Thermo Scientific Dionex UltiMate 3000 Series User manual

Thermo Scientific Dionex
UltiMate 3000 Series
Automated Fraction Collector
AFC-3000
Operating Instructions
(Original Operating Instructions)
Revision: 1.2
Date: October 2013
© 2013 Thermo Fisher Scientific
Doc No. 4820.7250

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Operating Instructions

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Operating Instructions Page I
Declaration of Conformity
(Original Declaration)
Product: Thermo Scientific Dionex UltiMate 3000 - Fraction Collector
Type: AFC-3000
Dionex Softron GmbH herewith declares conformity of the above products with
the respective requirements of the following regulations:
•EMC Directive 2004/108/EC
•Low Voltage Directive 2006/95/EC
The electrical safety of the products was evaluated based on the following
standard:
•DIN EN 61010-1:2001
Safety requirements for electrical equipment for measurement, control and
laboratory use, Part 1: General Requirements
The Electromagnetic Compatibility (EMC) of the products was evaluated based
on the following standard:
•DIN EN 61326: 2006
Electrical equipment for measurement, control and laboratory use
EMC Requirements
This declaration is issued for the manufacturer
Dionex Softron GmbH
Part of Thermo Fisher Scientific Inc.
Dornierstraße 4
D-82110 Germering
by the Managing Director, Rüdiger Obst and
the Vice President HPLC, Fraser McLeod.
August 30th, 2013

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Page II Operating Instructions

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Operating Instructions Page i
Table of Contents
1Introduction................................................................................................................... 1
1.1 How to Use This Manual ........................................................................................... 1
1.2 Safety Information ..................................................................................................... 2
1.2.1 Symbols on the Fraction Collector and in the Manual ......................................2
1.2.2 Safety Precautions.............................................................................................. 3
1.2.3 Consignes de Sécurité........................................................................................ 6
1.3 Intended Use ............................................................................................................ 10
1.4 Federal Communications Commission (FCC) Note................................................ 11
2Overview ...................................................................................................................... 13
2.1 Unit Description....................................................................................................... 13
2.2 Operating Principle.................................................................................................. 14
2.3 Fraction Collector Configurations ........................................................................... 15
2.4 Front Panel Elements............................................................................................... 17
2.5 Rear Panel ................................................................................................................ 18
2.5.1 Power Switch ................................................................................................... 19
2.5.2 USB Port.......................................................................................................... 19
2.5.3 RS-232 (Serial) Port......................................................................................... 19
2.5.4 Auxiliary I/O Connection ................................................................................ 19
2.6 Universal Fraction Tray, Racks and Tubes.............................................................. 20
2.7 Chromeleon Software .............................................................................................. 21
3Installation................................................................................................................... 23
3.1 Facility Requirements .............................................................................................. 23
3.2 Unpacking................................................................................................................ 24
3.3 Installing the Fraction Collector .............................................................................. 26
3.3.1 Mounting the Diverter Valve Assembly.......................................................... 27
3.3.2 Diverter Valve Connections............................................................................. 28
3.3.3 Attaching the Rinse Station ............................................................................. 29
3.3.4 Connecting the Drain Tubing .......................................................................... 29
3.3.5 Placing Fraction Racks on the Universal Drip Tray........................................ 30
3.3.6 Adjusting the Drop Former Height.................................................................. 33
3.4 Connecting the Fraction Collector........................................................................... 35
3.4.1 Connecting the External Desktop Power Supply............................................. 35
3.4.2 General Communications Information ............................................................ 36
3.4.3 Communication via RS-232............................................................................. 36
3.4.4 Communication via USB................................................................................. 36
3.5 Setting Up the Fraction Collector in Chromeleon ................................................... 39
3.5.1 Installing the Fraction Collector ...................................................................... 39
3.5.2 Configuring the Fraction Collector.................................................................. 40
4Verifying Installation.................................................................................................. 43
4.1 Overview of Actions................................................................................................ 43
4.2 Inspecting Components Prior to Fluidic Operation ................................................. 43

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Page ii Operating Instructions
4.3 Testing the Interface.................................................................................................43
4.4 Testing the Drop Former Alignment........................................................................44
5Operation and Maintenance ......................................................................................45
5.1 Power-Up .................................................................................................................45
5.2 Operation with Chromeleon.....................................................................................45
5.2.1 Connecting to Chromeleon ..............................................................................46
5.2.2 Direct Control ..................................................................................................46
5.2.3 Setting the Rack Configuration........................................................................49
5.2.4 Defining the Collect Mode...............................................................................50
5.2.5 Defining the Movement Mode.........................................................................51
5.2.6 Automated Fraction Collection with Chromeleon...........................................52
5.3 Shutting Down the Fraction Collector .....................................................................57
5.4 Flushing the Rinse Station and Eluent Flow Path....................................................57
5.5 Routine and Preventive Maintenance ......................................................................58
6Troubleshooting ..........................................................................................................59
6.1 General Notes...........................................................................................................59
6.2 Power and Communication Problems......................................................................59
6.3 Messages in the Chromeleon Audit Trail ................................................................60
7Service ..........................................................................................................................61
7.1 General Notes and Safety Precautions .....................................................................61
7.2 Cleaning the Fraction Collector ...............................................................................62
7.2.1 Daily External Cleaning...................................................................................62
7.2.2 Weekly Cleaning..............................................................................................63
7.3 Checking for Leaks ..................................................................................................63
7.4 Installing the Kit for Normal-Phase LC...................................................................64
7.5 Installing the Kit for Low Flow Rates .....................................................................66
7.6 Replacing the Diverter Valve...................................................................................67
7.7 Replacing the Universal Drip Tray ..........................................................................69
7.8 Updating the Firmware ............................................................................................69
8Technical Information ................................................................................................71
9Accessories, Spare Parts, and Consumables.............................................................73
9.1 Standard Accessories (included in the shipment) ....................................................73
9.2 Optional Accessories................................................................................................74
9.3 Consumables and Spare Parts ..................................................................................75
10 Appendix - Chromeleon Example Program .............................................................77
11 Index.............................................................................................................................81

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Operating Instructions Page 1
1 Introduction
1.1 How to Use This Manual
The layout of this manual is designed to provide quick reference to the sections of interest
to the reader. However, in order to obtain a full understanding of the fraction collector,
Thermo Fisher Scientific recommends that you review the manual thoroughly before
operating the fraction collector.
All descriptions in the manual apply to the AFC-3000 Automated Fraction Collector.
Therefore, the term "the fraction collector" or "the AFC-3000" is used throughout the manual.
Notes: The device configuration may vary, for example, the fraction collector may be
equipped with differing rack configurations; therefore, not all descriptions
necessarily apply to your particular instrument. If some detail applies to only
one fraction collector model or version, that model (version) is identified by
name.
It may happen that the representation of a component in this manual is different
from the real component. However, this does not influence the descriptions.
The descriptions in this manual refer to firmware version 1.03 and
ChromeleonTM 6.80 Service Release 13.
This manual is provided "as is." Every effort has been made to supply complete and
accurate information and all technical specifications have been developed with utmost
care. The information contained in this manual should not be construed as a commitment
by Thermo Fisher Scientific. Thermo Fisher Scientific assumes no responsibility for any
errors that may appear in this document that is believed to be complete and accurate at the
time of publication and, in no event shall Thermo Fisher Scientific be liable for incidental
or consequential damages in connection with or arising from the use of this document. We
appreciate your help in eliminating any errors that may appear in this document. The
information contained in this document is subject to change without notice.
All rights reserved, including those for photomechanical reproduction and storage on
electronic media. No part of this publication may be copied or distributed, transmitted,
transcribed, stored in a retrieval system, or transmitted into any human or computer language,
in any form or by any means, electronic, mechanical, magnetic, manual, or otherwise, or
disclosed to third parties without the express written permission of Thermo Fisher Scientific
Inc.
Trademarks
PEEK is a trademark of Victrex PLC.
Simriz is a trademark of Carl Freudenberg KG.
Windows and Windows Vista are registered trademarks of Microsoft Corp.
All other trademarks are property of Thermo Fisher Scientific Inc. and its subsidiaries.

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Page 2 Operating Instructions
1.2 Safety Information
The CE Mark label on the instrument indicates that the instrument is compliant with the
related standards (→page I).
1.2.1 Symbols on the Fraction Collector and in the Manual
The table below shows the symbols used on the fraction collector:
Symbol Description
Direct current—Courant continu
Power supply is on (−) — L'instrument est mis sous tension (−) and
Power supply is off (O)— L'instrument est mis hors tension (O)
Pinch point hazard—Risque de pincement
Refer to the Operating Instructions to prevent risk of harm to the operator and to
protect the instrument against damage.
Référez-vous à ce manuel pour éviter tout risque de blessure à l'opérateur et/ou
protéger l'instrument contre tout dommage.
Label according to the "Measures for Administration of the Pollution Control of
Electronic Information Products" (China RoHS) guideline
Étiquette "Measures for Administration of the Pollution Control of Electronic
Information Products" (China RoHS)
WEEE (Waste Electrical and Electronic Equipment) label—For more
information, see the WEEE Information section in the "Installation and
Qualification Documents for Chromatography Instruments" binder.
Étiquette DEEE (Déchets d'Equipements Electriques et Electroniques) — Pour
plus d'informations, référez-vous au chapitre WEEE Information dans le
classeur "Installation and Qualification Documents for Chromatography
Instruments".

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Operating Instructions Page 3
At various points throughout the manual, messages of particular importance are indicated by
certain symbols:
Tip: Indicates general information, as well as information intended to
optimize the performance of the instrument.
Important: Indicates that failure to take note of the accompanying information
could cause wrong results or may result in damage to the instrument.
Important: Indique que ne pas tenir compte de l'information jointe peut conduire
à de faux résultat ou endommager l'instrument.
Warning: Indicates that failure to take note of the accompanying information
may result in personal injury.
Avertissement: Indique que ne pas tenir compte de l'information jointe peut entraîner
des blessures corporelles.
1.2.2 Safety Precautions
When working with analytical instrumentation, you must know the potential hazards of
using chemical solvents.
Tip: Before initial operation of the fraction collector, make yourself
familiar with the contents of this manual.
For the safety precautions in French, see page Fehler! Textmarke
nicht definiert..
Warning: All users of the device must observe the following safety precautions
and all additional safety precautions in this manual to avoid the
possibility of personal injury or damage to the device when
operating the device or carrying out any maintenance or service
procedures.
Observe any warning labels on the device and refer to the related
sections in these Operating Instructions.
•Protective equipment
When performing any work on or near the HPLC system, wear personal protective
equipment (protective clothing, safety gloves, safety glasses) as required by the hazard of
the mobile phase and sample. For information about the proper handling of a particular
substance and for advice on specific hazards, refer to the material safety data sheet for the
substance you are using. Observe the guidelines of Good Laboratory Practice (GLP).
An eyewash facility and a sink should be close to the device. If any substance splashes on
the eyes or skin, wash the affected area and seek medical attention.

UltiMate 3000 Series:
AFC-3000 Automated Fraction Collector
Page 4 Operating Instructions
•Hazardous substances
Many organic solvents, mobile phases and samples are harmful to health. Be sure that
you know the toxic and infectious properties of all substances that you are using. You
may not know the toxic or infectious properties of many substances that you are using. If
you have any doubt about a substance, treat it as if it contains a potentially harmful
substance. For advice on the proper handling of a particular substance, refer to the Safety
Data Sheet (SDS) of the manufacturer. Observe the guidelines of Good Laboratory
Practice (GLP).
Dispose of waste substance in an environmentally safe manner that is consistent with all
local regulations. Do not allow flammable, toxic, and/or infectious substances to
accumulate. Follow a regulated, approved waste disposal program. Never dispose of
flammable, toxic, and/or infectious substances through the municipal sewage system.
•Hazardous gases
Install the HPLC system in a well-ventilated laboratory. If the mobile phase or sample
includes volatile or flammable solvents, do not allow them to enter the workspace. If the
mobile phase or sample includes volatile or flammable solvents, avoid open flames and
sparks.
•Electrostatic discharge
Discharge of electrostatic energy may lead to sparking and can constitute a fire hazard.
This effect is particularly pronounced in insulating capillaries and with non-conductive
solvents (for example, pure acetonitrile).
Take appropriate measures to prevent the generation of static electricity near the HPLC
system. For example, make sure that the air humidity level in the laboratory is
sufficiently high and provide proper ventilation, wear anti-static clothing or shoes,
prevent accumulation of air bubbles in waste lines, and use grounded waste containers.
Use only non-conductive capillaries to direct solvents into the waste container. With
electrically conductive capillaries, make sure that they are properly grounded.
Operation with Normal-Phase Eluents:
Do not perform normal-phase applications without a proper grounding protection for the
drop former. Non-conductive, non-polar normal-phase eluents, for example hexane, can
lead to a build-up of electrostatic charges on an ungrounded drop former. The
electrostatic discharge can create a fire and/or explosion hazard.
Note that a grounded drop former (part no 6702.0400) is available for normal-phase (NP)
applications. Use normal-phase eluents with the AFC-3000 Automated Fraction
Collector only after it has been modified with this grounded drop former. Operating the
device without the grounded drop former can result in a fire and/or explosion
hazard!
•Self-ignition of solvents
Do not use solvents for which the self-ignition temperature is below 150 °C. In case of
leakage, these solvents may self-ignite on a hot surface.