Agilent Technologies 1260Infinity II Bio-inert FractionCollector User manual

Agilent Technologies
Agilent InfinityLab LC Series
1260 Infinity II Analytical
Fraction Collector & 1260
Infinity II Bio-inert Fraction
Collector
User Manual

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
Notices
© Agilent Technologies, Inc. 2017
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Manual Part Number
G1364-90040
Edition
09/2017
Printed in Germany
Agilent Technologies
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1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 3
In This Guide
In This Guide
This manual contains technical reference information about:
•Agilent InfinityLab LC Series 1260 Infinity II Analytical Fraction Collector
(G1364F)
•Agilent InfinityLab LC Series 1260 Infinity II Bio-inert Fraction Collector
(G5664B)
1Introduction
This chapter gives an introduction to the module and an instrument overview.
2 Site Requirements and Specifications
This chapter provides information on environmental requirements, physical
and performance specifications.
3 Using the Module
This chapter explains the essential operational parameters of the module.
4 Preparing the Fraction Collector
This chapter explains the operational parameters of the module.
5 Troubleshooting and Diagnostics
This chapter gives an overview about the troubleshooting and diagnostic
features and the different user interfaces.
6 Error Information
This chapter describes the meaning of error messages, and provides
information on probable causes and suggested actions how to recover from
error conditions.
7 Maintenance
This chapter describes the maintenance of the module.

4 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
In This Guide
8 Parts for Maintenance and Repair
This chapter provides information on parts for maintenance and repair.
9 Identifying Cables
This chapter provides information on cables used with the module.
10 Hardware Information
This chapter describes the module in more detail on hardware and electronics.
11 Appendix
This chapter provides additional information on safety, legal, and web.

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 5
Contents
Contents
1Introduction 9
Product Description 10
Features 12
Overview of the Module 13
Fraction Collector Principle 14
Leak and Waste Handling 15
Bio-inert Materials 17
2 Site Requirements and Specifications 19
Site Requirements 20
Physical Specifications 23
Performance Specifications 24
3 Using the Module 31
Configuration and Operation of the Fraction Collector 32
Solvent Information 54
Turn on/off 56
Status Indicators 58
Agilent Local Control Modules 59
4 Preparing the Fraction Collector 61
Best Practices 62
Solvent Information 63
Capillary Color Coding Guide 69
Install Capillary Connections 70
Setting up the Fraction Collector with the Instrument Control Interface 73
Method Parameter Settings 78
5 Troubleshooting and Diagnostics 87
User Interfaces 88
Agilent Lab Advisor Software 89

6 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
Contents
6 Error Information 91
What Are Error Messages 93
General Error Messages 94
Module Error Messages 100
7 Maintenance 111
Introduction to Maintenance 112
Warnings and Cautions 113
Cleaning the Module 115
Overview of Maintenance 116
Replace the Inlet/Waste Tubings (Analytical and Bio-inert) 117
Replace the Valve to Needle Tubing (Analytical and Bio-inert) 122
Exchange the Analytical Needle Assembly 125
Exchange the Needle/Capillary Carrier Assembly (Analytical and Bio-inert) 128
Exchange the Diverter Valve 132
Exchange the Internal Tray 135
Repair or Exchange a Funnel of the Internal Tray 137
Exchange the Leak Sensor 139
Replace the Module Firmware 141
8 Parts for Maintenance and Repair 143
Analytical-Scale Fraction Collector Parts 144
Bio-inert Fraction Collector Parts 148
Diverter-Valve Assembly 153
Supported Trays for a Fraction Collector 154
List of Recommended Test Tubes 155
List of Recommended Vials and Caps 156
List of Recommended Plates and Closing Mats 160
Fraction Collector Accessory Kits 162
Fraction Collector Thermostat 163
9 Identifying Cables 165
Cable Overview 166
Analog Cables 168
Remote Cables 170
CAN/LAN Cables 174
RS-232 Cables 175
USB 176

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 7
Contents
10 Hardware Information 177
Firmware Description 178
Electrical Connections 181
Interfaces 184
Setting the 6-bit Configuration Switch 192
Early Maintenance Feedback 196
Instrument Layout 197
11 Appendix 199
General Safety Information 200
Waste Electrical and Electronic Equipment Directive 206
Radio Interference 207
Sound Emission 208
Installation of Stainless Steel Cladded PEEK Capillaries 209
Agilent Technologies on Internet 215

8 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
Contents

9
1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User
Manual
Agilent Technologies
1
Introduction
Product Description 10
Product Description (G1364F) 10
Product Description (G5664B) 11
Features 12
Features (G1364F) 12
Features (G5664B) 12
Overview of the Module 13
Overview of the Analytical and Bio-inert Fraction Collector 13
Fraction Collector Principle 14
Leak and Waste Handling 15
Leak and Waste 15
Waste Concept 16
Leak Sensor 16
Bio-inert Materials 17
This chapter gives an introduction to the module and an instrument overview.

10 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
1 Introduction
Product Description
Product Description
Product Description (G1364F)
The 1260 Infinity II Analytical Fraction Collector is designed for optimized
fraction collection at flow rates between 100 L/min and 10 mL/min. This
module fits within any Infinity II LC stack and is ideal for compound
purification in the nanogram to milligram range using columns with internal
diameters between 2.1 and 9.4 mm. For lower flow rates and smaller column
inner diameters, a low-dispersion tubing kit is available, which helps to
maintain the post-column integrity of the separated peaks. Unique fraction
delay sensor technology determines fraction delay volumes automatically and
ensures that fractions are collected just-in-time without the need to collect
extra volume. The optional 1260 Infinity II Multicolumn Thermostat enables
precise control of column temperature from cooling down to 10 degrees below
ambient up to 85 °C for applications involving thermally-labile chemical or
biochemical samples.
Figure 1 Overview of the fraction collector
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3RZHUVZLWFK

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 11
Introduction
1
Product Description
Product Description (G5664B)
The 1260 Infinity II Bio-inert Fraction Collector is the ideal extension to your
system when you need to investigate separated compounds further. It fits
perfectly in Agilent‘s modular LC design and does not require extra bench
space. Patented fraction delay calibration and time- or peak-triggered fraction
collection facilitates superior recovery and purity.
A wide range of collection vessels, including vials, microtiter plates or custom
vessels, provide highest collection flexibility. With flow rates up to 10 mL/min
even run separations using columns with larger inside diameters for small
scale prep applications are possible. An additional cooling module is available
to prevent degradation of thermally-labile bio-molecules.
Figure 2 Overview of the fraction collector
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3RZHUVZLWFK

12 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
1 Introduction
Features
Features
Features (G1364F)
Purification efficiency
•Lowest delay volumes for minimum peak dispersion and carryover
•Automated delay calibration facilitates highest fraction purity while
maintaining high-precision sample recovery
Instrument efficiency
•Per module collection of up to 216 fractions in glass tubes with 4 outer
diameters of tubes available, or in microtiter plates
•Multiple collection modes with fraction triggering based on time, peak, or
mass for exact collection of required fractions
Laboratory efficiency
•Expandable capacity up to 864 fractions within the same footprint
•Smooth upgrade paths allow you to increase capacity based on demand
•Forced fume extraction enables use of fraction collector outside a fume
cupboard
Features (G5664B)
•Bio-inert fraction collection for automated bio-purification and semi-prep
work with larger column dimensions
•Automated peak based fraction collection facilitates bio-analysis workflows
•Novel capillary and connection design
•High salt tolerance (2 M) and wide pH range (1 – 13, short term 14) for
increased flexibility
•Steel and iron-free wetted parts ensure the integrity of bio-molecules and
minimize unwanted surface interactions
•Peltier temperature control from 4 to 40 °C for thermally labile samples
(upgrade from non-thermostatted to thermostatted version possible)
•Controlled by OpenLAB CDS software

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 13
Introduction
1
Overview of the Module
Overview of the Module
Overview of the Analytical and Bio-inert Fraction Collector
Figure 3 Overview of the Analytical and Bio-inert Fraction Collector
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3RZHUVZLWFK

14 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
1 Introduction
Fraction Collector Principle
Fraction Collector Principle
The movements of the Fraction Collector components during the sequence are
monitored continuously by the Fraction Collector processor. The processor
defines specific time windows and mechanical ranges for each movement. If a
specific step of the sequence is not completed successfully, an error message is
generated.
The standard fractioning sequence occurs in the following order:
1The Fraction Collector starts always from the home position.
2When the sample is injected, the fraction probe with diverter valve moves to
the required position.
3When the trigger is given by the detector, the diverter valve opens to collect
the fraction.
4When the trigger is given by the detector, the diverter valve closes and the
arm moves to the next fraction position or back to the home position if this
function is chosen in the CDS.
Fractioning Sequence
Before the start of the sequence, and during an analysis, the diverter valve is
in the fraction start position. In this position, the mobile phase flows through
the diverter valve towards waste.

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 15
Introduction
1
Leak and Waste Handling
Leak and Waste Handling
Leak and Waste
1

16 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
1 Introduction
Leak and Waste Handling
Waste Concept
1Agilent recommends using the 6 L waste can with 1 Stay Safe cap GL45
with 4 ports (5043-1221) for optimal and safe waste disposal. If you decide
to use your own waste solution, make sure that the tubes don't immerse in
the liquid.
Leak Sensor
CAUTION
Solvent incompatibility
The solvent DMF (dimethyl formamide) leads to corrosion of the leak sensor. The
material of the leak sensor, PVDF (polyvinylidene fluoride), is incompatible with DMF.
➔Do not use DMF.

1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual 17
Introduction
1
Bio-inert Materials
Bio-inert Materials
For the Bio-inert LC system, Agilent Technologies uses highest quality
materials in the flow path (also referred to as wetted parts), which are widely
accepted by life science scientists, as they are known for optimum inertness to
biological samples and ensure best compatibility with common samples and
solvents over a wide pH range. Explicitly, the complete flow path is free of
stainless steel and free of other alloys containing metals such as iron, nickel,
cobalt, chromium, molybdenum or copper, which can interfere with biological
samples. The flow downstream of the sample introduction contains no metals
whatsoever.
Table 1 Used Bio-inert materials
Module Materials
Agilent 1260 Infinity II Bio-inert Pump
(G5654A)
Titanium, gold, platinum-iridium, ceramic,
ruby, PTFE, PEEK
Agilent 1260 Infinity II Bio-inert Multisampler
(G5668A)
Upstream of sample introduction:
•Titanium, gold, PTFE, PEEK, ceramic
Downstream of sample introduction:
•PEEK, ceramic
Agilent 1260 Infinity II Bio-inert Manual Injector
(G5628A)
PEEK, ceramic
Agilent 1260 Infinity II Bio-inert Analytical Fraction Collector
(G5664B)
PEEK, ceramic, PTFE
Bio-inert Flow Cells:
Standard flow cell bio-inert, 10 mm, 13 µL, 120 bar ( 12 MPa) for MWD/DAD,
includes Capillary Kit Flow Cells BIO (p/n G5615-68755) (G5615-60022)
(for Agilent 1260 Infinity II Diode Array Detectors DAD G7115A)
PEEK, ceramic, sapphire, PTFE
Bio-inert flow cell, 8 µL, 20 bar (pH 1–12) includes Capillary Kit Flow Cells BIO
(p/n G5615-68755) (G5615-60005)
(for Agilent 1260 Infinity II Fluorescence Detector FLD G7121A/B)
PEEK, fused silica, PTFE

18 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
1 Introduction
Bio-inert Materials
Bio-inert Heat Exchangers, Valves and Capillaries:
Quick-Connect Heat Exchanger Bio-inert (G7116-60009)
(for Agilent 1260 Infinity II Multicolumn Thermostat G7116A)
PEEK (steel-cladded)
Bio-inert Valve heads (G4235A, G5631A, G5632A, G5639A) PEEK, ceramic (Al
2
O
3
based)
Bio-inert Connection capillaries Upstream of sample introduction:
•Titanium
Downstream of sample introduction:
•Agilent uses stainless-steel-cladded
PEEK capillaries, which keep the flow
path free of steel and provide
pressure stability to more than
600 bar.
Table 1 Used Bio-inert materials
Module Materials
NOTE
To ensure optimum bio-compatibility of your Agilent 1260 Infinity II Bio-inert LC system, do
not include non-inert standard modules or parts to the flow path. Do not use any parts that
are not labeled as Agilent “Bio-inert”. For solvent compatibility of these materials, see
“Material Information” on page 64.

19
1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User
Manual
Agilent Technologies
2
Site Requirements and Specifications
Site Requirements 20
Physical Specifications 23
Performance Specifications 24
This chapter provides information on environmental requirements, physical
and performance specifications.

20 1260 Infinity II Analytical-Scale & Bio-inert Fraction Collector User Manual
2 Site Requirements and Specifications
Site Requirements
Site Requirements
A suitable environment is important to ensure optimal performance of the
instrument.
Power Considerations
The module power supply has wide ranging capability. It accepts any line
voltage in the range described in Table 2 on page 23. Consequently there is no
voltage selector in the rear of the module. There are also no externally
accessible fuses, because automatic electronic fuses are implemented in the
power supply.
WARNING
Hazard of electrical shock or damage of your instrumentation
can result, if the devices are connected to a line voltage higher than specified.
➔Connect your instrument to the specified line voltage only.
WARNING
The module is partially energized when switched off, as long as the power cord is
plugged in.
Repair work at the module can lead to personal injuries, e.g. electrical shock, when
the cover is opened and the module is connected to power.
➔Always unplug the power cable before opening the cover.
➔Do not connect the power cable to the instrument while the covers are removed.
WARNING
Inaccessible power plug.
In case of emergency it must be possible to disconnect the instrument from the
power line at any time.
➔Make sure the power connector of the instrument can be easily reached and
unplugged.
➔Provide sufficient space behind the power socket of the instrument to unplug the
cable.