or helpful information that
can make a task easier or optimize the performance of the device.

1 • Using this Manual
Page 14 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
1.2.3 Typographical Conventions
These typographical conventions apply to the descriptions in this
manual:
Data Input and Output
•The following appears in bold type:
¨Input that you enter by the keyboard or that you select with the
mouse
¨Buttons that you click on the screen
¨Commands that you enter by the keyboard
¨Names of, for example, dialog boxes, properties, and parameters
•For brevity, long expressions and paths appear in the condensed
form, for example: Click Start > All Programs > Thermo
Chromeleon7 > Services Manager > Start Instrument Controller.
References and Messages
•References to additional documentation appear italicized.
•Messages that appear on the screen are identified by quotation
marks.
Viewpoint
If not otherwise stated, the expressions left and right in this manual
always refer to the viewpoint of a person that is facing the device from
the front.
Particularly Important Words
Particularly important words in the main flow of text appear italicized.
Electronic Manual Version (PDF)
The electronic version (PDF) of the manual contains numerous links that
you can click to go to other locations within the manual. These include:
•Table of contents entries
•Index entries
•Cross-references (in blue text), for example, to sections and figures

1 • Using this Manual
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 15
1.3 Reference Documentation
In addition to this operating manual, other documentation is available
for reference.
Hardware Documentation
Additional hardware documentation includes the following:
•Operating manuals for the other modules of the Vanquish system
A printed version of the manual is shipped with the device.
•Vanquish System Operating Manual
A printed version of the manual is shipped with the Vanquish system
base and solvent rack.
•Instrument Installation Qualification Operating Instructions
TIP Electronic versions of these manuals are available as PDF (Portable
Document Format) files. To open and read the PDF files, Adobe™
Reader™ or Adobe™ Acrobat™ is required.
Software Documentation
Additional software documentation includes the following:
•Chromeleon™ Help and documents
The Chromeleon Help provides extensive information and
comprehensive reference material for all aspects of the software.
In addition, the following documentation is available (availability
depends on the software version):
•Installation Guide
For basic information about device installation and configuration,
refer to the Installation Guide.
•Instrument Configuration Manager Help
For specific information about a certain device, refer to the
Instrument Configuration Manager Help. In Chromeleon7, devices
are called modules.
•Quick Start Guide
For information about the main elements of the user interface and
step-by-step guidance through the most important workflows, refer
to the Quick Start Guide.
•Reference Card
For a concise overview of the most important workflows, refer to
the Reference Card.

1 • Using this Manual
Page 16 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
TIP The Chromeleon Help and documents are included in the software
shipment.
Third-Party Documentation
Refer also to the user documentation provided by the manufacturers of
third-party components and materials, for example, Safety Data Sheets
(SDSs).

2 • Safety
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 17
2 Safety
This chapter provides general and specific safety information and
informs about the intended use of the device.

2 • Safety
Page 18 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
2.1 Safety Symbols and Signal Words
2.1.1 Safety Symbols and Signal Words in This Manual
This manual contains safety messages to prevent injury of the persons
using the device.
The safety symbols and signal words in this manual include the
following:
Always be aware of the safety information. Do not proceed until you
have fully understood the information and consider the consequences of
what you are doing.
CAUTION
Indicates a hazardous situation that, if not avoided, could result in minor
or moderate injury.
WARNING
Indicates a hazardous situation that, if not avoided, could result in
serious injury.
2.1.2 Observing this Manual
Observe the following:
•Before installing or operating the device, read this manual carefully
to be familiar with the device and this manual. The manual contains
important information with regard to user safety as well as use and
care of the device.
•Always keep the manual near the device for quick reference.
•Save this manual and pass it on to any subsequent user.
Read, understand, and comply with all safety messages and
precautionary statements presented in this manual.

2 • Safety
Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
Page 19
2.1.3 Safety Symbols on the Device
The table lists the safety symbols that appear on the device or on labels
affixed to the device. Follow the safety notices in this manual to prevent
the risk of operator injury or damage to the device.
Symbol Description
Indicates a potential hazard. Refer to this manual to avoid the risk of
personal injury and/or to prevent damage to the device.
—
Ο
Power supply is on
Power supply is off
Indicates alternating current.
2.1.4 Rating Plate
The rating plate is present on the device near the electrical connections.
The rating plate indicates the serial number, part number, module
name, revision number (if any), line and fuse rating, and the
manufacturer's address.
TIP An additional type label on the leak tray of the device indicates the
module name, serial number, part number, and revision number (if any).
To facilitate device identification, have the information from this label
available when communicating with Thermo Fisher Scientific.

2 • Safety
Page 20 Pumps C, Pumps F ( VC-Pxx, VF-Pxx)
Operating Manual
2.2 Intended Use
The device is intended to be part of the Vanquish system.
The intended use of the Vanquish system is to analyze mixtures of
compounds in sample solutions.
The device is for use by qualified personnel and in laboratory
environment only.
The device and Vanquish system are intended to be used as General
Laboratory Equipment (GLE).
They are not intended for use in diagnostic procedures.
Laboratory Practice
Thermo Fisher Scientific recommends that the laboratory in which the
Vanquish system is used follow best practices for LC analyses. This
includes among others:
•Using appropriate standards
•Regularly running calibration
•Establishing shelf life limits and following them for all consumables
used with the system
•Running the system according to the laboratory's verified and
validated 'lab developed test' protocol