Thermo Scientific thermoscientific Vanquish UHPLC System User manual

thermoscientific
Vanquish
UHPLC System
Operating Manual
4820.3601-EN Revision 4.0 •December 2019

Copyright © 2019 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Manual
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Contact Us on http://www.thermofisher.com.
Contacting Us
UHPLC System
Operating Manual
Page 3

Contacting Us
Page 4 UHPLC System
Operating Manual

Contents
UHPLC System
Operating Manual
Page 5
Contents
1 Using this Manual ........................................................................ 9
1.1 About this Manual ................................................................................................10
1.2 Conventions..........................................................................................................11
1.2.1 Safety Messages....................................................................................... 11
1.2.2 Special Notices and Informational Notes ................................................. 11
1.2.3 Typographical Conventions ...................................................................... 12
1.3 Reference Documentation ...................................................................................13
2 Safety......................................................................................... 15
2.1 Safety Symbols and Signal Words.........................................................................16
2.1.1 Safety Symbols and Signal Words in This Manual .................................... 16
2.1.2 Observing this Manual ............................................................................. 16
2.1.3 Safety Symbols on the System ................................................................. 17
2.2 Intended Use ........................................................................................................18
2.3 Safety Precautions................................................................................................19
2.3.1 General Safety Information...................................................................... 19
2.3.2 Qualification of the Personnel ................................................................. 19
2.3.3 Personal Protective Equipment................................................................ 21
2.3.4 General Residual Hazards......................................................................... 22
2.3.5 In Case of Emergency ............................................................................... 24
2.4 Solvent and Additive Information ........................................................................25
2.4.1 General Compatibility .............................................................................. 25
2.4.2 Allowed pH Ranges................................................................................... 26
2.4.3 Allowed Concentrations ........................................................................... 26
2.4.4 Further Information ................................................................................. 27
3 System Overview ....................................................................... 29
3.1 System Description (Standard Configuration) ......................................................30
3.1.1 Solvent Rack ............................................................................................. 31
3.1.2 System Base ............................................................................................. 32
3.2 Operation .............................................................................................................33
4 Unpacking .................................................................................. 35
4.1 Unpacking.............................................................................................................36
4.2 Scope of Delivery..................................................................................................37

Contents
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Operating Manual
5 Installation................................................................................. 39
5.1 Safety Guidelines for Installation .........................................................................40
5.2 Installing the System ............................................................................................41
5.3 Site Requirements ................................................................................................43
5.3.1 Workbench............................................................................................... 43
5.3.2 Power Considerations .............................................................................. 44
5.3.3 Power Cord............................................................................................... 44
5.3.4 Condensation ........................................................................................... 45
5.3.5 Operating Conditions ............................................................................... 45
5.4 Setting Up the Hardware......................................................................................46
5.4.1 System Stack Setup .................................................................................. 46
5.4.2 Signal Cable Connections ......................................................................... 54
5.4.3 Power Connections .................................................................................. 59
5.4.4 Cable Clips ................................................................................................ 60
5.4.5 System Base Lock ..................................................................................... 61
5.5 Setting Up the Flow Connections .........................................................................64
5.5.1 General Information and Guidelines........................................................ 64
5.5.2 Flow Connections Overview..................................................................... 65
5.5.3 Guiding Capillaries and Tubing Through the System................................ 66
5.5.4 Connecting Fittings, Capillaries, and Tubing ............................................ 68
5.5.5 Connecting the Waste Lines..................................................................... 70
5.6 Turning On the System .........................................................................................78
5.7 Setting Up the System in the Software.................................................................79
5.8 Flushing the System..............................................................................................81
6 Operation................................................................................... 83
6.1 Introduction to this Chapter.................................................................................84
6.2 Safety Guidelines for Operation ...........................................................................85
6.3 Power On/Off Control ..........................................................................................86
6.4 Preparing the System for Operation.....................................................................87
6.5 Use of Solvents and Additives ..............................................................................89
6.6 Operating the System from the Software ............................................................92
6.6.1 Starting the Instrument Controller and Client ......................................... 92
6.6.2 Controlling the System from the ePanel Set ............................................ 93
6.6.3 Monitoring the Baseline........................................................................... 94
6.6.4 Running Automated Sample Analysis....................................................... 95
6.7 Shutting Down the System ...................................................................................97

Contents
UHPLC System
Operating Manual
Page 7
7 Maintenance and Service ......................................................... 101
7.1 Introduction to Maintenance and Service......................................................... 102
7.2 Safety Guidelines for Maintenance and Service................................................ 103
7.3 General Rules for Maintenance and Service ..................................................... 105
7.4 Routine and Preventive Maintenance............................................................... 106
7.4.1 Maintenance Plan .................................................................................. 106
7.4.2 Cleaning or Decontaminating the System .............................................. 106
7.5 Transporting or Shipping the System ................................................................ 109
8 Troubleshooting....................................................................... 113
8.1 General Information about Troubleshooting .................................................... 114
8.2 System Troubleshooting.................................................................................... 115
8.2.1 Peak Shape ............................................................................................. 115
8.2.2 Ghost Peaks, Negative Peaks and Spikes ............................................... 116
8.2.3 Peak Area Precision................................................................................ 117
8.2.4 Flow........................................................................................................ 119
8.2.5 Pressure.................................................................................................. 120
8.2.6 Retention Time Variation ....................................................................... 121
8.2.7 Baseline .................................................................................................. 121
8.2.8 Temperature Control ............................................................................. 123
8.2.9 Power and Communication.................................................................... 124
8.2.10 System Diagnostics................................................................................. 125
9 Specifications ........................................................................... 129
9.1 System Specifications ........................................................................................ 130
9.2 Solvent Rack and System Base Specifications ................................................... 131
10 Accessories, Consumables and Replacement Parts ................... 133
10.1 General Information.......................................................................................... 134
10.2 Ship Kit............................................................................................................... 135
10.3 Optional Accessories ......................................................................................... 137
10.4 Consumables and Replacement Parts ............................................................... 138
10.4.1 Capillaries and Tubing ............................................................................ 138
10.4.2 Solvents and Wash Systems ................................................................... 139
10.4.3 Fuses and Cables .................................................................................... 140
10.4.4 Other Parts ............................................................................................. 140

Contents
Page 8 UHPLC System
Operating Manual
11 Appendix.................................................................................. 141
11.1 Compliance Information.................................................................................... 142
11.1.1 Declarations of Conformity .................................................................... 142
11.1.2 WEEE Compliance .................................................................................. 143
11.1.3 FCC Compliance...................................................................................... 143
11.1.4 Manual Release History.......................................................................... 143
Index........................................................................................ 145

1 • Using this Manual
UHPLC System
Operating Manual
Page 9
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 10 UHPLC System
Operating Manual
1.1 About this Manual
This manual provides instructions for installation, set up, start up, shut
down, operation, maintenance and troubleshooting of your system.
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
system, read this manual thoroughly.
This manual also contains safety messages, precautionary statements,
and special notices that can prevent personal injury, damage to the
system, or loss of data when followed properly.
Note the following:
•The descriptions in this manual refer to a standard one-stack
VanquishTM system configuration. Not all descriptions necessarily
apply to your particular system.
•Illustrations in this manual are provided for basic understanding.
They can vary from the actual model of the system. However, this
does not influence the descriptions. No claims can be derived from
the illustrations in this manual.

1 • Using this Manual
UHPLC System
Operating Manual
Page 11
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 system 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 system.

1 • Using this Manual
Page 12 UHPLC System
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 system 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
UHPLC System
Operating Manual
Page 13
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 modules of the Vanquish system
A printed version of the manual is shipped with each device.
•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.
TIP The Chromeleon Help and documents are included in the software
shipment.

1 • Using this Manual
Page 14 UHPLC System
Operating Manual
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
UHPLC System
Operating Manual
Page 15
2 Safety
This chapter provides general and specific safety information and
informs about the intended use of the system.

2 • Safety
Page 16 UHPLC System
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 system.
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 system and this manual. The manual contains
important information with regard to user safety as well as use and
care of the system.
•Always keep the manual near the system 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
UHPLC System
Operating Manual
Page 17
2.1.3 Safety Symbols on the System
For a list of the safety symbols that appear on a Vanquish system
module or on labels affixed to a module, refer to the Operating Manual
of the module. Follow the safety notices in these manuals to prevent the
risk of operator injury or damage to the system.
Safety Symbols on the System Base
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.
Indicates a power button that switches the system between on and
off states.

2 • Safety
Page 18 UHPLC System
Operating Manual
2.2 Intended Use
The intended use of the Vanquish system is to analyze mixtures of
compounds in sample solutions.
The system is for use by qualified personnel and in laboratory
environment only.
The Vanquish system and its modules 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

2 • Safety
UHPLC System
Operating Manual
Page 19
2.3 Safety Precautions
2.3.1 General Safety Information
All users must observe the general safety information presented in this
section and all specific safety messages and precautionary statements
elsewhere in this manual during all phases of installation, operation,
troubleshooting, maintenance, shutdown, and transport of the system.
If the system is used in a manner not specified by Thermo Fisher
Scientific, the protection provided by the system could be impaired.
Observe the following:
•Operate the system only within its technical specifications.
•Use only the replacement parts and additional components, options,
and peripherals specifically authorized and qualified for the system
by Thermo Fisher Scientific.
•Perform only the procedures that are described in this operating
manual and in supporting documents for the system. Follow all
instructions step by step and use the tools recommended for the
procedure.
•Open the enclosure of the system and other components only if
specifically instructed to do so in this manual.
•Thermo Fisher Scientific cannot be held liable for any damage,
material or otherwise, resulting from inappropriate or improper use
of the system. If there is any question regarding appropriate usage,
contact Thermo Fisher Scientific before proceeding.
2.3.2 Qualification of the Personnel
Observe the information below on the proper qualification of the
personnel installing and/or operating the system.

2 • Safety
Page 20 UHPLC System
Operating Manual
Installation
System configuration without Charger
Only skilled personnel are permitted to install the system and to
establish the electrical connections according to the appropriate
regulations.
•Thermo Fisher Scientific recommends always having service
personnel certified by Thermo Fisher Scientific perform the
installation (for brevity, referred to as Thermo Fisher Scientific
service engineer).
•If a person other than a Thermo Fisher Scientific service engineer
installs and sets up the system, the installer is responsible for
ensuring the safety of the system.
System configuration with Charger: Installation by Service Engineer
only
Service personnel certified by Thermo Fisher Scientific must perform the
installation (for brevity, referred to as Thermo Fisher Scientific service
engineer).
Operation
General Operation
The system is designed to be operated only by trained and qualified
personnel in a laboratory environment.
All users must know the hazards presented by the system and the
substances they are using. All users should observe the related Safety
Data Sheets (SDSs).