Amersham™ WB system - GE Healthcare Life Sciences

Amersham™ WB system
User Manual
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Table of Contents
Table of Contents
1
Introduction ..........................................................................................................
1.1
1.2
1.3
1.4
2
8
9
11
12
System description ..............................................................................................
14
2.1
2.2
2.3
15
18
22
Instrument overview ...........................................................................................................................
Elpho & scan unit ..................................................................................................................................
Western unit ............................................................................................................................................
2.3.1
2.3.2
2.3.3
2.4
2.5
2.6
Overview ............................................................................................................................................
Western unit compartments ....................................................................................................
Liquid flow paths ............................................................................................................................
23
26
31
Accessories and consumables overview ..................................................................................
Pre-labeling consumables ................................................................................................................
Accessories and consumables for electrophoresis ..............................................................
35
40
42
2.6.1
2.6.2
2.6.3
2.6.4
2.7
Amersham WB molecular weight markers ........................................................................
Amersham WB gel card ..............................................................................................................
Amersham WB buffer strip and Amersham WB buffer strip holder ........................
Amersham WB paper comb ......................................................................................................
43
45
48
50
Accessories and consumables for Western blot steps ......................................................
51
2.7.1
2.7.2
2.7.3
2.7.4
2.8
2.9
Accessories and consumables for transfer .........................................................................
Secondary antibodies – probing .............................................................................................
Drying holder – PVDF card drying ..........................................................................................
Membrane adapter – PVDF card scan ..................................................................................
52
57
59
60
Other accessories .................................................................................................................................
Amersham WB software overview ...............................................................................................
61
63
2.9.1
2.9.2
2.9.3
2.9.4
2.9.5
2.9.6
2.9.7
3
7
About this manual ................................................................................................................................
Important user information ............................................................................................................
Regulatory information and safety instructions ....................................................................
Amersham WB system documentation .....................................................................................
Amersham WB software start screen ...................................................................................
Amersham WB software main screen ..................................................................................
Menu bar ............................................................................................................................................
Workflow panel ...............................................................................................................................
Instrument status panel ..............................................................................................................
Help panel .........................................................................................................................................
Keyboard shortcuts .......................................................................................................................
64
65
67
72
76
78
79
Plan an experiment ..............................................................................................
80
3.1
3.2
81
83
Electrophoresis and Western experiments ..............................................................................
Pre-labeling of proteins ......................................................................................................................
3.2.1
3.2.2
3.3
3.4
Protein pre-labeling concept .....................................................................................................
Pre-labeling pre-requisites and protocols ...........................................................................
84
86
Plan electrophoresis experiments ................................................................................................
Plan Western experiments ...............................................................................................................
90
93
3.4.1
3.4.2
3.4.3
3.4.4
Fluorescent Western blotting ....................................................................................................
Western normalization strategies ..........................................................................................
Experimental setup .......................................................................................................................
Western experiments setup overview ..................................................................................
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96
98
101
3
Table of Contents
3.4.5
4
Western experiment buffers and solutions ........................................................................
102
Perform an experiment .......................................................................................
105
4.1
4.2
4.3
106
108
110
Overview ...................................................................................................................................................
Start the Amersham WB analyzer ...............................................................................................
Set up an experiment in Amersham WB software ................................................................
4.3.1
4.3.2
4.3.3
4.3.4
4.3.5
4.3.6
4.3.7
4.3.8
4.4
Start the software and create an experiment ...................................................................
Set up experiment and samples ..............................................................................................
Set up electrophoresis and gel scanning protocols ........................................................
Set up the transfer parameters ...............................................................................................
Set up the probing protocol .......................................................................................................
View membrane scanning setup ............................................................................................
View or enter experiment information .................................................................................
Save experiment .............................................................................................................................
111
119
131
136
139
145
147
152
Prepare samples ...................................................................................................................................
153
4.4.1
4.4.2
4.4.3
4.5
Perform pre-labeling of samples .............................................................................................
Prepare unlabeled samples .......................................................................................................
Prepare Amersham WBmolecular weight markers ........................................................
154
161
162
Perform electrophoresis and gel scanning ...............................................................................
163
4.5.1
4.5.2
4.5.3
4.6
Preparations before starting electrophoresis ....................................................................
Run electrophoresis ......................................................................................................................
Procedures after electrophoresis and gel card scanning .............................................
164
169
182
Perform the Western Blot steps (Western experiments only) ..........................................
184
4.6.1
4.6.2
4.6.3
4.6.4
4.6.5
4.6.6
4.6.7
4.6.8
4.6.9
5
Prepare and connect transfer solutions ...............................................................................
Prepare the transfer sandwich ................................................................................................
Run transfer ......................................................................................................................................
Procedures after transfer ...........................................................................................................
Prepare and connect probing and antibody solutions ..................................................
Run probing ......................................................................................................................................
Procedures after probing ............................................................................................................
Run drying .........................................................................................................................................
Scan membrane and view results ..........................................................................................
185
186
200
205
208
211
218
222
224
Evaluate an experiment ......................................................................................
237
5.1
5.2
5.3
238
239
247
Introduction .............................................................................................................................................
Perform evaluation and check results ........................................................................................
Analyze the results of an experiment type ...............................................................................
5.3.1
5.3.2
5.3.3
5.3.4
5.3.5
5.3.6
5.4
Analyze an Easy Western experiment ..................................................................................
Analyze a Western experiment with endogenous protein normalization ............
Analyze a Western experiment with total protein normalization ............................
Analyze an Easy SDS-PAGE experiment ..............................................................................
Analyze an Easy SDS-PAGE experiment with quantity calibration ..........................
Analyze an Easy Western experiment with quantity calibration ..............................
248
250
252
255
258
260
Result views in Amersham WB software ...................................................................................
262
5.4.1
5.4.2
5.4.3
5.4.4
5.4.5
5.4.6
4
Image view .......................................................................................................................................
The Bar chart tab ...........................................................................................................................
The Lane profile tab ......................................................................................................................
The Band table tab ........................................................................................................................
The Quantity calibration tab .....................................................................................................
The Protein table tab ....................................................................................................................
263
272
278
281
285
288
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5.5
Edit analysis settings ...........................................................................................................................
5.5.1
5.5.2
5.5.3
5.5.4
6
291
Edit lane detection .........................................................................................................................
Edit band detection .......................................................................................................................
Edit band matching .......................................................................................................................
Edit molecular weight calibration ...........................................................................................
292
297
304
309
Maintenance .........................................................................................................
317
6.1
6.2
319
324
Maintenance program .......................................................................................................................
Maintenance instructions .................................................................................................................
6.2.1
6.2.2
6.2.3
Weekly cleaning of the transfer and probing flow paths .............................................
Replacement procedures ............................................................................................................
Moving the instrument units .....................................................................................................
325
328
339
7
Troubleshooting ...................................................................................................
340
8
Reference information ........................................................................................
352
8.1
8.2
System specifications .........................................................................................................................
Chemical resistance guide ...............................................................................................................
353
358
Ordering information ..........................................................................................
360
9
Appendix A
The Amersham WB watch app ........................................................
363
Index .......................................................................................................................
371
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1 Introduction
1
Introduction
The Amersham WB system
The Amersham WB system is an integrated system for SDS-PAGE and Western blotting
analysis of proteins based on fluorescence detection. Electrophoresis, scanning, transfer
and automated probing steps are all performed by the same system. Reagents for prelabeling and antibody detection, as well as gel and membrane consumables, are available.
The Amersham WB system includes the instrument, the Amersham WB analyzer,
Amersham WB software (software) and accessories and consumables. The Amersham
WB analyzer comprises of two units, the Amersham WB elpho & scan unit and the
Amersham WB western unit.
The system supports many applications, from quick screening of protein composition
or abundance to advanced quantitative analysis for comparisons of protein levels
between samples. The proteins can be pre-labeled with the dye reagent Amersham WB
Cy™5 and can therefore directly be detected in the gel after electrophoresis. In Western
experiments, unlabeled or Cy5 pre-labeled protein samples are transferred to membranes,
and target proteins can be detected using Cy3 and/or Cy5 conjugated secondary antibodies. The fluorescence based detection gives high sensitivity and a broad dynamic
range, and enables multiplex analysis of the same Western blot membrane.
Multiplex analysis of total protein pre-labeled with Cy5 and target detected with Cy3
labeled secondary antibody enables normalization of target signals using total protein
in each lane. Easy to use Amersham WB software for controlling the different steps of
the workflow and for automated or manual evaluation of your results is part of the system.
In this chapter
This chapter contains the the following sections:
Section
See page
1.1 About this manual
8
1.2 Important user information
9
1.3 Regulatory information and safety instructions
11
1.4 Amersham WB system documentation
12
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1 Introduction
1.1 About this manual
1.1
About this manual
Purpose of this manual
The User Manual provides you with the instructions needed to plan, set up, run and
evaluate experiments as well as instructions needed to safely operate and maintain the
Amersham WB system.
Typographical conventions
Software items are identified in the text by bold italic text. A colon separates menu levels,
thus File:Open refers to the Open command in the File menu.
Hardware items are identified in the text by bold text (e.g., Power switch).
8
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1 Introduction
1.2 Important user information
1.2
Important user information
Read this before operating the
Amersham WB analyzer
All users must read the entire Operating Instructions before installing, operating, or
maintaining the instrument. Always keep the Operating Instructions at hand when operating the Amersham WB analyzer.
Do not operate the Amersham WB analyzer in any other way than described in the user
documentation.
If you do, you may be exposed to hazards that can lead to personal injury, and you may
cause damage to the equipment.
Intended use
Amersham WB system is a protein electrophoresis and Western blotting system that
includes scanning of gel cards and PVDF cards. Proteins can be pre-labeled with Cy5
and can therefore directly be detected in the gel after electrophoresis. In Western experiments, unlabeled or Cy5 pre-labeled protein samples are transferred to membranes,
and target proteins can be detected using Cy3 and/or Cy5 conjugated secondary antibodies. The fluorescence-based detection gives high sensitivity and a broad dynamic
range, and enables multiplex analysis of the same Western blot membrane.
Amersham WB system is intended for research use only, and shall not be used in any
clinical procedures, or for diagnostic purposes.
Prerequisites
In order to operate the system in the way it is intended, the following pre-requisites must
be fulfilled:
•
You should have a general understanding of how the PC and Microsoft® Windows®
work.
•
You should understand the concepts of electrophoresis and Western blotting.
•
The instrument and software must be installed according to the instructions in
Amersham WB system Operating Instructions.
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1 Introduction
1.2 Important user information
Tip:
To read more about the principles and methods of Western blotting and for
guidance on how to perform successful Western blotting, download or order
the handbook, Western Blotting – Principles and Methods 28-9998-97, from
www.gelifesciences.com.
Safety notices
This user documentation contains WARNINGS, CAUTIONS and NOTICES concerning the
safe use of the product. See definitions below.
Warnings
WARNING
WARNING indicates a hazardous situation which, if not avoided,
could result in death or serious injury. It is important not to proceed
until all stated conditions are met and clearly understood.
Cautions
CAUTION
CAUTION indicates a hazardous situation which, if not avoided,
could result in minor or moderate injury. It is important not to
proceed until all stated conditions are met and clearly understood.
Notices
NOTICE
NOTICE indicates instructions that must be followed to avoid
damage to the product or other equipment.
Notes and tips
10
Note:
A note is used to indicate information that is important for trouble-free and
optimal use of the product.
Tip:
A tip contains useful information that can improve or optimize your procedures.
Amersham WB system User Manual 29-0214-88 AC
1 Introduction
1.3 Regulatory information and safety instructions
1.3
Regulatory information and safety instructions
Regulatory information
For regulatory information regarding Amersham WB system, refer to Section 1.3 in
Amersham WB system Operating Instructions.
Safety instructions
For safety instructions regarding Amersham WB system, refer to Chapter 2 in Amersham
WB system Operating Instructions.
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1 Introduction
1.4 Amersham WB system documentation
1.4
Amersham WB system documentation
Introduction
This section describes the user documentation and associated documentation for the
Amersham WB system.
User documentation
The table below lists the user documentation delivered with Amersham WB system:
Document
Main contents
Availability
Amersham WB analyzer
Unpacking Instruction
This instruction describes how to unpack the Amersham WB analyzer.
Inside the Amersham WB
analyzer delivery box.
Amersham WB system
Operating Instructions
This manual contains the information
needed to:
English version in printed
format is delivered with the
system.
•
install, handle and maintain the
Amersham WB system in a safe way
•
perform a typical experiment in a
safe way
Translated versions are
available as PDF files on the
User Documentation CD.
It also contains safety and regulatory
information, a description of the system
and reference information.
Amersham WB system User
Manual
This manual contains the information
needed to:
•
operate and maintain the
Amersham WB system in a safe way
•
plan, perform and evaluate electrophoresis and Western experiments
•
troubleshoot the system and results
Integrated with Amersham
WB software as HTML manual in the Help menu.
Also available as a PDF file
on the User Documentation
CD.
It also contains a description of the
system, reference information and ordering information.
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1 Introduction
1.4 Amersham WB system documentation
Document
Main contents
Availability
Amersham WB software
Help
The Amersham WB software Help contains information about:
Integrated with Amersham
WB software (in the right
panel of the software).
•
user workflows for performing
electrophoresis and Western experiments
•
software descriptions
•
links to the Amersham WB system
User Manual for detailed information about handling of the instrument, accessories and consumables
Method handbook
The handbook Western Blotting – Principles and Methods gives guidance for the complete
Western blotting workflow. It describes theoretical and practical aspects of the technique,
together with useful hints and tips. The aim of the handbook is to guide and inspire beginners, as well as experts, towards successful Western blotting.
Download or order the handbook, Western Blotting – Principles and Methods 28-999897, from www.gelifesciences.com.
Data files and application notes
Data files and application notes can be ordered or downloaded from
www.gelifesciences.com.
Amersham WB system User Manual 29-0214-88 AC
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2 System description
2
System description
About this chapter
Amersham WB system consists of:
•
Amersham WB analyzer (two units)
•
accessories and consumables to be used with the instrument
•
a computer (not included in the delivery)
•
Amersham WB software
This chapter describes the different parts of the Amersham WB system.
In this chapter
This chapter contains the following sections:
Section
14
See page
2.1 Instrument overview
15
2.2 Elpho & scan unit
18
2.3 Western unit
22
2.4 Accessories and consumables overview
35
2.5 Pre-labeling consumables
40
2.6 Accessories and consumables for electrophoresis
42
2.7 Accessories and consumables for Western blot steps
51
2.8 Other accessories
61
2.9 Amersham WB software overview
63
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2 System description
2.1 Instrument overview
2.1
Instrument overview
Introduction
This section provides an overview of the Amersham WB analyzer.
The Amersham WB analyzer consists of two units:
•
Amersham WB elpho & scan unit
•
Amersham WB western unit
The instrument units are controlled from a PC running Amersham WB software.
Note:
The instrument units must always be connected to each other during a run.
Both units must be turned on when running an experiment in the Western
unit.
Safety switches
There is high voltage and two lasers inside the Elpho & scan unit. The unit has double
safety switches that stop the power to the high voltage converter and lasers when the
loader is opened.
There is high voltage inside the transfer tank in the Western unit. The unit has safety
switches that stop the power when the transfer tank lid is opened.
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2 System description
2.1 Instrument overview
Illustration of the Amersham WB
analyzer
The illustration below shows the Amersham WB analyzer, with the Elpho & scan unit to
the left and the Western unit to the right.
Illustration of the instrument
panels
The same setup of indicator lamps are available for each compartment on the instrument
units (electrophoresis and scanning, transfer, probing and drying). When the instrument
units are turned on, the lamps showing the compartment names are lit. The indicators
are located on the instrument panel on each unit.
The illustration below shows the instrument panels on the two units, with the compartment names lit.
16
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2.1 Instrument overview
Indicators on the instrument
The table below describes the different indicators. The indicators (Ready/run finished,
Run and Error or warning) are identical for all instrument unit compartments. In this example, the TRANSFER indicators are described.
Status indicators
TRANSFER
Status
Description
Start-up
The text is lit when the unit is starting
up and performing internal tests.
Ready/run finished
The lamp is lit when:
TRANSFER
TRANSFER
TRANSFER
TRANSFER
•
the unit/compartment is ready for
a new experiment
•
a step (i.e., electrophoresis, scanning, transfer, probing or drying) has
been completed
TRANSFER
TRANSFER
TRANSFER
TRANSFER
TRANSFER
Run
The lamp is lit:
•
when the unit/compartment is running
•
during cleaning of the transfer or
probing flow paths
TRANSFER
TRANSFER
Note:
TRANSFER
Do not open the related lid(s) while running. For example, opening the transfer
lid during transfer will stop the transfer
run and may affect the result.
TRANSFER
TRANSFER
Error or warning
The lamp is lit when an error has occurred
Refer to the Amersham WB software
for information about the error.
Suggestions about how to correct the
problem are provided by the software.
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2 System description
2.2 Elpho & scan unit
2.2
Elpho & scan unit
Introduction
The Elpho & scan unit is used to separate SDS treated sample proteins in a polyacrylamide
gel. It is also used to scan gels after electrophoresis and PVDF cards after probing and
drying in a Western experiment.
This section provides an overview of the Elpho & scan unit.
Illustration of the Elpho & scan
unit
The illustration below shows the main parts of the Elpho & scan unit:
1
2
3
4
Part
Description
1
Instrument panel (with status indicators)
2
Elpho & scan loader
For loading gel cards or PVDF cards.
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2 System description
2.2 Elpho & scan unit
Part
Description
3
Eject button
To open/close the loader of the electrophoresis and scanning compartment.
Note:
The loader can only be opened when no electrophoresis or scanning experiment is running. Any ongoing run first has to be stopped using the appropriate software instruction to be able to eject the loader.
4
Adjustable feet (4 feet, one foot at each corner)
Illustration of the Elpho & scan
unit rear panel
The illustration below shows the main parts of the Elpho & scan unit rear panel:
1
7
Part
Description
1
USB cable connector (USB type B)
2
6
5
4
3
For connecting the Elpho & scan unit to a computer.
2
Communication connection for the Western unit (use ethernet cable)
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2 System description
2.2 Elpho & scan unit
Part
Description
3
Air inlet
4
Mains power switch
ON=I, OFF=O
5
Fuse drawer (5x20 mm)
6
Power cord connector (60320/C14)
7
Air outlets
Elpho & scan loader
The Elpho & scan loader is used to load:
•
gel cards for electrophoresis and scanning
•
PVDF cards for scanning. When loading PVDF cards for scanning, an Amersham WB
membrane adapter must first be placed on the card plate (see Section 4.6.9 Scan
membrane and view results, on page 224 for more information).
The loader is ejected from the Elpho & scan unit by pressing the eject button on the front
panel.
20
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2 System description
2.2 Elpho & scan unit
Illustration of the Elpho & scan
loader
The illustration below shows the Elpho & scan unit with the loader ejected and the sealing
lids of the left card plate opened.
1
3
2
7
6
5
4
Part
Description
1
Latch
For opening the sealing lid.
2
Sealing lid
3
Indicator of position A and position B
4
Cavities
For buffer strip holders with electrical connectors for the buffer electrodes.
5
Guiding pins
For correct placement of gel cards or membrane adapters including PVDF
cards.
6
Card plate
For cooling of gel cards and holding cards flat while scanning.
7
Protective glass
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2 System description
2.3 Western unit
2.3
Western unit
Introduction
The Western unit is used to:
•
transfer the separated proteins in the gel to the membrane
•
probe the proteins on the membrane with primary antibodies and then secondary
antibodies conjugated to a CyDye™
•
dry the PVDF cards (before scanning in the Elpho & scan unit)
This section provides an overview of the Western unit.
In this section
This section contains the following subsections:
Section
22
See page
2.3.1 Overview
23
2.3.2 Western unit compartments
26
2.3.3 Liquid flow paths
31
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2 System description
2.3 Western unit
2.3.1 Overview
2.3.1
Overview
Introduction
This section describes an overview of the front and rear panels of the Western unit.
Illustration of the Western unit
The illustration below shows the main parts of the Western unit:
6
7
5
8
4
3
2
1
Part
Description
1
Antibody compartment lid
2
Area pressed to open the antibody compartment lid
3
Instrument panel (for the status indicators)
4
Transfer tank lid
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2 System description
2.3 Western unit
2.3.1 Overview
Part
Description
5
Bottle rack (and service compartment lid)
Note:
Only remove the bottle rack when the pumps and tubing are inspected or
when parts are replaced as described in Chapter6 Maintenance, on page317.
6
Tubing holders
7
Probing compartment lid
8
Drying compartment lid
Illustration of the Western unit
rear panel
The illustration below shows the main parts of the Western unit rear panel:
1
7
24
2
3
4
5
1
6
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2 System description
2.3 Western unit
2.3.1 Overview
Part
Description
1
Outlets for waste and overflow tubing
2
Communication connection for the Elpho & scan (use ethernet cable)
3
Power cord connector (60320/C14)
4
Fuse drawer (5x20 mm)
5
Mains power switch (ON=I, OFF=O)
6
Air outlets
7
Air inlet
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2 System description
2.3 Western unit
2.3.2 Western unit compartments
2.3.2
Western unit compartments
Introduction
This section describes the different compartments of the Western unit with the lids
opened.
Illustration of the transfer tank
The illustration below shows the transfer tank of the Western unit.
1
5
26
2
3
4
Part
Description
1
Sandwich guiding tracks
2
Indicator of position A and position B
3
Right transfer electrode
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2 System description
2.3 Western unit
2.3.2 Western unit compartments
Part
Description
4
Transfer tank filter
5
Left transfer electrode
Illustration of the probing
compartment
The illustration below shows the probing compartment of the Western unit.
1
2
3
4
5
6
Part
Description
1
Probing chamber
2
Probing chamber lid
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2 System description
2.3 Western unit
2.3.2 Western unit compartments
Part
Description
3
Indicator of position A and position B
4
Guiding pins for PVDF card (marked by orange circles)
5
Probing compartment lid
6
Probing chamber lid hatch
Illustration of the drying
compartment
The illustration below shows the drying compartment of the Western unit.
28
1
2
Part
Description
1
Membrane dryer guides
2
Indicator of position A and position B locations
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2 System description
2.3 Western unit
2.3.2 Western unit compartments
Illustration of the antibody
compartment
The illustration below shows the antibody compartment where 15 ml antibody solution
tubes with primary and secondary antibodies are inserted before probing (left side). See
Connect the antibody solution tubes, on page 209 for more information.
The right side of the compartment is used for storage of the Amersham WB membrane
adapters (Membrane adapters).
1
2
7
3
6
4
5
Part
Description
1
Tube holder
2
Tubing
3
Door lock (magnetic)
4
Membrane adapters
5
Holder for membrane adapters
6
Door lock
7
Indicator of antibody solution tube position A PRIMARY, A SECONDARY, B
PRIMARY, and B SECONDARY.
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2 System description
2.3 Western unit
2.3.2 Western unit compartments
Illustration of the service
compartment
The illustration below shows the service compartment of the Western unit.
1
2
3
4
5
30
Part
Description
1
Transfer valve block
2
Probing pump
3
Transfer pump
4
Air filter compartment lid
5
Probing valve block
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2 System description
2.3 Western unit
2.3.3 Liquid flow paths
2.3.3
Liquid flow paths
Introduction
This section shows the transfer and probing liquid flow paths in the Western unit and
describes the basic principles of operation.
Illustration of the transfer liquid
flow path
The illustration below shows a detailed flow chart for the transfer process. The flow chart
shows interconnections between instrument components. The white labels refer to
tubing labels. The blue numbers refer to instrument components.
5
T WASTE
T BUFFER
T WATER
1
3
4
2
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2.3 Western unit
2.3.3 Liquid flow paths
The table below describes the components in the flow chart:
Part
Description
1
Transfer valve block
For selecting which solution should be pumped through the liquid flow
path.
2
Transfer tank
3
Transfer pump
For pumping the solution through the liquid flow path.
4
Transfer cooling unit
For cooling down the transfer buffer to keep it at room temperature.
5
Transfer tank overflow
Basic principle of the transfer
process
During the transfer, an electrophoretic transfer of the separated proteins in the gel onto
the membrane is performed. The basic principle of the transfer process is described
below.
Stage
Description
1
When the Amersham WB transfer holder(s) (transfer holder) has been loaded
into the transfer tank, the transfer tank is filled with transfer buffer (the tube
marked with T Buffer).
2
During the transfer step, the transfer buffer is pumped through the transfer
tank, transfer cooling unit, transfer pump and the transfer valve block, circulating the transfer buffer during the run.
The transfer cooling unit makes sure that the transfer buffer is kept at room
temperature during the run.
3
32
After a run, and after removal of the transfer holders, ultra pure water is
used to clean the liquid flow path (the tube marked with T Water is used for
cleaning).
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2.3 Western unit
2.3.3 Liquid flow paths
Illustration of the probing liquid
flow path
The illustration below shows a detailed flow chart for the probing process. The flow chart
shows interconnections between instrument components. The white labels refer to
tubing labels. The blue numbers refer to instrument components.
P WASTE
P WASTE
P CUSTOM
P WATER
P WASH
P FINAL
WASH
P BLOCK
2
4
Prim A
Sec A
Prim B
5
Sec B
3
1
6
A
B
The table below describes the components in the flow chart:
Part
Description
1
Antibody compartment with antibody solution tubes containing primary
and secondary antibodies for positions A and B.
2
Probing valve block
Used to select solution to be pumped through the flow path.
3
Probing pump
For pumping the solution through the liquid flow path.
4
Air sensor
To detect if air is present in the tubing. The air detector pauses the run if
a solution bottle is empty.
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2 System description
2.3 Western unit
2.3.3 Liquid flow paths
Part
Description
5
Probing chamber selector valve
To select whether to direct the solution to the probing chambers or from
the probing chambers to waste outlet.
6
Probing chambers
Basic principle of the probing
process
In probing, primary antibodies are bound to the proteins on the membrane and then
secondary antibodies conjugated to a CyDye are bound to the primary antibodies.
The basic principle of the probing process is described below.
Stage
Description
1
The probing chamber is pre-filled with the first solution, as entered in the
probing protocol in the software (blocking solution is used as the default).
Pre-filling of the probing chamber is started by the user from selecting the
appropriate software instruction.
2
34
The PVDF cards are inserted into the probing chambers and sequential incubations (including wash steps) of membrane with blocking solution, primary
antibodies and secondary antibodies are performed.
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2.4 Accessories and consumables overview
2.4
Accessories and consumables overview
Introduction
This section gives an overview of the accessories and consumables to be used with the
Amersham WB analyzer. It also contains storage information for the consumables and
information about how to order consumables.
Accessories and consumables
The table below lists the accessories and consumables to be used with the instrument
in relation to the operational task to be performed. The instrument accessories are delivered with the system and the consumables are ordered separately.
Accessories to be installed are described in Amersham WB system Operating Instructions
and accessories for user maintenance tasks are described in Maintenance accessories,
on page 328.
For a detailed description of the accessories and consumables, see the subsequent
sections.
Task
Required consumables
Pre-labeling of
samples
•
Amersham WB Cy5
•
Amersham WB labeling buffer (Labeling
buffer)
•
Amersham WB loading buffer (Loading
buffer)
•
Amersham WB MiniTrap™ kit (optional)
•
Amersham WB molecular weight markers (Molecular weight markers)
•
Amersham WB gel card (Gel card)
•
Amersham WB buffer strip (Buffer strip)
•
Amersham WB loading buffer
•
Amersham WB paper comb (optional)
(Paper comb)
Electrophoresis
run
Amersham WB system User Manual 29-0214-88 AC
Required
accessories
For details, see...
N/A
Section 2.5
Amersham WB buffer
strip holder 1 (Buffers
strip holder)
Section 2.6
35
2 System description
2.4 Accessories and consumables overview
Task
Required consumables
Required
accessories
For details, see...
Amersham WB transfer holder1 (Transfer
holder)
Section
2.7.1
Antibody solution
tubes1
Section
2.7.2
Western blot steps
Transfer
Probing
•
Amersham WB gel card from the electrophoresis run
•
Amersham WB PVDF card (PVDF card)
•
Amersham WB transfer paper (Transfer
paper)
•
Amersham WB sponge (Sponge)
•
Laboratory prepared transfer solutions
(for recipes, see Transfer solution recipes,
on page 103)
•
Laboratory prepared primary antibody
solutions
•
Secondary antibody:
Amersham WB goat anti-mouse Cy3/Cy5
(goat anti-mouse Cy3/Cy5) or
Amersham WB goat anti-rabbit Cy3/Cy5
(goat anti-rabbit Cy3/Cy5)
•
PVDF card from the transfer step
•
Laboratory prepared probing solutions
(for recipes, see Probing and antibody
solution recipes, on page 104)
Drying
PVDF card from the probing step
Amersham WB drying holder (Drying
holder)
N/A
Scanning of the
PVDF card in the
Elpho & scan unit
PVDF card from the drying step
Amersham WB membrane adapter1
(Membrane adapter)
Section
2.7.4
Other
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2.4 Accessories and consumables overview
Task
Required consumables
Required
accessories
For details, see...
Scanning data
matrix tags on
gel cards and
PVDF card single
packages (optional)
N/A
Matrix tag reader (order separately)
Section 2.8
1
Included in delivery of Amersham WB analyzer.
Order consumables
Depending on the experiments to be performed, different combinations of consumables
are required. A selection guide for putting a kit of consumables together is available at
www.gelifesciences.com.
For ordering information for separate consumables, see Chapter 9 Ordering information,
on page 360.
Storage of consumables
The table below summarizes the storage and environmental conditions for the different
consumables. The expiry date of the consumables is printed on the package.
Consumable
Storage temperature
Environment
Pre-labeling consumables
-15°C to -30°C
Protect contents from direct
sunlight. Avoid repeated
freeze-thaw cycles of the Cy5
dye reagent.
Diluted Cy5 dye reagent should
be used within 30 min and not
be frozen.
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2.4 Accessories and consumables overview
Consumable
Storage temperature
Environment
Amersham WB molecular
weight markers
-15°C to -30°C
Protect the molecular weight
(MW) markers from direct sunlight. The MW markers must
always be stored in the freezer.
Minimize time in room temperature before use and avoid refreezing.
MW markers diluted in Loading
buffer with DTT can be dispensed in aliquots for singletime use, if frozen directly after
dilution. The aliquots should
not be stored for longer than
one week.
Amersham WB gel card
4°C to 8°C
Store in refrigerator or cold
room.
Amersham WB buffer strips
4°C to 8°C
Store in refrigerator or cold
room.
Amersham WB PVDF card
Room temperature
Store the PVDF card in the single package, inside the the box
in which they are delivered.
Store the box in a clean and
dry place, protected from light.
Amersham WB transfer paper
Room temperature
Store the transfer papers in a
dry place, in the box in which
they are delivered.
Protect from dust.
Amersham WB paper comb
Room temperature
Store the paper combs in a dry
place, in the box in which they
are delivered.
Protect from dust.
Amersham WB sponge
Room temperature
Protect from dust and direct
sunlight.
Amersham WB goat antimouse Cy3/Cy5 or Amersham
WB anti-rabbit Cy3/Cy5,
lyophilized
2°C to 8°C
Protect secondary antibodies
from light.
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2.4 Accessories and consumables overview
Consumable
Storage temperature
Environment
Reconstituted secondary antibodies (reconstituted in ultra
pure water to a concentration
of 1 μg/μl)
Store aliquots at -15°C to -30°C
Protect reconstituted secondary antibodies from light.
Primary antibodies
See manufacturer's instructions.
The aliquots should not be
stored for longer than 6
months. Avoid repeated freezethaw cycles.
Amersham WB system User Manual 29-0214-88 AC
See manufacturer's instructions.
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2 System description
2.5 Pre-labeling consumables
2.5
Pre-labeling consumables
Introduction
The pre-labeling consumables are used for the pre-labeling of protein samples with a
fluorescent dye.
Fluorescent pre-labeling of samples:
•
enables total protein detection when scanning the gel card,
•
eliminates the need for post-staining the gel.
When to use pre-labeling of
proteins
Pre-labeling of proteins is always performed before the electrophoresis step when performing:
•
electrophoresis experiments,
•
Western experiments with total protein normalization.
Pre-labeling consumables
Pre-labeling consumables are packed in separate foil bags. Each foil bag contains solution
reagents sufficient for running 10 gel cards (where 14 lanes/gel card are loaded with
pre-labeled samples), that is, 140 individual labeling reactions.
The table below summarizes the contents of the pre-labeling consumables.
Pre-labeling consumable
Content
Amount
Amersham WB Cy5
0.25 mg/ml (approximately
250 pmol/μl) Cy5 dye in
DMSO
5 vials (blue caps)
Amersham WB labeling buffer
(Labeling buffer)
Tris-based buffer containing
SDS with pH 8.7 (at 25°C)
5 vials (black caps)
Amersham WB loading buffer
(Loading buffer)
50 mM Tris-Cl, 0.25% (w/v)
Orange G, 4% SDS, 0.5 mM
Lysine
5 vials (orange caps)
40
35 μl Cy5 dye solution per vial
(enough for two gel cards)
0.7 ml Labeling buffer solution per
vial (enough for two gel cards)
0.7 ml Loading buffer solution per
vial (enough for two gel cards)
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2.5 Pre-labeling consumables
Sample preparation consumable
The table below describes the Amersham WB MiniTrap kit.
Sample preparation consumable
Function
Amount
Amersham WB MiniTrap kit
The kit is designed for rapid
and convenient clean-up of
protein samples (>5000 Mr)
containing interfering substances, e.g., imidazole.
•
30 prepacked disposable PD
MiniTrap G-25 columns containing Sephadex G-25 medium
•
1 bottle of 10× Amersham WB
labeling buffer (14 ml stock
solution)
•
Integrated column stand,
waste tray and tube holder
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2.6 Accessories and consumables for electrophoresis
2.6
Accessories and consumables for electrophoresis
Introduction
The following accessories and consumables are needed for protein electrophoresis:
•
Amersham WB buffer strip
•
Amersham WB buffer strip holder
•
Amersham WB molecular weight markers
•
Amersham WB gel card
•
Amersham WB paper comb, if sample well clean up will be performed
•
Amersham WB loading buffer (see Section 2.5 Pre-labeling consumables, on page 40
for information about the Loading buffer)
In this section
This section contains the following subsections:
Section
42
See page
2.6.1 Amersham WB molecular weight markers
43
2.6.2 Amersham WB gel card
45
2.6.3 Amersham WB buffer strip and Amersham WB buffer strip
holder
48
2.6.4 Amersham WB paper comb
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2.6 Accessories and consumables for electrophoresis
2.6.1 Amersham WB molecular weight markers
2.6.1
Amersham WB molecular weight markers
Introduction
Amersham WB molecular weight markers are a mixture of nine native and recombinant
proteins, Mr: 10 000 to 225 000, labeled with both Cy3 and Cy5, for molecular weight
determination of proteins on scanned gel cards and PVDF cards.
The software calculates molecular weight calibration curves. When two molecular weight
calibration curves are used, interpolated data from the curves are used to create sample
lane specific calibration curves. The molecular weights of all detected bands in each
lane are then calculated.
Content
Each package of Amersham WB molecular weight markers contains solution for running
10 gel cards (where 2 lanes/gel card are loaded with Amersham WB molecular weight
markers).
Illustration of MW markers
The illustration below shows the sizes of the Amersham WB molecular weight markers
separated on a gradient gel card (left image) and a homogeneous gel card (right image):
Mr×103
225
97
66
50
225
97
66
50
35
25
35
20
20
14
10
14
25
10
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2.6 Accessories and consumables for electrophoresis
2.6.1 Amersham WB molecular weight markers
MW marker proteins
The table below shows the proteins that are included:
44
Protein
Molecular weight (Mr×103)
Recombinant protein
225
Phosphorylase b, rabbit muscle
97
Albumin, bovine serum
66
Recombinant protein
50
Recombinant protein
35
Recombinant protein
25
Trypsin inhibitor, soybean
20
Alpha-Lactalbumin, bovine milk
14
Recombinant protein
10
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2.6 Accessories and consumables for electrophoresis
2.6.2 Amersham WB gel card
2.6.2
Amersham WB gel card
Introduction
This section describes the gel card details.
Gel card types
There are two types of gel cards:
•
Homogeneous gel card: Amersham WB gel card 14, 13.5%
•
Gradient gel card: Amersham WB gel card 14, 8-18%
Gel composition
The gels are pre-cast in the gel card casette. The gels are polyacrylamide/bisacrylamide
gels containing a Tris-acetate buffer.
Protein separation resolution
The table below lists the protein separation resolution for the gel card types:
Gel card type
Separation resolution, Mr×103
Amersham WB gel card 14, 13.5%,
Homogeneous
10 to 225
Amersham WB gel card 14, 8-18%,
Gradient
•
6 to 225 (pre-labeled proteins)
•
3.5 to 225 (Western experiments, antibody
detection)
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2.6 Accessories and consumables for electrophoresis
2.6.2 Amersham WB gel card
Illustration of the front side of a
gel card
The illustration below shows the gel card with the front side facing upwards:
4
4
3
5
6
2
5
1
Part
Description
1
Writing surface for your own annotation
Note:
Always use a pencil when writing the annotation.
The annotation can be entered in the software as well.
2
Label with gel card type
3
Sample well cover
that must be removed when the sealing lid in the Elpho & scan unit has
been closed, prior to applying the samples.
4
Gel handles
to ease handling of the gel when it has been removed from its support for
Western blotting.
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2.6 Accessories and consumables for electrophoresis
2.6.2 Amersham WB gel card
Part
Description
5
Guiding holes
for the correct placement of the gel cards in the Elpho & scan loader and
transfer holder.
6
Label with Data matrix tag, Lot number and ID
Illustration of the reverse side of
a gel card
The illustration below shows the gel card with the reverse side facing upwards:
1
2
1
Part
Description
1
Protective films
that are removed prior to electrophoresis to enable contact between the
gel and buffer strips.
2
Protective film
that is removed when preparing the transfer sandwich (only relevant in
Western experiments).
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2.6 Accessories and consumables for electrophoresis
2.6.3 Amersham WB buffer strip and Amersham WB buffer strip holder
2.6.3
Amersham WB buffer strip and Amersham WB buffer
strip holder
Introduction
The buffer strip holders hold the buffer strips in place during an electrophoresis run. The
buffer strip holders have built-in electrodes, providing contact between the electrode
and buffer strip, enabling an electric current for the run.
The buffer strips are loaded into the holders before starting the run and are discarded
after the run. The shape of the holder guides the user when placing the buffer strips in
the holders, and when placing the holders into the Elpho & scan unit.
See Preparations before starting electrophoresis, on page 164 for more information.
Buffer used in the buffer strips
The buffer used in the buffer strips is Tris-tricine.
Illustration of the buffer strips
The illustration below shows a buffer strip.
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2.6 Accessories and consumables for electrophoresis
2.6.3 Amersham WB buffer strip and Amersham WB buffer strip holder
Illustration of the buffer strip
holders
The illustration below shows a buffer strip holder.
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2.6 Accessories and consumables for electrophoresis
2.6.4 Amersham WB paper comb
2.6.4
Amersham WB paper comb
Introduction
The paper comb is used to clean up the sample wells when proteins have migrated into
the gel for a few minutes. Sample well cleanup is recommended to remove excess dye
when pre-labeled samples are used. This reduces the background, which improves the
detection and quantification of low abundant proteins (<1 ng/band) and low molecular
weight proteins (Mr<40 000).
Sample well cleanup will generally improve band resolution, also for unlabeled samples
of high protein concentrations or large sample volumes.
For more information about how to use the paper comb, see Run electrophoresis and
gel scanning, on page 169.
Illustration of the paper comb
The illustration below shows a paper comb.
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2.7 Accessories and consumables for Western blot steps
2.7
Accessories and consumables for Western blot steps
Introduction
This section describes the accessories and consumables used for the transfer of proteins
from the gel onto the membrane, the probing of the membrane with primary and secondary antibodies, and the scanning of PVDF cards.
In this section
This section contains the following subsections:
Section
See page
2.7.1 Accessories and consumables for transfer
52
2.7.2 Secondary antibodies – probing
57
2.7.3 Drying holder – PVDF card drying
59
2.7.4 Membrane adapter – PVDF card scan
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2 System description
2.7 Accessories and consumables for Western blot steps
2.7.1 Accessories and consumables for transfer
2.7.1
Accessories and consumables for transfer
Introduction
This section describes:
•
Amersham WB transfer holder (accessory)
•
Amersham WB PVDF card (consumable)
•
Amersham WB transfer paper (consumable)
•
Amersham WB sponge (consumable)
Amersham WB transfer holder
The transfer holder is used during transfer. It contains the transfer sandwich (sponge,
transfer paper, gel card, PVDF card, transfer paper and sponge) prepared before starting
transfer. The separated proteins are transferred from the gel to the membrane during
the transfer run.
Guiding pins in the transfer holder will make sure that the gel card and PVDF card are
positioned correctly when preparing the transfer sandwich.
By using the built-in roller (when moving the roller over the sandwich in the roller tracks),
air bubbles will be removed and a reproducible pressure will be applied on the gel card
and PVDF card for an even transfer process.
See Start building the transfer sandwich, on page 192 for more information about how to
prepare the transfer sandwich.
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2.7 Accessories and consumables for Western blot steps
2.7.1 Accessories and consumables for transfer
Illustration of the transfer holder
when closed
The image below shows the transfer holder when it is closed:
Illustration of the transfer holder
when disassembled
The image below shows the transfer holder when it has been disassembled.
3
1
4
5
2
6
7
The table below describes the different parts of the transfer holder.
Part
Function
Bottom part (black lid)
1
Latches
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2.7 Accessories and consumables for Western blot steps
2.7.1 Accessories and consumables for transfer
Part
Function
2
Guiding pins for gel card and PVDF card
3
Roller tracks (for roller pins)
Top part (white lid)
4
Roller pins (fit in roller tracks to assemble the lids)
5
Roller
6
Handle
7
Holes for the latches
Amersham WB PVDF card
In the transfer step, proteins are transferred from the gel to the blotting area of the PVDF
card. The PVDF card is a low fluorescent PVDF membrane.
The illustration below shows the different parts of the PVDF card and the PDVF card
single package.
2
1
1
3
1
4
5
6
7
3
The following table describes the different parts of the PVDF card and PDVF card single
package.
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2.7 Accessories and consumables for Western blot steps
2.7.1 Accessories and consumables for transfer
Part
Description
1
Guiding holes
Note:
The guiding holes assist the correct placement of the card in the transfer
holder, the probing chamber, the drying holder and the Elpho & scan loader.
2
Writing surface for your own annotation
Note:
Always use a pencil when writing the annotation.
The annotation can be entered in the software as well.
3
Card handles
4
Blotting area
5
PDVF card single package
6
PDVF card with protective papers
7
Label with Product code, Lot number, Identity number and Data matrix
tag (contains Product code, Lot number and ID number)
Amersham WB transfer paper
The transfer papers are used when preparing the transfer sandwich.
The illustration below shows a transfer paper:
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2 System description
2.7 Accessories and consumables for Western blot steps
2.7.1 Accessories and consumables for transfer
Amersham WB sponge
Two sponges are used when preparing the transfer sandwich. The sponges need to be
replaced after each run.
The illustration below shows a sponge.
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2.7 Accessories and consumables for Western blot steps
2.7.2 Secondary antibodies – probing
2.7.2
Secondary antibodies – probing
Introduction
The target proteins are identified by probing the membrane with primary antibodies and
species-specific secondary CyDye conjugated antibodies. By using two different species
of primary antibodies (mouse and rabbit) and one Cy3 conjugated secondary antibody
and one Cy5 conjugated secondary antibody, a multiplex experiment detecting two
proteins simultaneously on the same membrane can be performed.
The following variants of CyDye conjugated secondary antibodies are available:
•
Amersham WB goat anti-mouse Cy3 (goat anti-mouse Cy3)
•
Amersham WB goat anti-rabbit Cy3 (goat anti-rabbit Cy3)
•
Amersham WB goat anti-mouse Cy5 (goat anti-mouse Cy5)
•
Amersham WB goat anti-rabbit Cy5 (goat anti-rabbit Cy5)
CyDye (conjugated to the
secondary antibodies)
The CyDye conjugated to the secondary antibodies have their own specific excitation
and emission wavelengths in the visible light spectra and are spectrally differentiated
from each other, resulting in minimum cross-talk, see the table below.
CyDye
Excitation wavelength
Emission wavelength
Cy3
550 nm
570 nm
Cy5
649 nm
670 nm
After excitation, the resulting fluorescent emission signals are captured using the multichannel fluorescent scanner in the Elpho & scan unit.
The CyDye have a high photostability. The signal on probed membrane is stable for >3
months, if stored in the dark.
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2.7 Accessories and consumables for Western blot steps
2.7.2 Secondary antibodies – probing
Preparation and storage of
reconstituted secondary
antibodies
Reconstitute the secondary antibodies in 150 μl ultra pure water per vial, to a concentration of 1 μg/μl. Vortex and spin down the reconstituted secondary antibodies.
It is recommended to store the secondary antibodies in aliquots at -15°C to -30°C, and
protect from light. Avoid repeated freeze-thaw cycles.
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2.7 Accessories and consumables for Western blot steps
2.7.3 Drying holder – PVDF card drying
2.7.3
Drying holder – PVDF card drying
Introduction
The Amersham WB drying holder (drying holder) orients and fixes the PVDF card in the
correct position for the best possible drying result.
Illustration of the drying holder
The illustrations below show the drying holder when closed (top) and the drying holder
when opened (below).
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2.7 Accessories and consumables for Western blot steps
2.7.4 Membrane adapter – PVDF card scan
2.7.4
Membrane adapter – PVDF card scan
Introduction
The Amersham WB membrane adapter (membrane adapter) orients and fixes the PVDF
card in the correct position for the best possible scanning and detection in the Elpho &
scan unit.
Illustration of the membrane
adapter
The illustrations below show the membrane adapter when closed (left) and the membrane
adapter when opened (right):
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2.8 Other accessories
2.8
Other accessories
Matrix tag reader
The matrix tag reader is used to enter gel card and PVDF card information (product code,
ID and lot number) into the software by scanning the data matrix tags on the gel card
and on the PVDF card single package label. It must be ordered separately (see Chapter 9
Ordering information, on page 360).
The illustration below shows the matrix tag reader.
Inlet filter holder
The inlet filter holders, with inlet filters, are attached on the inlet tubes that are inserted
in the bottles on the bottle rack. Particles are filtered by the inlet filter and the inlet filter
holder itself is a weight that holds the tubing in place at the bottom of the bottles.
The illustration below shows an inlet filter holder, with an inlet filter mounted and attached
to tubing.
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2 System description
2.8 Other accessories
Tubing holders
To compensate for tensions when tubing is placed in bottles, and to avoid bottles falling
when liquid level decreases, a tubing holder must be attached to the tubing. See illustration below:
Additional accessories to be
installed by the user
The transfer electrodes and the membrane dryer guides must be installed by the user.
See Amersham WB system Operating instructions for more information.
Accessories for user
maintenance
For a description of accessories for user maintenance, see Maintenance accessories, on
page 328.
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2.9 Amersham WB software overview
2.9
Amersham WB software overview
About this chapter
This section gives an overview of the Amersham WB software.
In this chapter
This chapter contains the following sections:
Section
See page
2.9.1 Amersham WB software start screen
64
2.9.2 Amersham WB software main screen
65
2.9.3 Menu bar
67
2.9.4 Workflow panel
72
2.9.5 Instrument status panel
76
2.9.6 Help panel
78
2.9.7 Keyboard shortcuts
79
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2.9 Amersham WB software overview
2.9.1 Amersham WB software start screen
2.9.1
Amersham WB software start screen
In the software start screen it is possible to create new experiments and open previously
saved experiments. For information about how to create/open experiments in the software, see Section 4.3.1 Start the software and create an experiment, on page 111.
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2.9.2 Amersham WB software main screen
2.9.2
Amersham WB software main screen
The illustration below shows the software main screen for a Western experiment.
Area
Description
1
Menu bar
The menu bar consists of four menus:
•
File: Create, open and save experiments. Print information and exit software.
•
Control: Abort run, empty transfer and probing chamber, start cleaning of transfer and
probing flow paths.
•
Remote: Connect and disconnect to instrument remote access. Retrieve instrument
access codes and manage remote user. Edit the remote connection configuration.
Note:
Only visible when an instrument is connected.
•
Help: Generate system reports. Open the help panel, the user manual and the About
Amersham WB dialog.
For more information see Section 2.9.3 Menu bar, on page 67.
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2.9.2 Amersham WB software main screen
Area
Description
2
Workflow panel
The workflow panel shows the different workflow steps in the software for an experiment.
It is possible to go forward and backward to view and edit information and parameters in
the different workflow steps before starting a run (i.e., electrophoresis, transfer, probing,
drying or membrane scanning).
It is always possible to go back and edit text in information fields in the different workflow
steps during and after a run. For example, the sample table can be filled in after electrophoresis has started.
Note:
For an electrophoresis experiment, the workflow steps TRANSFER, PROBING & DRYING and
MEMBRANE SCANNING are dimmed. These steps are only included in Western experiments.
For more information see Section 2.9.4 Workflow panel, on page 72.
3
Work area
The work area shows the text information, parameters and controls for the currently displayed workflow step.
4
Instrument status panel
The instrument status panel shows the instrument connection status. When the instrument
is connected the status of each hardware module (electrophoresis and scanning compartment, transfer tank, probing compartment, and drying compartment) and the progress of
any run in the modules is shown.
Several experiments can be open at the same time. Each experiment requires that a new
instance of the software is opened. The instrument status panel will show the status of the
instrument for all open experiments. One hardware module can be used by one experiment
at a time. This means that four different workflow steps from four different experiments
can be run in parallel.
5
Help panel
The help panel shows the help instructions for the screen currently displayed in the work
area. When selecting a new step in the workflow, the help instructions are automatically
updated to display help for the active screen.
Tip:
To view the user manual containing detailed information about the system, select Help:View
user manual in the menu bar, or press Ctrl+F1.
For more information see Section 2.9.6 Help panel, on page 78.
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2.9.3 Menu bar
2.9.3
Menu bar
File menu
Command
Description
New (Ctrl+N)
Select to open a new instance of the
software showing the Amersham WB
software start screen.
Up to four instances (experiments) of the
software can be run on one instrument
in parallel.
New from existing
Select to create a new experiment based
on an existing experiment.
A dialog will open in which to select the
experiment to base the new experiment
on.
A number of settings from the previous
experiment will be copied to the new experiment. See Create a new experiment
based on a previous run, on page 117 for
more information.
Open (Ctrl+O)
Select to open an existing experiment.
Exit
Select to exit the software.
Save (Ctrl+S)
Click to save the experiment. If you are
saving the experiment for the first time,
a dialog will appear where you must enter a name for the experiment. Save is
not available when editing an image.
Save as
Click to save the experiment with another
name. Save as is not available during a
run or when editing an image.
Print (Ctrl+P)
This selection is only available for the
EXPERIMENT & SAMPLES and PROBING
& DRYING screens.
Click to print the experiment and samples
information or the probing protocol, depending on which screen is displayed.
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2.9.3 Menu bar
Control menu
Command
Description
Empty Transfer tank
Select to empty the transfer tank, for example, if cleaning of the transfer flow
path was not performed.
Note:
Make sure that the transfer holders have
been removed from the transfer tank before emptying the transfer tank.
Empty Probing chamber
Select to empty the probing chamber, for
example, if cleaning of the probing flow
path was not performed.
Note:
Make sure that the membranes have been
removed from the probing chamber before emptying the probing chamber.
Clean Transfer flow path
Select to clean the transfer flow path.
Follow the instructions in the dialog that
is displayed.
Note:
Make sure that the transfer holders have
been removed from the transfer tank before cleaning the transfer flow path.
Clean Probing flow path
Select to clean the probing flow path.
Follow the instructions in the dialog that
is displayed.
Note:
Make sure that the membranes have been
removed from the probing chamber before cleaning the probing flow path.
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2.9.3 Menu bar
Command
Description
Maintenance clean Transfer flow path
Select to perform a maintenance cleaning of the transfer flow path. See Maintenance cleaning of transfer flow path, on
page 325.
Note:
Make sure that the transfer holders have
been removed from the transfer tank before cleaning the transfer flow path.
Maintenance clean Probing flow path
Select to perform a maintenance cleaning of the Probing flow path. See Maintenance cleaning of probing flow path, on
page 326.
Note:
Make sure that the membranes have been
removed from the probing chamber before cleaning the probing flow path.
Abort run
Select to abort an ongoing run. A dialog
will open and ask for your confirmation
before aborting the run.
Click OK to abort the run.
Remote menu
The Remote menu is only visible when the computer is connected to an instrument.
Command
Description
Activate/Deactivate remote access
Select to activate/deactivate instrument
remote access.
When the instrument is activated for the
first time, the Remote access settings
dialog opens, where the system name
and settings can be edited.
See AppendixA The Amersham WB watch
app, on page 363 for more information.
Add WB watch user
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Select to receive the instrument access
code to be entered in the Amersham WB
watch app.
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2.9.3 Menu bar
Command
Description
List of WB users
Select to open the List of WB users dialog to view the remote users that are
connected to the instrument. The user
First name, Last name, and E-mail is
displayed.
It is also possible to remove a user by
clicking the Remove user button.
Remote access settings
Select to edit the system name, and if
snapshots of the last images scanned
and service information should be uploaded to the cloud.
See AppendixA The Amersham WB watch
app, on page 363 for more information.
Help menu
Command
Description
Generate system report
Select to generate a system report.
The system report will contain information about the status of the connected
instruments as well as of the software
installation.
It also contains a text field for entering
information if a problem has been encountered.
When finished the system report is saved
in a compressed file by clicking the Save
system report button.
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Show/hide help panel (F1)
Select to hide or show the help panel.
View user manual (Ctrl+F1)
Select to view the Amersham WB system
User Manual.
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2.9.3 Menu bar
Command
Description
About Amersham WB
Select to open the About Amersham WB
dialog.
The dialog contains information on:
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Amersham WB software version
•
Elpho & scan unit and Western unit
firmware versions
•
Elpho & scan unit and Western unit
serial numbers
•
trademark and address information
(press Details button)
•
license agreement (press License
agreement button)
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2.9.4 Workflow panel
2.9.4
Workflow panel
About the workflow panel
The workflow panel displays the workflow steps associated with the selected experiment.
Panel display
The workflow panel can be minimized or maximized by clicking the arrow,
in the upper left corner.
,
In the maximized view the images and names of the workflow steps are displayed. In
the minimized view, the images of the workflow steps are displayed.
Navigate between the workflow steps by clicking on the steps or by using the available
keyboard shortcuts, see the table below.
A yellow check mark indicates that the workflow step has been completed or, for the
EXPERIMENT & SAMPLES workflow step, all required data has been entered.
Workflow panel overview
Workflow step
Description
EXPERIMENT & SAMPLES (Ctrl + 1)
In this workflow step the user can:
•
select number of gel cards
•
select gel card type
•
enter sample information
•
enter antibody information
See Section 4.3.2 Set up experiment and
samples, on page 119 for more information.
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2.9.4 Workflow panel
Workflow step
Description
ELECTROPHORESIS & GEL SCANNING
(Ctrl + 2)
In this workflow step the user can:
•
enter gel card information
•
edit the parameters for the Electrophoresis Protocol
•
edit the parameters for the Gel
Scanning Protocol
•
select automatic or manual Scanning
Sensitivity
•
start electrophoresis and gel scanning
•
perform a re-scan of a gel
See Section 4.3.3 Set up electrophoresis
and gel scanning protocols, on page 131
for more information.
TRANSFER (Ctrl + 3)
In this workflow step the user can:
•
enter membrane information
•
view gel card information
•
edit solution information
•
edit the parameters for the Transfer
Protocol.
•
start transfer
Note:
For an electrophoresis experiment, the
workflow step TRANSFER is dimmed. This
step is only included in Western experiments.
See Section 4.3.4 Set up the transfer parameters, on page 136 for more information.
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2.9.4 Workflow panel
Workflow step
Description
PROBING & DRYING (Ctrl + 4)
In this workflow step the user can:
•
view membrane and antibody information
•
select Recover primary antibodies
•
edit solution information
•
edit probing protocol
•
start pre-fill of probing chamber
•
start probing
•
start drying
Note:
For an electrophoresis experiment, the
workflow step PROBING & DRYING is
dimmed. This step is only included in
Western experiments.
See Section 4.3.5 Set up the probing protocol, on page 139 for more information.
MEMBRANE SCANNING (Ctrl + 5)
In this workflow step the user can:
•
start membrane scanning
•
view membrane information
•
select automatic or manual Scanning
Sensitivity
Note:
For an electrophoresis experiment, the
workflow step MEMBRANE SCANNING is
dimmed. This step is only included in
Western experiments.
See Section 4.3.6 View membrane scanning setup, on page145 for more information.
EVALUATION (Ctrl + 6)
74
Evaluate the experiment. See Chapter 5
Evaluate an experiment, on page 237 for
more information.
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2.9.4 Workflow panel
Workflow step
Description
Experiment Information (Ctrl + I)
Enter or edit experiment information. See
Section 4.3.7 View or enter experiment
information, on page147 for more information.
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2.9.5 Instrument status panel
2.9.5
Instrument status panel
About the instrument status
panel
When the instrument is connected, the status of each hardware module (electrophoresis
and scanning compartment, transfer tank, probing compartment, and drying compartment) and the progress of any run in the modules is shown in the instrument status bar
for all open experiments.
The instrument status panel shows the status for the four modules:
•
electrophoresis and scanning in the Elpho & scan unit
•
transfer, probing, and drying in the Western unit
Four different workflow steps from four different experiments can be run in parallel. If
several experiment workflow steps are run in parallel, the module being used by the
displayed experiment will be highlighted blue.
For an ongoing run, the experiment name is shown in the instrument status panel for
that workflow step.
To open a running experiment in any instance of the software you can click on the experiment name to display it.
Panel display
The instrument status panel can be minimized/maximized by clicking the arrow
.
In the minimized view the progress bar is displayed.
In the maximized view the progress bar and status message is displayed.
Status messages
Status messages include:
76
•
the name of an experiment, while running. To open the experiment, click the experiment name.
•
the instrument connection status
•
if a compartment is ready for a new run
•
if the run is in progress
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2.9.5 Instrument status panel
•
if the run is completed
•
if cleaning/maintenance cleaning of the transfer or probing flow path is in progress
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2.9.6 Help panel
2.9.6
Help panel
About help panel
Help information for a workflow step in the software is automatically displayed in the
help panel on the right side of the screen. Software information and short laboratory
work descriptions are provided.
When selecting a new workflow step, the help instructions are automatically updated
to show help information connected to the workflow step.
Help panel display
To hide/show the help panel:
•
press F1 on the keyboard
or
•
click the hide/show icon on the top right
To increase/decrease the width of the help panel, drag the help panel list.
Where more detailed information is available for a help instruction step, a link is provided
to the User Manual.
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2.9.7 Keyboard shortcuts
2.9.7
Keyboard shortcuts
Shortcut
Description
Ctrl + N
Opens a new instance of the software
showing the Amersham WB software
start screen.
Ctrl + O
Opens an existing experiment.
Ctrl + S
Saves an experiment.
Ctrl + P
Prints the experiment and samples information or the probing protocol, depending on which screen that is displayed.
F1
Opens/closes the help panel in the software.
Ctrl + F1
Opens the Amersham WB system User
Manual.
Ctrl + 1
Opens the EXPERIMENT & SAMPLES step
in the workflow area.
Ctrl + 2
Opens the ELECTROPHORESIS & GEL
SCANNING step in the workflow area.
Ctrl + 3
Opens the TRANSFER step in the workflow area.
Ctrl + 4
Opens the PROBING & DRYING step in
the workflow area.
Ctrl + 5
Opens the MEMBRANE SCANNING step
in the workflow area.
Ctrl + 6
Opens the EVALUATION step in the
workflow area.
Ctrl + I
Opens the Experiment Information dialog.
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3
Plan an experiment
Introduction
This chapter describes:
•
the two main experiment types: electrophoresis experiments and Western experiments
•
Cy5 pre-labeling of proteins
•
planning of electrophoresis and Western experiments
In this chapter
This chapter contains the following sections:
Section
80
See page
3.1 Electrophoresis and Western experiments
81
3.2 Pre-labeling of proteins
83
3.3 Plan electrophoresis experiments
90
3.4 Plan Western experiments
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3.1 Electrophoresis and Western experiments
3.1
Electrophoresis and Western experiments
Introduction
Two main types of experiments can be performed using Amersham WB system:
•
Electrophoresis experiments
•
Western experiments
This section briefly describes the different experiment types.
Electrophoresis experiments
In electrophoresis experiments, samples are pre-labeled using Cy5 dye reagent prior to
electrophoresis. This enables direct detection of pre-labeled proteins in the sample,
eliminating the need for post-staining the gel. In the Evaluation step after gel scanning,
automatic analysis of the protein bands is performed and the results are presented in
the software.
See Section 3.2 Pre-labeling of proteins, on page 83 and Section 3.3 Plan electrophoresis
experiments, on page 90 for more information.
Western experiments
In Western experiments, unlabeled or Cy5 pre-labeled proteins are separated in the gel
during electrophoresis and then transferred from the gel to a membrane. The membrane
is probed with primary antibodies and secondary antibodies conjugated with Cy3 or Cy5
dye for target protein detection. For total protein detection the sample is pre-labeled
with Cy5. After probing, the membrane is dried and then scanned. In the Evaluation step,
automatic analysis of the protein bands is performed and the results are presented in
the software.
See Section 3.2 Pre-labeling of proteins, on page 83 and Section 3.4 Plan Western experiments, on page 93 for more information.
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3.1 Electrophoresis and Western experiments
General workflow overview
The illustration below shows the main steps in Electrophoresis and Western experiments.
Electrophoresis experiment
Western experiment
Start instrument
Set up experiment in
software
Perform pre-labeling
Prepare unlabeled samples
OR
for loading
Run elecrophoresis &
Prepare and connect
gel scanning
transfer solutions
Prepare transfer
sandwich
Prepare and connect
Evaluate results
Run transfer
probing and antibody
solutions
Perform probing &
drying
Scan membrane(s)
Evaluate results
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3.2
Pre-labeling of proteins
Introduction
This section describes Cy5 pre-labeling of proteins for detection in the Amersham WB
experiments. It gives information about:
•
The protein pre-labeling concept
•
Amersham WB Cy5
•
Sample types and compatible and interfering buffer substances
•
Available labeling protocols
In this section
This section contains the following subsections:
Section
See page
3.2.1 Protein pre-labeling concept
84
3.2.2 Pre-labeling pre-requisites and protocols
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3.2 Pre-labeling of proteins
3.2.1 Protein pre-labeling concept
3.2.1
Protein pre-labeling concept
Introduction
This section describes the protein pre-labeling concept in the Amersham WB system. It
gives general information about protein pre-labeling, the fluorescent dye reagent, and
the labeling reaction.
Pre-labeling of proteins
Pre-labeling of proteins enables protein detection after electrophoresis and Western
experiments by automated scanning of gel cards and PVDF cards. The proteins are labeled
prior to electrophoresis using the Cy5 dye reagent, enabling detection of protein in the
sample, eliminating the need for post-staining the gel or membrane.
Pre-labeled samples can be used for normalization, in which the total protein signal on
the membrane is used as loading control. See Section 3.4.2 Western normalization
strategies, on page 96 for more information.
Cy5 dye reagent
The Cy5 dye reagent has an N-Hydroxy succinimidyl (NHS ester) reactive group, which
forms covalent bonds with the epsilon amino group of lysine and the N-terminus of
proteins via an amide linkage. Samples with a wide range of protein concentrations
(1 ng/μl - 20 μg/μl) can be labeled. Labeling proteins with Cy5 adds approximately 700
to the protein mass. The Cy5 dye reagent is provided in solution (dissolved in DMSO).
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3.2.1 Protein pre-labeling concept
Schematic illustration of labeling
reaction
The illustration below shows a schematic overview of the labeling reaction.
Dye
H2 N
Protein
Dye
O
O
O N
O
NHS ester
reactive group
O
O N
H
Protein
The table below describes the main steps of the labeling reaction:
Stage
Description
1
The labeling reaction is started by addition of Cy5 dye reagent to the samples.
2
The reaction is stopped by addition of Amersham WB loading buffer, followed
by heating.
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3.2.2 Pre-labeling pre-requisites and protocols
3.2.2
Pre-labeling pre-requisites and protocols
Introduction
This section describes:
•
different sample types
•
compatible and interfering substances
•
required consumables and products
•
protocols
Sample types
When performing pre-labeling of samples, the samples can be divided into three sample
types:
•
protein samples in compatible buffers
•
protein samples in buffer containing interfering substances
•
cell lysates or tissue extracts
Depending on the sample type, different pre-labeling procedures are recommended.
Sample concentration
The total protein concentration should be between 1 ng/μl and 20 μg/μl in the original
sample. However, the exact protein concentration of the sample does not need to be
known.
If samples need to be diluted, it is recommended to dilute protein samples in Amersham
WB labeling buffer and cell/tissue samples in their original lysis buffer.
Compatible buffer substances
(protein samples)
Buffer salts are compatible in commonly used working concentrations. Additives are
compatible in common concentrations or in the indicated concentration ranges.
Examples of buffer substances that are compatible with pre-labeling of protein samples
using the SDS-PAGE labeling protocol (described in Available protocols, on page 89) are
listed below.
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Buffer salts
Additives
•
Acetate
•
Acetonitrile
•
Bicine
•
Beta-mercaptoethanol (<10 mM)
•
Bis-Tris
•
CHAPS
•
Borate
•
DTT (<20 mM)
•
Carbonate
•
EDTA
•
Citrate
•
Ethanol
•
HEPES
•
Glycerol
•
MES
•
MgCl2
•
MOPS
•
Protease inhibitor mix
•
Phosphate (PBS)
•
SDS (<1%)
•
PIPPS
•
Sucrose
•
Tricine
•
TCEP (<20 mM)
•
Tris
•
Triton X-100 (<1%)
•
Tween™ (<1%)
•
Urea
Interfering substances (protein
samples)
The sample buffer may contain interfering substances that:
•
inhibit the labeling reaction and require buffer exchange
or
•
lower the labeling efficiency
If the sample buffer contains interfering substances that lower the labeling efficiency,
then further dilution (default 1:10 in SDS PAGE pre-labeling protocol) of the sample in
Labeling buffer, or a buffer exchange using Amersham WB MiniTrap kit into Labeling
buffer, may be required to reduce the amount of interfering substances.
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3.2.2 Pre-labeling pre-requisites and protocols
Interfering substances requiring buffer exchange
The following substances require a buffer exchange using Amersham WB MiniTrap kit
before pre-labeling of samples:
•
Imidazole
•
Glycine buffers (>100 mM)
•
Ammonium sulfate
•
Guanidinium-Cl
Interfering substances lowering labeling efficiency
Interference can be reduced or eliminated by dilution or buffer exchange.
Examples of substances that lower the labeling efficiency are listed below:
•
Thiols, for example DTT
•
Primary amines, for example amino acids and ethanol amine
•
Piperazine
•
Extreme pH: pH>10, pH<4
Compatible lysis buffers
Common Tris-based lysis buffers with pH 7 to 9, and with various detergents and salts,
are compatible with pre-labeling of cell/tissue samples, for example:
•
GE mammalian protein extraction buffer
•
RIPA buffer
Required consumables and
products
The following reagents and solutions are needed for pre-labeling:
•
Amersham WB Cy5
•
Amersham WB labeling buffer
•
Amersham WB loading buffer
See Section 2.5 Pre-labeling consumables, on page 40 for a description of the pre-labeling
consumables components.
If the protein sample buffer contains interfering substances, buffer exchange using the
Amersham WB MiniTrap kit may be required. The Amersham WB MiniTrap kit can be
ordered separately, see Chapter 9 Ordering information, on page 360.
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Available protocols
Three protocols are available for pre-labeling of samples: the SDS-PAGE pre-labeling
protocol, Western pre-labeling protocol and the Quick SDS-PAGE pre-labeling protocol.
The Quick SDS-PAGE pre-labeling protocol has a decreased incubation time and should
only be used for qualitative analysis.
The SDS-PAGE/Quick SDS-PAGE pre-labeling protocols are designed to minimize sample
buffer effects on labeling efficiency. A 10 fold dilution of the sample in Amersham WB
labeling buffer ensures optimal labeling conditions (see Compatible buffer substances
(protein samples), on page 86).
The table below summarizes when to use the different protocols:
Protocol
Description
Labeling pH
SDS PAGE pre-labeling
protocol
Main protocol for pre-labeling of protein samples.
pH 8.5 to 9.0
Incubation at room temperature for 30 minutes.
pH between 8.5 and 9.0 is
obtained by 10 times dilution
in Amersham WB labeling
buffer.
If buffer exchange into Labeling buffer has been performed, pH is optimal.
Western pre-labeling protocol
Total protein normalization for cell and tissue
samples.
pH 7 to 9
Quick SDS-PAGE pre-labeling protocol
Quick protocol used for
pre-labeling of protein
samples mainly for qualitative analysis.
pH 8.5 to 9.0. See SDS PAGE
pre-labeling protocol above.
Incubation at 95ºC for 35 minutes.
Sample loading capacity
The table below describes the loading capacities of pre-labeled proteins:
1
Loading volume/well
Protein amount
15-30 μl 1
Maximum 20 μg/well
20 μl, recommended
<0.5 μg/protein band
Difference between wells should be <10 μl. Adjust with Amersham WB loading buffer (diluted with an
equal volume of ultra pure water).
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3.3
Plan electrophoresis experiments
Introduction
This section describes how to plan and set up an electrophoresis experiment.
Select an appropriate gel card
type
There are two types of gel cards, homogeneous and gradient gel cards. Choose a suitable
gel card type depending on the molecular weight range of your target proteins. Gradient
gel cards give a better resolution in the low molecular weight area, and homogeneous
gel cards give a better resolution in the high molecular weight area.
Gel card type
Separation resolution, Mr×103
Amersham WB gel card 14, 13.5%,
Homogeneous
10 to 225
Amersham WB gel card 14, 8-18%,
Gradient
•
6 to 225 (pre-labeled proteins)
•
3.5 to 225 (Western experiments, antibody
detection)
Reagents for pre-labeling of
samples
Pre-labeling of samples is required in an Electrophoresis experiment. Reagents and solutions for pre-labeling of proteins (including Labeling buffer, Cy5 dye reagent and
Loading buffer) can be ordered separately. See Section 3.2 Pre-labeling of proteins, on
page 83 for more information.
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Amersham WB molecular weight
markers
It is recommended to include two MW markers in the run to obtain best possible results
in the automatic molecular weight calibration of sample proteins in the image analysis
step.
Sample lanes between the two molecular weight marker lanes will use interpolated
calibration curves. See Description of the molecular weight calibration algorithm, on
page 315 for more information.
Electrophoresis running buffer
The electrophoresis running buffer for a run is included in the buffer strips.
Electrophoresis experiments
overview
There is one experiment type available for Electrophoresis experiments, the Easy SDSPAGE experiment type.
The table below gives an overview of the different examples of objectives for this experiment type.
For information about automatically calculated results for the experiment type and further
analyses that can be performed, see Chapter 5 Evaluate an experiment, on page 237.
Objective
Description
Confirmatory analysis
•
Confirm presence/absence of a protein
•
Estimate low/high level of the protein of interest
•
Confirm molecular weight of sample proteins
Purity check
Estimate target protein:impurity ratio (% purity)
Protein characterization
Protein composition analysis (e.g., molecular weight shift
analysis, protein stability, enzymatic cleavage etc.)
LC fractionation analysis
Comparison of different chromatography fractions or pools
during protein purification.
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3.3 Plan electrophoresis experiments
Objective
Description
Quantity calibration
Determine amount of target protein in different samples.
Tip:
Use similar buffer conditions for labeling of sample and
quantity calibrant.
Note:
Labeling efficiencies will vary from protein to protein. For
quantity measurements, use the same quantity calibrant
protein as the sample protein of interest.
Note:
The software uses linear regression (not forced through the
origin) to create the calibration curve.
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3.4
Plan Western experiments
Introduction
This section briefly describes the principles of fluorescent detection and multiplexing
and Western normalization strategies in Western experiments in Amersham WB system.
It also describes what to consider when setting up an experiment and what solutions
are needed for a run.
In this section
This section contains the following subsections:
Section
See page
3.4.1 Fluorescent Western blotting
94
3.4.2 Western normalization strategies
96
3.4.3 Experimental setup
98
3.4.4 Western experiments setup overview
101
3.4.5 Western experiment buffers and solutions
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3.4.1 Fluorescent Western blotting
3.4.1
Fluorescent Western blotting
Introduction
This section briefly describes the principles of fluorescent detection and multiplexing in
Amersham WB system.
Multiplex detection
Multiplexed fluorescent Western blotting enables simultaneous detection on the same
blot of:
•
two target proteins (by using Cy3 and Cy5 conjugated secondary antibodies)
The target proteins may have the same molecular weight. One of the target proteins
can be a housekeeping protein that is used as internal control in Western normalization experiments.
•
Cy5 pre-labeled total protein and one target protein (by using secondary antibody
conjugated to Cy3)
Cy5 labeled total protein will be transferred to the membrane, since it is a covalent
bond between dye and protein. Cy5 pre-labeled total protein can be used as loading
control in Western normalization experiments.
Principle of multiplexing using
Cy3 and Cy5 secondary
antibodies
The illustration below shows primary antibodies against protein targets on the membrane
that are recognized by species-specific Cy3 and Cy5 conjugated secondary antibodies.
Excitation
Cy5
Emission Excitation
Emission
Cy3
CyDye conjugated
secondary antibodies
Primary antibodies
Proteins on membrane
Protein 1
94
Protein 2
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3.4.1 Fluorescent Western blotting
Principle of multiplexing by
combining Cy5 total protein
pre-labeling and Cy3 secondary
antibody
The illustration below shows Cy5 total protein labeled cell lysate on the membrane and
a target protein detected by a species specific Cy3 conjugated secondary antibody. Cy5
pre-labeled protein is transferred from the gel to the membrane.
Excitation
Cy3
Excitation
Emission
Emission
CyDye conjugated
secondary antibody
Primary antibody
Cy5
Cy5
Cy5
Cy5
Cy5
Cy5
Cy5
Pre-labeled total protein
Target protein
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3.4.2 Western normalization strategies
3.4.2
Western normalization strategies
Introduction
In this section, principles and differences between the Western normalization strategies
for quantitative comparison of target protein levels between samples using Amersham
WB system are briefly described.
Normalization for accurate
quantitation
To reliably quantitate protein levels in Western experiments between different samples,
levels of the protein of interest should be normalized to an internal reference proportional
to sample load. Normalization corrects for variations in the amount of total protein
loaded between lanes due to errors such as pipetting of sample, incorrect protein
quantitation of sample or cell number of sample, that otherwise may result in uneven
sample loading.
Normalization options
There are two different Western normalization options for a Western experiment in
Amersham WB system:
•
Normalization using Cy5 pre-labeled total protein
•
Normalization using endogenous or housekeeping protein
Normalization using pre-labeled
protein
Total protein labeling of cell lysates or tissue samples can be used as a loading control
since the total protein signal is proportional to protein amount. The labeled proteins are
transferred and can be detected on the membrane at the same time as a Cy3 antibody
against a target protein (see illustration in Principle of multiplexing by combining Cy5
total protein pre-labeling and Cy3 secondary antibody, on page 95.
Note:
96
For linearity of results it is important to use identical labeling conditions (i.e.,
pH, temperature, volume and dye concentration should not vary between
samples).
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3.4.2 Western normalization strategies
Normalization using endogenous
protein
If the sample is a cell lysate, an endogenous constitutively expressed "housekeeping"
protein (i.e., usually a structural cellular protein which is expressed at a relatively constant
rate reflecting cell number) may be used as an internal control.
Commonly used housekeeping proteins for mammalian cells are GAPDH, Tubulin and
Actin. The target protein and the housekeeping protein can be detected simultaneously
on the membrane by multiplexing using Cy3 and Cy5 secondary antibodies (see illustration
in Principle of multiplexing using Cy3 and Cy5 secondary antibodies, on page 94).
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3.4.3 Experimental setup
3.4.3
Experimental setup
Introduction
This section describes what to consider when setting up a Western experiment.
Select an appropriate gel card
type
There are two types of gel cards, homogeneous and gradient gel cards. Choose a suitable
gel card type depending on the molecular weight range of your target proteins. Gradient
gel cards give a better resolution in the low molecular weight area, and homogeneous
gel cards give a better resolution in the high molecular weight area.
Gel card type
Separation resolution, Mr×103
Amersham WB gel card 14, 13.5%,
Homogeneous
10 to 225
Amersham WB gel card 14, 8-18%,
Gradient
•
6 to 225 (pre-labeled proteins)
•
3.5 to 225 (Western experiments, antibody
detection)
Amersham WB molecular weight
markers
•
In Western experiments, Amersham WB molecular weight markers should be diluted
1:20 in Loading buffer before loading on the gel card. Before use, the supplied
Loading buffer must be diluted with ultra pure water and contain added DTT. For
preparation, see Section 4.4.3 Prepare Amersham WBmolecular weight markers, on
page 162.
•
The molecular weight markers can be diluted further in prepared Loading buffer to
match samples with weak signals. However, it is then recommended to select the
option Stop electrophoresis on time
•
It is recommended to include two marker lanes in the run to obtain best possible
result in the automatic molecular weight calibration of sample proteins in the image
analysis step.
Sample lanes between the two molecular weight marker lanes will use interpolated
calibration curves. See Description of the molecular weight calibration algorithm, on
page 315 for more information.
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3.4.3 Experimental setup
Pre-labeling of samples
Pre-labeling of samples must be performed in normalized Western experiments where
pre-labeled protein is used as a total protein control. See Section 3.2 Pre-labeling of
proteins, on page 83 for more information.
Select primary and secondary
antibodies for an experiment
To be able to distinguish between the two targets in a multiplex Western, the primary
antibodies must be of two different species and the secondary antibodies need to be
species specific and be conjugated with two different CyDyes (Cy3 and Cy5, see illustration
in Principle of multiplexing using Cy3 and Cy5 secondary antibodies, on page 94).
Cy3 and Cy5 conjugated secondary antibodies directed against both mouse and rabbit
primary antibodies are available. Select the appropriate secondary antibody matching
the primary antibody species.
Note:
If Cy5 pre-labeling is performed, use Cy3 conjugated secondary antibody for
detection of the target protein.
The table below shows possible combinations of primary and secondary antibodies.
Setup
Primary antibody
species
Secondary antibody selections
Detecting one target protein
Mouse
Select one of the secondary antibodies below:
Rabbit
Detecting two target proteins
One mouse and
one rabbit
•
Goat anti-mouse Cy3
•
Goat anti-mouse Cy5
Select one of the secondary antibodies below:
•
Goat anti-rabbit Cy3
•
Goat anti-rabbit Cy5
Select one of the secondary antibody combinations below:
•
Goat anti-mouse Cy3 and
Goat anti-rabbit Cy5
or
•
Goat anti-mouse Cy5 and
Goat anti-rabbit Cy3
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3.4.3 Experimental setup
Setup
Primary antibody
species
Secondary antibody selections
Detecting Cy5 pre-labeled
protein and one target
protein
Mouse
Goat anti-mouse Cy3
Rabbit
Goat anti-rabbit Cy3
Detecting more than two
target bands that differ in
molecular weight
Mouse and/or rabbit
Appropriate mix of secondary
antibodies
Note:
Pre-run individual antibodies
separately to determine what
bands each antibody detects.
Probing time
Optimal probing time varies between different primary antibodies from approximately
15 minutes (high abundant target or high affinity of antibody) to overnight (low abundant
or low affinity). 1 hour probing time is sufficient for most primary antibodies and is set
as default, but for low abundant targets it is recommended to optimize/prolong the
probing time for best results.
The secondary antibody probing time is optimized to 30 minutes (set as default) and
works for targeting most primary antibodies.
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3.4.4 Western experiments setup overview
3.4.4
Western experiments setup overview
Introduction
This section gives an overview of the Western experiment types.
Western experiments overview
The table below gives an overview of the different Western experiment types and examples of objectives for an experiment type.
For information about automatically calculated results for the experiment types and
further analyses that can be performed, see Chapter 5 Evaluate an experiment, on
page 237.
Experiment type
Example of objectives
Easy Western
•
Confirm presence/absence of up to two proteins
•
Estimate low/high level of the target protein(s)
•
Confirm molecular weight of target protein
Western with total protein normalization
Compare normalized target protein levels between samples.
Western with endogenous protein normalization
Compare normalized target protein levels between samples.
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For example: Study the effect of various treatments and
conditions on target protein levels.
For example: Study the effect of various treatments and
conditions on target protein levels.
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3.4.5 Western experiment buffers and solutions
3.4.5
Western experiment buffers and solutions
Introduction
This section describes the recommended secondary antibody dilutions and how to determine optimum antibody concentrations. It also lists the buffers and solutions that
need to be prepared for a Western experiment.
Recommended dilution for
secondary antibodies
The recommended dilution for secondary antibodies (1 μg/μl) is 1:2500, but the optimal
dilution (between 1:2500 to 1:4000) should be determined for each Western experiment
setup. See below for information about how to optimize the primary and secondary antibody dilution.
Primary and secondary antibody
optimization
Note:
102
The signal-to-noise ratio is not the only parameter to look at. The linearity of
the response is equally important for normalization purposes. This is valid for
both primary and secondary antibodies.
Step
Action
1
Make a serial dilution of the protein that the primary antibody is directed
against.
2
Perform full Western blotting procedure.
3
Block the membranes.
4
Wash and incubate the membranes with several dilutions of the primary
antibody, for example, 1:100, 1:500, 1:1000 and 1:1500.
5
Wash and incubate the membranes with the secondary antibody, using the
same dilutions that were used for the primary antibody.
6
Select the optimal antibody dilution as the maximal signal-to-noise ratio.
7
Make a serial dilution of the protein that the primary antibody is directed
against.
8
Perform full Western blotting procedure.
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3.4.5 Western experiment buffers and solutions
Step
Action
9
Block the membranes.
10
Wash and incubate the membranes with the optimal dilution of the primary
antibody.
11
Wash and incubate the membranes with several dilutions of the secondary
antibody, for example, 1:1250, 1:1500, 1:3500 and 1:4000.
12
Select the optimal antibody dilution for maximal signal-to-noise ratio with
linear and proportional response.
Transfer solution recipes
WARNING
Place the Amersham WB analyzer in a room with exhaust ventilation if methanol or other chemicals that need ventilation will be
used.
CAUTION
Fire hazard. Do not use transfer buffer solutions consisting of more
than 40% ethanol or 40% methanol. It is recommended to only use
20% ethanol in transfer buffers.
Solution
Recipe
Amount/run
Transfer buffer
25 mM Tris, 192 mM glycine, 20% ethanol
1000 ml
pH 8.3
It is possible to use methanol instead of ethanol in the transfer
buffer.
Note:
Some ethanols have auto fluorescent properties which will lead
to a high membrane background. Make sure that the ethanol used
during transfer is not auto fluorescent.
Ultra pure water
(used for cleaning)
Ultra pure water
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1000 ml
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3.4.5 Western experiment buffers and solutions
Probing and antibody solution
recipes
Solution
Recipe
Amount/run
Blocking solution
The system is compatible with most blocking solutions,
for example 2% ECL PRIME agent in PBS-T (0.1%
Tween™-20 in 1×PBS), or 5% Bovine Serum Albumin in
PBS.
70 ml
Use blocking solutions with low auto fluorescence, see
Western Blotting – Principles and Methods handbook
for recommendations.
Wash buffer
PBS-T (0.1% Tween-20 in 1×PBS)
560 ml
Final wash buffer
PBS pH 7.4
290 ml
Antibody solution
Antibodies in PBS-T (0.1% Tween-20 in 1×PBS).
5 to 12 ml
See Primary and secondary antibody optimization, on
page 102 for how to determine optimum antibody concentrations.
Ultra pure water (used for
rinsing between probing
steps and cleaning of probing
flow path)
104
Ultra pure water
760 ml
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Perform an experiment
About this chapter
Electrophoresis (gel electrophoresis and scanning) experiments and Western experiments
(gel electrophoresis and Western blot steps) can be performed using Amersham WB
system. This chapter describes how to set up and run an experiment.
For information about evaluation of experiments, see Chapter 5 Evaluate an experiment,
on page 237.
For information about workflows and background information for pre-labeling of samples,
electrophoresis and Western experiments, see Chapter 3 Plan an experiment, on page 80.
In this chapter
This chapter contains the following sections:
Section
See page
4.1 Overview
106
4.2 Start the Amersham WB analyzer
108
4.3 Set up an experiment in Amersham WB software
110
4.4 Prepare samples
153
4.5 Perform electrophoresis and gel scanning
163
4.6 Perform the Western Blot steps (Western experiments only)
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4.1 Overview
4.1
Overview
Introduction
This section gives a workflow overview for Electrophoresis and Western experiments.
For more information about the different types of experiments and pre-labeling of
samples, see Chapter 3 Plan an experiment, on page 80.
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4.1 Overview
General workflow overview
The illustration below shows the main steps in Electrophoresis and Western experiments.
Electrophoresis experiment
Western experiment
Start instrument
Set up experiment in
software
Perform pre-labeling
Prepare unlabeled samples
OR
for loading
Run elecrophoresis &
Prepare and connect
gel scanning
transfer solutions
Prepare transfer
sandwich
Prepare and connect
Evaluate results
Run transfer
probing and antibody
solutions
Perform probing &
drying
Scan membrane(s)
Evaluate results
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4.2 Start the Amersham WB analyzer
4.2
Start the Amersham WB analyzer
Introduction
This section describes how to start up the Amersham WB analyzer units. It is possible to
set up an experiment in advance on an office computer with no connection to the instrument.
Note:
Both instrument units must always be turned on during a run.
Start the Amersham WB elpho &
scan unit
Step
Action
1
On the rear panel of the Elpho & scan unit, press the mains power switch to
I (ON).
Result: The Elpho & scan unit is started.
2
During start-up, the indicator panel displays the following:
When the instrument unit is ready to use, a white square is displayed.
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4.2 Start the Amersham WB analyzer
Start the Amersham WB western
unit
Step
Action
1
On the rear panel of the Western unit, press the mains power switch to I
(ON).
Note:
The Elpho & scan unit must be turned on before it is possible to run the Western
unit.
Result: The Western unit is started.
2
During start-up, the indicator panel displays the following:
When the Western unit compartments are ready to use, a white square is
displayed for each of the three compartments (transfer, probing and drying).
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4.3 Set up an experiment in Amersham WB software
4.3
Set up an experiment in Amersham WB software
Introduction
This section describes how to start the Amersham WB software and how to create, set
up and save an experiment in the software.
Help instructions for each workflow step are also available in the Amersham WB software
help in the right software panel.
In this section
This section contains the following subsections:
Section
110
See page
4.3.1 Start the software and create an experiment
111
4.3.2 Set up experiment and samples
119
4.3.3 Set up electrophoresis and gel scanning protocols
131
4.3.4 Set up the transfer parameters
136
4.3.5 Set up the probing protocol
139
4.3.6 View membrane scanning setup
145
4.3.7 View or enter experiment information
147
4.3.8 Save experiment
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4.3 Set up an experiment in Amersham WB software
4.3.1 Start the software and create an experiment
4.3.1
Start the software and create an experiment
Start the software
Step
Action
1
Start the computer and log on to Microsoft Windows.
2
Double-click the Amersham WB software icon on the desktop.
Result: The software start screen is displayed.
Tip:
To show the help panel with help instructions for the active screen, click the
or press F1.
help panel button
To open the user manual, select Help:View user manual or press Ctrl + F1.
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4.3.1 Start the software and create an experiment
Create a new Electrophoresis
experiment
Step
Action
1
In the Amersham WB software start screen, select the Easy SDS-PAGE experiment type in the Create New Experiment area.
Result: A description of the experiment type is displayed on the right side of
the start screen.
For further information about examples of objectives within this experiment
type, see Electrophoresis experiments overview, on page 91.
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4.3.1 Start the software and create an experiment
Step
Action
2
Click Create.
Result: The Amersham WB software main screen opens displaying the EXPERIMENT & SAMPLES workflow step.
The workflow steps associated with electrophoresis and gel scanning and
evaluation are enabled in the workflow panel.
For a description of the different areas in the main screen, see Section 2.9.2
Amersham WB software main screen, on page 65.
Continue with the instructions in Section 4.3.2 Set up experiment and samples,
on page 119.
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4.3.1 Start the software and create an experiment
Create a new Western
experiment
Step
Action
1
In the Amersham WB software start screen, select the appropriate Western
experiment type in the Create New Experiment area.
Result: A description of the selected experiment type is displayed on the right
side of the software start screen.
Note:
Make sure to select the correct experiment type when creating a new experiment. It is not possible to edit the experiment type within the experiment once
created.
For further information about the experiment types, see Section 3.4.4 Western
experiments setup overview, on page 101.
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4.3.1 Start the software and create an experiment
Step
Action
2
Click Create.
Result: The Amersham WB software main screen opens displaying the EXPERIMENT & SAMPLES workflow step.
The workflow steps associated with electrophoresis and gel scanning,
transfer, probing & drying, membrane scanning and evaluation are enabled
in the workflow panel.
For a description of the different areas in the main screen, see Section 2.9.2
Amersham WB software main screen, on page 65.
Continue with the instructions in Section 4.3.2 Set up experiment and samples,
on page 119.
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4.3.1 Start the software and create an experiment
Open a previously saved
experiment
Step
Action
1
Click the Open... button or select File:Open... (Ctrl + O) in the menu bar in the
Amersham WB software start screen.
Result: The Open dialog opens.
2
Browse and select the appropriate Amersham WB experiment file (*.AWBexp)
and click Open.
Result: The selected Amersham WB experiment file opens up in the main
screen and:
•
the EXPERIMENT & SAMPLES screen is displayed
or
•
116
if all workflow steps have been run, the EVALUATION workflow step is
displayed
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4.3.1 Start the software and create an experiment
Create a new experiment based
on a previous run
Step
Action
1
Click the New from existing... button or select File:New from existing... in
the menu bar in the Amersham WB software start screen.
Result: The Open dialog opens.
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4.3.1 Start the software and create an experiment
Step
Action
2
Browse and select the appropriate Amersham WB experiment file (*.AWBexp)
and click Open.
Result: The selected Amersham WB experiment file opens up in the main
screen and the EXPERIMENT & SAMPLES workflow step is displayed.
The following information in the selected experiment is transferred to the
new experiment that is created:
•
•
EXPERIMENT & SAMPLES:
-
Experiment type (cannot be edited)
-
Gel card type
-
Sample type
-
Amount (only for sample types Quantity calibrant)
-
Unit (for Amount)
-
Secondary antibody type
-
Primary antibody name
ELECTROPHORESIS & GEL IMAGING, TRANSFER, PROBING & DRYING:
Any default settings that have been edited are transferred.
•
EVALUATION:
All settings for the different image positions in the experiment are
transferred. The actual images and associated data are not transferred.
•
Experiment Information:
Information entered about consumables (Consumable type) in the Cards
& reagents tab is transferred.
Note:
Experiment specific data such as consumable ID, batch data and general
comments about the experiment are not transferred.
3
118
Continue with the instructions in Section 4.3.2 Set up experiment and samples,
on page 119.
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4.3 Set up an experiment in Amersham WB software
4.3.2 Set up experiment and samples
4.3.2
Set up experiment and samples
Choose gel cards
Step
Action
1
Choose the number of gel cards for the experiment in the Number of Gel
cards area in the EXPERIMENT & SAMPLES screen. If one gel card is included,
position A must be used.
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4.3.2 Set up experiment and samples
Step
Action
2
Select the type of gel card to be used in the Gel card drop-down list.
See Section 3.3 Plan electrophoresis experiments, on page 90 for information
of the separation resolution for the different types of gel cards
Note:
The A and B gel cards must be of the same type.
Result: The Gel Card A tab displays the sample table where sample information can be entered.
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4.3.2 Set up experiment and samples
Sample table overview
On the Gel card A tab (and Gel card B tab if included in the experiment), the sample table
is displayed. Each row in the table corresponds to a well in the gel card.
By default:
•
the first and last well on the gel card (in the Type column of the table) are set to
Blank,
Note:
It is recommended to load lane 1 and 16 with Loading buffer to optimize
the performance and minimize the potential outer lane artifacts.
•
the second and the fifteenth well are set to Amersham™ WB MW markers,
•
the other wells are set to Sample.
If you are performing a quantity calibration experiment, the samples to be used as calibrants, should be set to type Quantity calibrant.
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4.3.2 Set up experiment and samples
Set up the samples for the gel
card(s)
Step
Action
1
To change the type of sample for a well, select the drop-down arrow for the
well in the Type column and select the appropriate sample type.
See Sample table – Type column options, on page 124 for a description of the
sample types and when to use a sample type.
2
For Quantity calibration experiments only (otherwise proceed with step
3)
Note:
For information about when to use the quantity calibration sample type, see
Sample table – Type column options, on page 124 below.
To set samples to quantity calibrants and enter amounts:
•
In the Amount column header, click the drop-down arrow and select
the appropriate unit.
•
For each well containing a quantity calibrant:
- In the Type column drop-list, select Quantity calibrant.
Result: The corresponding Amount field is indicated with a red frame.
- Click in the Amount field with a red frame and enter the protein amount.
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4.3.2 Set up experiment and samples
Step
Action
3
Enter sample ID and comments for a sample (optional).
For each well, click in the appropriate:
•
Sample ID field and enter an ID for the sample
•
Comments field and enter a comment, for example, sample concentration, sample volume, buffer used etc.
Tip:
Sample IDs and Comments can be entered at any time, also during or after
a run.
Tip:
It is possible to add general comments about the experiment at any time by
clicking the Experiment Information icon in the workflow panel.
See Section 4.3.7 View or enter experiment information, on page 147 for more
information.
4
Repeat the steps for Gel card B if included in the experiment.
Tip:
It is possible to copy and paste the whole sample table or parts of the sample
table. See Copy and paste in the sample table, on page 125.
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4.3.2 Set up experiment and samples
Sample table – Type column
options
Type
Description & when to use
Sample
Use this type for a sample to be investigated.
Amersham™ WB MW
markers
One or several lanes can be used for Amersham WB
molecular weight markers. Make sure that the lanes containing the MW markers are set to Type: Amersham™ WB
MW markers. When a new experiment is set up the second and the fifteenth well are set to Amersham™ WB MW
markers by default.
The lanes set to Amersham™ WB MW markers are used
by the software to automatically calculate the molecular
weight calibration curves. Then, by using the calibration
curves, the molecular weights of all detected bands on
the image are automatically calculated.
See Description of the molecular weight calibration algorithm, on page315 for information about how the molecular
weight calibration curve is calculated.
Quantity calibrant
In quantity calibration (i.e., an experiment where the
amount of target protein in different samples should be
determined using a calibration curve), the sample type
Quantity calibrant must be used for the calibrants.
This sample type is available for quantity calibration in
Easy SDS-PAGE and Easy Western experiments.
The lanes set to Type: Quantity calibrant are used by the
software to automatically calculate the calibration curve.
Then, by using the calibration curve, the absolute protein
amount for the samples are automatically calculated.
Blank
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Generally used as default type for the outer lanes where
the wells are loaded with Amersham WB loading buffer
(diluted with an equal volume of ultra pure water). This
sample type can also be used for any other lanes loaded
with Loading buffer.
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4.3.2 Set up experiment and samples
Copy and paste in the sample
table
It is possible to copy the whole sample table or cells of the sample table and paste into
the sample table on another tab (e.g., from Gel Card A tab to Gel card B tab) or into, for
example, a Microsoft Excel® sheet.
Step
Action
1
To select cells in the sample table:
•
To select one cell in the sample table:
Click in the cell.
•
To select a number of cells:
Click in a cell, hold down the left mouse button and drag a rectangle to
include the cells to be copied/pasted.
•
To select the whole sample table for copy/paste:
Click in a cell in the sample table and press Ctrl + A.
It is also possible to click on 1 in the upper left corner of the sample table
(representing well number 1), hold down the left mouse button and drag
a rectangle to include all cells in the sample table.
You do not need to select the column headers.
Result: Selected cells are highlighted in blue.
2
To copy the selected cells:
•
press Ctrl + C on the keyboard,
or
•
3
right-click on the sample table and select Copy.
To paste the selected cells into the sample table for another position:
•
Click the cell which corresponds to the top left cell of your selection and
press Ctrl + V on the keyboard.
or
•
Right-click the cell which corresponds to the top left cell of your selection
and select Paste.
Result: The cells are pasted into the sample table.
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Step
Action
4
To paste the selected cells into, for example, Microsoft Excel:
Click a cell in an Excel sheet and press Ctrl+V on the keyboard or use the
paste control in the application.
Result: The selected cells and the table columns of the sample table are
pasted into the work sheet.
Select antibodies for probing
(Western experiments only)
Depending on the type of Western experiment, one or two sets of antibodies can be
entered in the Antibodies for Membrane A (or B) area.
Antibodies for probing of membranes in positions A and B are entered under the gel
card A and B tabs. The type of secondary antibody to be used needs to be entered before
probing can be started. If there are two primary antibodies used, the selection in the gel
card tab will determine which antibody is displayed as target and which is displayed as
control in further analysis. The first selected primary antibody will be shown in the
membrane target image and the second selected primary antibody will be shown in the
membrane control image.
See Select primary and secondary antibodies for an experiment, on page99 for information
of how to combine antibodies.
Select antibodies for Easy
Western experiments
In Easy Western experiments, one or two different target proteins can be detected. To
enter information:
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Step
Action
1
Enter a description for the primary antibody in the Primary antibody field
(optional).
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Step
Action
2
Select the appropriate secondary antibody from the Labeled secondary ab
drop-down list.
Note:
The secondary antibody must match the primary antibody species (if the primary antibody species is mouse, the secondary antibody must be of type
anti-mouse).
3
If a second target protein should be detected check the Primary antibody
2 box.
Result: Fields for the antibodies to be used for detecting a second target
protein are displayed.
4
Type in a description for the second primary antibody in the Primary antibody 2 field (optional).
Note:
The Primary antibody 2 species should be a different species than the Primary
antibody species.
5
Select the appropriate secondary antibody 2 from the Labeled secondary
ab 2 drop-down list.
Note:
The Labeled secondary ab 2 must match the Primary antibody 2 species
and have another CyDye conjugated than the Labeled secondary ab.
Example:
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Select antibodies for Western
with total protein normalization
experiments
Step
Action
1
Type in a description for the primary antibody in the Primary ab (against
target) field (optional).
2
Select the appropriate secondary antibody from the Labeled Secondary ab
drop-down list (must match the primary antibody species).
Note:
In this case Cy5 has been used for pre-labeling, so only secondary antibodies
conjugated to Cy3 are available.
Select antibodies for Western
with endogenous protein
normalization experiments
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Step
Action
1
Type in a description for the primary antibody in the Primary ab (against
target) field (optional).
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Step
Action
2
Select the appropriate secondary antibody from the Labeled secondary ab
drop-down list.
Note:
The secondary antibody must match the primary antibody species (if the primary antibody species is mouse, the secondary antibody must be of type
anti-mouse).
3
Type in a description for the second primary antibody in the Primary ab
(against control) field (optional).
Note:
The Primary ab (against control) species should be a different species than
the Primary antibody (against target) species.
4
Select the appropriate secondary antibody 2 from the Labeled secondary
ab 2 drop-down list
Note:
The Labeled secondary ab 2 must match the Primary antibody (against
control) species and have another CyDye conjugated than the Labeled secondary ab.
Example:
Print the experiment & samples
information (optional)
To print the entered experiment and samples information, click the Print icon to the right
of the gel card tabs, or select File:Print, or press Ctrl + P. Select printer in the Print dialog
and print out the information.
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The following information will be printed:
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•
experiment name
•
the gel card type used in the experiment
•
the sample tables for gel card A and B
•
the antibodies to be used for probing (Western experiments only)
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4.3.3 Set up electrophoresis and gel scanning protocols
4.3.3
Set up electrophoresis and gel scanning protocols
Introduction
This section describes the electrophoresis and gel scanning parameters.
Enter gel card information
Step
Action
1
To enter the ID of a gel card:
In the ELECTROPHORESIS & GEL SCANNING screen, place the cursor in the
ID field for Position A and:
•
scan the data matrix code on the gel card using the data matrix tag
reader
or
•
enter the ID manually (five digits)
Tip:
Entering ID should be done just before the gel card is placed on the card plate
in the loader.
If a data matrix tag reader is a used, Code number and Lot number of the gel
card will be logged in the Experiment Information dialog.
2
To enter a note about a gel card, place the cursor in the Note field for Position A and type in a note. More information can be added in the Experiment
Information dialog.
Note:
A note can also be written in the writing surface of the physical gel card. Use
a pencil, not a pen.
3
Repeat the steps above for Position B, if included in the experiment.
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4.3.3 Set up electrophoresis and gel scanning protocols
View/edit the electrophoresis
protocol
Note:
The default settings for the Electrophoresis Protocol do not normally need
to be edited. By default, the electrophoresis is stopped using front detection,
that is, when the front has reached the end of the gel.
If you need to edit any settings in the Electrophoresis Protocol area, the table below
gives a description of the settings. To revert to default settings and values click the Default
button.
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Command
Description
Voltage limit 1
Shows the maximum voltage to be used
during the run. Decreasing this value will
extend the run time.
Current limit1
Shows the maximum current to be used
during a run. Decreasing this value will
extend the run time.
Pause for sample well cleanup after X
minutes 2
Check this box to pause the electrophoresis after the calculated time in minutes
and perform sample well cleanup. The
sample well cleanup is performed for prelabeled samples by dipping a paper comb
in the sample wells to remove excess dye
after the proteins have migrated into the
gel.
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4.3.3 Set up electrophoresis and gel scanning protocols
Command
Description
Stop electrophoresis on front detection
The electrophoresis run is stopped when
the front has reached the end of the gel
(i.e., right before the buffer strip opening
on the gel card).
An Estimated time for the run is shown
only when using default current and
voltage limits.
This radio button is selected by default.
Note:
If performing a Western experiment where
no molecular weight markers are included
and pre-labeling of samples is not performed, the electrophoresis can not be
stopped using front detection. Use the
option Stop electrophoresis on time instead.
Note:
If the molecular weight marker dilution is
higher then 20 times, it is recommended
to Stop electrophoresis on time .
Stop electrophoresis on time
Select this radio button to stop the run
after a specified time.
Enter the run time for the electrophoresis
run in the Stop electrophoresis on time
field.
The run will be stopped when the set time
has passed, regardless of the position of
the front.
Tip:
If you want to increase the separation of
larger proteins in the upper area of the
gel card and know what run time is suitable, it is possible to enter a duration time
for the run in the protocol to determine
the length of the run instead of stopping
it based on front detection. The front and
smaller proteins may then migrate
through and exit the gel.
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4.3.3 Set up electrophoresis and gel scanning protocols
1
2
Command
Description
Default
Click to revert to default parameters. A
dialog asking for your confirmation will
be displayed.
Maximum power is 20 W/gel card. The maximum values for the voltage and current parameters can not
be reached simultaneously.
The time will be calculated from the set current limit and voltage limit. The default limits will set the time
to 5 minutes.
View/edit the gel scanning
protocol
Note:
The default settings for gel scanning is adjusted to the experiment type to be
run. These settings do not normally need to be edited.
If you need to edit any settings in the Gel Scanning Protocol area, the table below gives
a description of the settings. To revert to default settings and values click the Default
button.
Command
Description
Scan gel automatically after electrophoresis
When this box is checked, the gel cards
are automatically scanned after the
electrophoresis run.
This box is checked by default for the
applications that requires pre-labeling of
samples, that is Easy SDS-PAGE and
Western with total protein normalization.
The status of the box can be altered for
all experiments, except for Easy SDSPAGE where the gel is always scanned
after the electrophoresis run.
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4.3.3 Set up electrophoresis and gel scanning protocols
Command
Description
Scanning sensitivity
Automatic sensitivity
Select this radio button to use the automatic sensitivity function at gel card
scanning.
The scanner and software automatically
optimize the scanning sensitivity level for
the gel images. The sensitivity level is set
so that the strongest protein signals in
the gel image do not become saturated
(the front and the outermost lanes are
not used when sensitivity is optimized).
This radio button is selected by default.
Manual sensitivity
Select this button to set/change the sensitivity level of the gel scanning manually.
For example:
•
if you get weak signals for your proteins of interest, try a higher sensitivity level and re-scan the gel cards
•
if you get saturated signals for your
proteins of interest (indicated by a
red color in the image preview), try a
lower sensitivity level and re-scan the
gel cards
Change the sensitivity level by dragging
the Cy5 sensitivity level slider.
Default
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values set in the software. A dialog asking
for your confirmation will be displayed.
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4.3.4 Set up the transfer parameters
4.3.4
Set up the transfer parameters
Introduction
This section describes the transfer parameters.
Enter transfer sandwich
assembly information
Gel cards and membranes description
•
In the TRANSFER workflow step in the software, in the Gel Cards & Membranes area,
both Membrane Position A and Position B boxes are checked if two gel cards were
run in the electrophoresis.
Note:
•
If you only want to continue with one of the gel cards from the electrophoresis in the transfer, uncheck the appropriate box (Membrane Position A or
Position B) in the Gel Cards & Membranes area.
If a Gel Card ID and a Gel Card Note have been entered for the gel card in the
ELECTROPHORESIS & GEL SCANNING workflow step, these are displayed in their
respective fields.
Enter membrane information
Perform the following steps for each position to be used in the transfer:
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4.3.4 Set up the transfer parameters
Step
Action
1
To enter the ID of a membrane, look at an Amersham WB PVDF card package.
The ID information is found on the label of the PVDF card single package.
Place the cursor in the ID field for the appropriate position in the software
and:
•
scan the data matrix code on the PVDF card single package using the
data matrix tag reader
or
•
type in the ID manually in the software
See also Prepare the PVDF card, on page 188 for more information about how
to prepare the PVDF card.
Note:
When preparing the transfer sandwich(es), make sure that the gel card and
the membrane for position A in the instrument/software are used together
and the gel card and membrane for position B in the instrument/software
are used together when assembling the transfer sandwiches.
See Section 4.6.2 Prepare the transfer sandwich, on page 186 for information
about how to assemble the transfer sandwich.
Note:
If a data matrix tag reader is a used, Code number and Lot number of the
membrane will be logged in the Experiment Information dialog.
2
To enter a note about the membrane, place the cursor in the Note field and
type in a note.
View/edit the transfer protocol
Note:
The default settings for the transfer protocol do not normally need to be edited.
If you need to edit any settings in the Transfer Protocol area, the table below gives a
description of the settings. To revert to default values click the Default button.
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4.3.4 Set up the transfer parameters
Command
Description
Duration
Shows the duration time for the transfer
run.
Tip:
It is possible to increase the duration time
if your sample contains larger proteins
and decrease the duration time if you
have smaller proteins.
1
Voltage limit 1
Shows the maximum voltage to be used
during the run.
Default
Click to revert to default transfer protocol.
A dialog asking for your confirmation will
be displayed.
Maximum power is 40 W. Maximum current is 400 mA.
Enter information about the
transfer solutions
The Description field shows the recommended Transfer buffer and Cleaning (ultra pure
water) solutions to be used for a run.
Edit the descriptions if you will use other solutions in the run.
See Transfer solution recipes, on page 103 for information about recipes.
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4.3.5 Set up the probing protocol
4.3.5
Set up the probing protocol
Introduction
This section describes how to view/edit the probing protocol. No specific parameters
need to be set for drying.
View/edit membrane information
In the Membranes area:
•
Both Membrane Position A and Position B boxes are checked if two PVDF cards
were run in the transfer.
If you only want to continue with one of the membranes from the transfer run, deselect the appropriate check box (Membrane Position A or Position B).
Results:
•
-
The information for an unused position in the Antibodies area will be dimmed.
-
The software will automatically calculate the volume/solution to be used in the
run according to that one membrane will be used.
If an ID or Note was entered in the TRANSFER workflow step, these are displayed in
their respective fields.
View antibodies information
In the Antibodies area (for the included positions):
•
•
The descriptions of the Primary antibody position A/position B are displayed (if they
have been entered in the EXPERIMENT & SAMPLES workflow step).
Under the Labeled secondary ab position A (and/or B):
The secondary antibody to be used is displayed (e.g., Cy5 labeled anti-mouse antibody).
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4.3.5 Set up the probing protocol
If two primary antibodies are used for one position, both antibodies are displayed. Then,
the antibodies must be mixed in the antibody solution tube to be used in the position A
Primary (or B Primary) in the antibody compartment. The same applies if two secondary
antibodies are used.
Note:
The type of secondary antibody to be used need to be entered in the gel card
tab before probing can be started. If there are two primary antibodies used,
the selection in the EXPERIMENT & SAMPLES Gel card tab A and B will determine which antibody is displayed as target and which is displayed as control
in further analysis. The first selected primary antibody will be shown in the
membrane target image and the second selected primary antibody will be
shown in the membrane control image.
Note:
The antibody solution tube positions are marked with A Primary/Secondary
and B Primary/Secondary on the inside of the lid. Make sure that tubes in
positions A/B in the software/antibody compartment match the PVDF card
positions A/B in the software/probing compartment.
Recovery of primary antibodies
If you want to recover your primary antibodies, check the Recover primary antibodies
box in the Antibodies area.
Recovered primary antibodies are automatically re-collected in their respective antibody
solution tubes in the antibody compartment.
Note:
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Not all of the primary antibody solution volume can be recovered and the recovered solution is diluted about 30%.
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4.3.5 Set up the probing protocol
Enter information about the
probing solutions
In the Solutions & Volumes area, default descriptions of the Water, Wash, Block and
Final Wash solutions are displayed.
If you are using other solutions, edit the Description field(s) for the appropriate solution(s).
Note:
Make sure the Water bottle is filled with ultrapure water. The solution is used
for rinsing of flow path between the probing steps. Wash solution is used for
rinsing between primary antibody to position A and B.
Probing protocol
In the Probing area, the probing sequence table is displayed showing the default steps
for probing.
For each step, the following is shown:
•
the solution to be used
•
the duration time for the step
•
how many times the step will be performed
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4.3.5 Set up the probing protocol
If you want to edit an existing step or the sequence of steps, continue with the instructions
below.
Edit a step in the probing
protocol
To edit information for an existing step:
Step
Action
1
To change the solution to be used, click the drop-down arrow and select the
appropriate solution inlet.
Tip:
The Custom inlet can be used for any additional probing solution. It is not
used in the default probing protocol. When selected, 16 ml of the custom
probing solution will be pumped into the probing chamber. The custom inlet
tubing is marked with P Custom.
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2
To change the duration time for a step, click in the appropriate Dur. (min)
field and enter a new time.
3
To edit the number of times for a step to be performed, click in the appropriate Repeat field and edit the number.
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4.3.5 Set up the probing protocol
Insert a new step in the probing
protocol
To insert a step in the probing sequence:
Step
Action
1
Select the row in the table, below which you want to add a step.
2
Click Insert step.
Result: A new row is added.
3
Select the solution to be used in the Probing steps column drop-down list
and enter duration time and the number of times the step should be performed.
Note:
The duration and repeats for the default protocol are automatically presented
on choosing the probing step.
Remove a step from the probing
protocol
To remove a step from the probing sequence:
•
Select the step to be removed in the probing sequence table.
•
Click Remove step.
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4.3.5 Set up the probing protocol
Print the probing information
To print the entered probing information, click the Print icon below the probing sequence
table, or select File:Print in the menu bar, or press Ctrl + P. Select printer in the Print dialog and print out the information.
The following information will be printed:
144
•
experiment name
•
PVDF card information
•
the antibodies to be used for probing and whether recovery of primary antibodies
will be performed
•
the probing sequence
•
the solutions and volumes to be used in the probing run
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4.3.6 View membrane scanning setup
4.3.6
View membrane scanning setup
Introduction
This section describes the membrane scanning parameters.
View membrane information
If an ID or Note was entered in the Membranes area in the TRANSFER workflow step,
these are displayed in their respective fields.
View/edit scanning sensitivity
parameters
In the Scanning Sensitivity area, the radio button Automatic sensitivity is selected by
default.
Note:
This setting do not normally need to be edited.
If you need to edit any settings in the Scanning Sensitivity area, the table below gives
a detailed description of the settings.
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4.3.6 View membrane scanning setup
Command
Description
Automatic sensitivity
Select this radio button to use the automatic sensitivity function at membrane
scanning.
The scanner and software automatically
optimize the scanning sensitivity level for
the membrane images. The sensitivity
level is set so that the strongest protein
signals in the membrane image do not
become saturated (the outer most lanes
are not used when sensitivity is optimized).
This radio button is selected by default.
Manual sensitivity
Select this button to set/change the sensitivity level of the membrane scanning
manually.
For example:
•
if you get saturated signals for your
protein of interest, try a lower sensitivity level and re-scan the membranes
•
if you get weak signals for your protein of interest, try a higher sensitivity
level and re-scan the membranes
Up to four gel scans per position can be
saved within an experiment.
Change the sensitivity level by dragging
the Cy5 sensitivity level and/or Cy3
sensitivity level slider.
Default
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Click to revert to default setting Automatic sensitivity. A dialog asking for your
confirmation will be displayed.
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4.3.7 View or enter experiment information
4.3.7
View or enter experiment information
Introduction
Experiment information can be entered/edited at any time during an experiment.
This section describes how to:
•
enter general comments for an experiment
•
view information about gel cards and PVDF cards
•
add/remove custom consumables
•
view the experiment log
Open the Experiment
information dialog
In the software workflow area to the left, click the experiment information icon.
Result: The Experiment information dialog opens displaying the Experiment comments
tab.
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4.3.7 View or enter experiment information
View/enter general experiment
comments
•
On the Experiment comments tab:
Enter any general comments about the experiment. Previously entered comments
can be viewed.
•
Click OK to save any changes and to close the dialog.
View/enter information about gel
cards and PVDF cards
In the Cards & reagents tab previously entered information about the gel cards and
membranes in the ELECTROPHORESIS & GEL IMAGING and TRANSFER workflow steps
is displayed. If the data matrix code on the gel card/PVDF card was scanned using the
data matrix tag reader, the Code No (code number), Lot No and ID are automatically
filled in on this tab.
•
On the Cards & reagents tab:
Enter or edit Lot No and ID information for the gel card/PVDF card. The Code No
cannot be edited or entered by the user.
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4.3.7 View or enter experiment information
•
Click OK to save any changes and to close the dialog.
Add a consumable to the Cards
& reagents tab
To add a new consumable to the Cards & reagents tab, for example, a buffer that is
used in the experiment:
Step
Action
1
Click the Add button.
Result: A new row for entering consumable information is displayed.
2
Enter a description of the consumable in the Consumable type field.
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4.3.7 View or enter experiment information
Step
Action
3
Enter information about the consumable (e.g., lot number) in the Consumable
information field.
4
Click OK to save any changes and to close the dialog.
Remove a consumable from the
Cards & reagents tab
To remove a manually entered consumable:
•
select the row with the consumable to be removed,
•
click the Remove button,
•
click OK to save any changes and to close the dialog.
View the experiment log
On the Experiment log tab, information about the events in the experiment is automatically logged.
For each event, the date and time for the event, the user logged in and a description of
the event are displayed.
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4.3.7 View or enter experiment information
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4.3.8 Save experiment
4.3.8
Save experiment
Introduction
An experiment can be saved as an experiment file (*.AWBexp). This section describes
when and how to save an experiment.
When to save an experiment?
You must save the experiment before a run is started. If the experiment has not been
saved when starting a run, the Save as dialog appears where you can save the experiment.
When the experiment file has been created, the experiment will automatically be saved
before and after every run.
Save an experiment
To save the experiment the first time:
•
Select File:Save in the menu bar.
Result: The Save as dialog opens.
•
Type in a name for the experiment and click Save.
To save an existing experiment, select File:Save in the menu bar or press Ctrl+S.
Note:
It is recommended to save the experiment to a local hard drive during a run
to avoid network connectivity problems.
Save an experiment with a new
name
To save an existing experiment with a new name:
•
Select File:Save as in the menu bar.
Result: The Save as dialog opens.
•
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Type in a name for the experiment and click Save.
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4.4 Prepare samples
4.4
Prepare samples
Introduction
Samples can be either unlabeled or pre-labeled depending on the application.
•
The Easy SDS-PAGE and Western with total protein normalization experiment types
require pre-labeling of samples.
•
In the Easy Western and Western with endogenous protein normalization experiment
types samples are not pre-labeled.
This section describes how to perform pre-labeling of samples and how to prepare unlabeled samples.
In this section
This section contains the following subsections:
Section
See page
4.4.1 Perform pre-labeling of samples
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4.4.2 Prepare unlabeled samples
161
4.4.3 Prepare Amersham WBmolecular weight markers
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4.4.1 Perform pre-labeling of samples
4.4.1
Perform pre-labeling of samples
Introduction
Pre-labeling of samples is required for detection when running electrophoresis experiments. It is also required in Western experiments when detecting the total protein on a
membrane.
This section describes:
•
pre-requisites for pre-labeling
•
materials required for pre-labeling
•
preparations before starting pre-labeling
•
labeling of samples (pre-labeling protocol)
For more information about pre-labeling, see Section 3.2 Pre-labeling of proteins, on
page 83.
Precautions
WARNING
When working with pre-labeling of protein samples:
•
Always wear protective clothing, gloves and protective glasses.
•
Read the Safety Data Sheet (SDS/MSDS) before performing prelabeling of samples.
CAUTION
When pre-labeling of proteins in samples has been performed a
strong odor may arise from trace amounts of dimethyl sulfide (DMS)
and dimethyl sulfoxide (DMSO). Local exhaust ventilation may be
required. Follow local regulations and instructions for safe operation.
Note:
154
To obtain comparable labeling efficiencies, important parameters such as pH,
reaction volume, temperature and buffer salts should be invariant.
Labeling efficiencies will also vary from protein to protein.
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4.4.1 Perform pre-labeling of samples
Pre-requisites for pre-labeling
and protocol selection
See Section 3.2.2 Pre-labeling pre-requisites and protocols, on page 86 for information
about pre-requisites for pre-labeling and how to select protocol.
Required solutions and materials
The following solutions and materials are required for the pre-labeling of proteins:
•
Pre-labeling consumables: Cy5 dye reagent, Labeling buffer, Loading buffer
•
1 M DTT (dithiothreitol) stock solution (DTT and ultra pure water) if reducing SDS-PAGE
will be performed
•
Ultra pure water for diluting the Cy5 dye reagent
•
Original lysis buffer for adjusting reaction volume (Western experiments only)
•
0.5 ml microfuge tubes
•
Heating block
•
Vortex
•
Centrifuge
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4.4.1 Perform pre-labeling of samples
Preparations before starting
pre-labeling
Step
Action
1
•
Take out one of each of the following vials (enough for running two gel
cards) from the freezer:
-
1 vial Amersham WB Cy5
-
1 vial Amersham WB labeling buffer (not needed if labeling samples
using the Western pre-labeling protocol)
-
1 vial Amersham WB loading buffer
•
Thaw the pre-labeling components completely.
•
Equilibrate the Cy5 vial to room temperature before opening to avoid
moisture condensation.
2
Briefly spin down the Cy5 dye reagent liquid using a centrifuge.
3
Set the temperature of the heating block to 95ºC.
4
For reducing SDS-PAGE, add reducing agent to the Loading buffer:
•
Note:
Add 29 µl 1 M DTT stock solution to 0.7 ml (one vial) Loading buffer, and
vortex to mix.
Prepare the Amersham WB molecular weight markers at the same time. See
Section 4.4.3 Prepare Amersham WBmolecular weight markers, on page 162.
Pre-labeling of quantity
calibrants
If purified protein samples are used as quantity calibrants, label each calibrant individually (i.e., one labeling reaction for each calibrant) for best possible quantity calibration.
Also, samples and quantity calibrants should be pre-labeled under the same conditions.
Note:
156
The slope and linearity of the calibration curve depends both on the protein
and the sample concentration range. For quantity calibration, use the same
calibrant protein as the sample protein of interest.
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4.4.1 Perform pre-labeling of samples
Perform sample pre-labeling
(SDS-PAGE pre-labeling protocol)
Note:
To adjust the amount of sample loaded per well (maximum 0.5 µg/protein
band for optimal resolution), dilute the sample prior to, or after, pre-labeling.
The Amersham WB labeling buffer is used to dilute samples prior to pre-labeling. For dilution after labeling, use the Amersham WB loading buffer (with or
without DTT) diluted with an equal volume of ultra pure water. For pre-labeling
of samples with a small number of proteins, a suitable starting concentration
is 1 mg/ml. The protocol below can be scaled up.
Step
Action
1
If the protein sample contains interfering substances, perform a buffer exchange using Amersham WB MiniTrap kit.
2
Perform labeling reaction in a 0.5 ml microfuge tube:
•
For protein samples: First add 17 μl of labeling buffer and then 2 μl of
protein sample (1 ng/µl - 20 μg/µl) and mix. 1
•
For proteins samples after buffer exchange: Add 2-19 μl of protein
sample (1 ng/µl - 20 μg/µl in Labeling buffer) to the tube. Fill up to a volume of 19 μl using Labeling buffer.
3
Heat the samples at 95ºC for 1 minute using a heating block. 2
4
•
Remove the microfuge tubes from the heating block.
•
Let the samples cool down for 5 minutes at room temperature.
•
Add 1 μl of Cy5 dye reagent.
•
Mix thoroughly by quickly vortexing.
5
6
Incubate at room temperature for 30 minutes.
Note:
It is important to make sure that the labeling volume and time are equal for
all samples.
7
Add 20 μl of Loading buffer.
8
Heat the samples at 95ºC for 3 minutes.
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4.4.1 Perform pre-labeling of samples
Step
Action
9
Spin down the samples. Total sample volume is 40 μl per reaction (recommended loading volume is 20 μl).
Proceed with the instructions in Section 4.5 Perform electrophoresis and gel
scanning, on page 163.
If the electrophoresis analysis will be performed at a later stage, store the
pre-labeled samples at -20°C.
1
2
158
A sample volume of 2 µl is sufficient for most protein samples with concentrations ranging from 1 ng/µl
to 20 µg/µl. The 10-fold dilution in Labeling buffer ensures optimal labeling conditions.
It is possible to skip the heating step for temperature sensitive samples
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4.4.1 Perform pre-labeling of samples
Perform sample pre-labeling
(Western pre-labeling protocol)
Tip:
The protocol below can be scaled up.
Step
Action
1
Perform the labeling reaction in a 0.5 ml microfuge tube:
•
Add 2-19 μl cell lysate or tissue extract sample (maximum 40 μg total
protein), and fill up to a volume of 19 μl using original sample lysis buffer.
•
Add 1 μl of Cy5 dye reagent diluted 1:10 in ultra pure water.
Note:
The diluted dye must be freshly prepared and used within 30 minutes. It
can not be frozen and re-used.
•
2
Briefly vortex to mix thoroughly.
Incubate at room temperature for 30 minutes.
Note:
Make sure that the labeling time and volume is equal for all samples.
For temperature sensitive samples, incubate on ice for 30 minutes.
3
Add 20 μl of Loading buffer.
4
Heat the samples at 95ºC for 3 minutes.
5
Spin down the samples. Total sample volume is 40 μl per reaction (recommended loading volume is 20 μl).
Proceed with the instructions in Section 4.5 Perform electrophoresis and gel
scanning, on page 163.
If the electrophoresis analysis will be performed at a later stage, store the
pre-labeled samples at -20°C.
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4.4.1 Perform pre-labeling of samples
Perform sample pre-labeling
(Quick SDS-PAGE pre-labeling
protocol)
Note:
To adjust the amount of sample loaded per well (maximum 0.5 µg/protein
band for optimal resolution), dilute the sample prior to, or after, pre-labeling.
The Amersham WB labeling buffer is used to dilute samples prior to pre-labeling. For dilution after labeling, use the Amersham WB loading buffer (with or
without DTT) diluted with an equal volume of ultra pure water. The reaction
below can be scaled up.
Step
Action
1
If the protein sample contains interfering substances, perform a buffer exchange using Amersham WB MiniTrap kit.
2
Perform labeling reaction in a 0.5 ml microfuge tube:
3
•
For protein samples: First add 17 μl of labeling buffer and then 2 μl of
protein sample (1 ng/μl - 20μg/μl) and mix. 1
•
For proteins samples after buffer exchange: Add 2-19 μl of protein
sample (1 ng/μl - 20μg/μl in Labeling buffer) to the tube. Fill up to a volume of 19 μl using Labeling buffer.
•
Add 1 μl of Cy5 dye reagent.
•
Mix thoroughly by a quick vortex.
4
Incubate at 95ºC for 3-5 minutes.
5
Add 20 μl of Loading buffer.
6
Heat the samples at 95ºC for 3 minutes.
7
Spin down the samples. Total sample volume is 40 μl per reaction (recommended loading volume is 20 μl).
Proceed with the instructions in Section 4.5 Perform electrophoresis and gel
scanning, on page 163.
1
160
A sample volume of 2 µl is sufficient for most protein samples with concentrations ranging from 1 ng/µl
to 20 µg/µl. The 10-fold dilution in labeling buffer ensures optimal labeling conditions.
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4.4.2 Prepare unlabeled samples
4.4.2
Prepare unlabeled samples
Introduction
This section describes how to prepare unlabeled samples and sample loading capacity.
Prepare samples
Step
Action
1
Set the temperature of the heating block to 95ºC.
2
For reducing SDS-PAGE, add reducing agent to the Loading buffer:
•
Add 29 µl 1 M DTT stock solution to 0.7 ml (one vial) Loading buffer and
vortex (final concentration 40 mM).
3
Mix equal volume of Loading buffer and sample.
4
Heat the samples at 95ºC for 3 minutes.
Sample loading capacity
The table below describes the loading capacities:
1
Loading volume/well
Protein amount
15-30 μl 1
Maximum 20 μg/well
20 μl, recommended
<0.5 μg/protein band
Difference between wells should be <10 μl. Adjust with Amersham WB loading buffer (diluted with an
equal volume of ultra pure water).
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4.4.3 Prepare Amersham WBmolecular weight markers
4.4.3
Prepare Amersham WBmolecular weight markers
Introduction
Take out one vial of Amersham WB molecular weight markers (molecular weight markers)
(enough for running two gel cards) from the freezer and thaw completely.
Western experiments
In Western experiments, Amersham WB molecular weight markers should be diluted
1:20 in Loading buffer before loading on the gel card. Before use, the supplied Loading
buffer must be diluted with ultra pure water and contain added DTT.
Step
Action
1
Add 29 μl of 1 M DTT stock solution to 0.7 ml (one vial) Loading buffer. Vortex
to mix.
2
Dilute the DTT-containing Loading buffer with an equal volume of ultra pure
water. Vortex to mix.
3
Dilute the molecular weight markers 1:20 with the prepared Loading buffer.
Note:
The molecular weight markers can be diluted further in prepared Loading
buffer to match samples with weak signals. However, it is then necessary to
select the option Stop electrophoresis on time.
Electrophoresis experiments
In Electrophoresis experiments, there is usually no need to dilute the Amersham WB
molecular weight markers. If needed, dilute the molecular weight markers with Loading
buffer containing DTT (diluted with an equal volume of ultra pure water).
Replicates
It is recommended to include two marker lanes in the run to obtain best possible results
in the automatic molecular weight calibration of sample proteins in the evaluation step.
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4.5
Perform electrophoresis and gel scanning
Introduction
This section describes how to perform protein electrophoresis including:
•
preparations before starting electrophoresis
•
start and monitor electrophoresis and gel card scanning
•
procedures after electrophoresis and gel card scanning
In this section
This section contains the following subsections:
Section
See page
4.5.1 Preparations before starting electrophoresis
164
4.5.2 Run electrophoresis
169
4.5.3 Procedures after electrophoresis and gel card scanning
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4.5.1 Preparations before starting electrophoresis
4.5.1
Preparations before starting electrophoresis
Introduction
This section describes how to load the buffer strips, gel card and samples for the electrophoresis run.
Preparations before starting
electrophoresis
WARNING
Exploding glass. Do not run the system if the glass in the sealing
lid in the Elpho & scan unit is scratched or broken. Switch off the
instrument, disconnect the power cord and contact an authorized
service engineer.
CAUTION
Moving parts. Be careful when opening/closing the loader to avoid
fingers or clothing becoming trapped when the loader is moving.
Never place any bottles or vials in front of the Elpho & scan unit.
They may fall when the loader is opened.
Step
1
Illustration of step
Operator actions
Place the buffer strips in the
buffer strip holders by pushing out two buffer strips from
their package directly into
the buffer strip holders.
Note:
To avoid contamination of
the buffer strips, do not touch
the buffer strips, or make sure
to use clean gloves.
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4.5.1 Preparations before starting electrophoresis
Step
Illustration of step
2
Operator actions
Press the eject button on the
Elpho & scan unit.
Result: The loader is ejected.
3
Open the sealing lid using
the latch.
4
Place the buffer strip holders
in the card plate cavities in
the loader.
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4.5.1 Preparations before starting electrophoresis
Step
5
Illustration of step
Operator actions
•
Take out a gel card from
its package (with the
front side facing up).
•
Optional: Place the cursor in the ID field in the
software at the ELECTROPHORESIS & GEL
SCANNING workflow
step of the software and
scan the gel card matrix
tag (indicated with an
orange circle) using the
matrix tag reader.
See Enter gel card information , on page 131 for
more information.
6
•
Turn the gel card so that
the reverse side is facing
up (blue gel handles
without labels are facing
up).
•
Grip the end of the protective film at the bottom
of the gel card and carefully remove it.
•
Grip the end of the protective film at the top of
the gel card and carefully
remove it.
By removing the protective
films, contact between the
gel and buffer is established
when placing the gel card on
the card plate. Be careful not
to touch the exposed gel
surfaces.
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4.5.1 Preparations before starting electrophoresis
Step
Illustration of step
7
Operator actions
•
Turn the gel so the front
side is facing up (i.e.,
sample well cover is facing up).
Note:
Make sure the card plate
is completely dry.
•
Place the gel card on the
card plate by aligning the
holes on the gel card
frame with the guiding
pins marked with orange
circles.
Note:
Be careful not to scratch the
card plate with any sharp
objects.
8
•
Close the sealing lid.
•
Grip the end of the sample well cover and carefully remove it.
Tip:
Change grip while removing
the sample well cover to be
able to hold as near the wells
as possible.
Note:
If the sample well cover
breaks: Let the gel card remain in the loader with the
sealing lid closed. Use for example tweezers to remove
the rest of the well cover.
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4.5.1 Preparations before starting electrophoresis
Step
9
Illustration of step
Operator actions
Load the samples, the Loading buffer, and/or the
molecular weight markers
into the wells (typically 20
μl/well) as set up in the EXPERIMENT & SAMPLES
screen in the software.
Note:
Never open the lid after the
samples have been loaded.
Note:
All wells must be loaded with
a sample, Loading buffer (diluted with an equal volume
of ultra pure water) or
molecular weight markers. It
is recommended to have
Loading buffer in wells 1 and
16, and molecular weight
markers in wells 2 and 15.
10
When all samples have been
loaded, press the eject button.
Result: The loader is inserted
into the Elpho & scan unit.
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4.5.2 Run electrophoresis
4.5.2
Run electrophoresis
Introduction
This section describes how to start and monitor the electrophoresis. How to view and
re-scan gel images is also described.
Run electrophoresis and gel
scanning
Step
Action
1
Make sure that:
2
•
buffer strip holders containing the buffer strips have been placed into
the Elpho & scan unit
•
gel card(s) have been placed on the card plate
•
samples have been loaded in the gel card(s) wells
•
the loader has been closed
Click Start in the Electrophoresis area.
Result: The run is started. The indicator lamp on the Elpho & scan unit
changes to a blue triangle.
Note:
If you have not saved the experiment earlier, the Save as dialog opens. The
experiment must be saved before the run can be started.
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4.5.2 Run electrophoresis
170
Step
Action
3
If sample well cleanup has been selected, the electrophoresis will stop after
the calculated time and a dialog is displayed.
•
Eject the Elpho & scan loader.
•
Apply an Amersham WB paper comb into the wells of the gel card for 5
seconds.
•
Close the Elpho & scan loader.
•
To continue the electrophoresis, click Continue run.
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4.5.2 Run electrophoresis
Step
Action
4
The progress of the electrophoresis run is viewed in the Electrophoresis
area and graphs.
•
Graphs
By default, the graph shows the current for the progressing run. Graphs
for both gel card positions are displayed in the same view (color coded
lines).
Click a tab (Voltage, Current, Power, Temp) to view the corresponding
graph for that parameter and the progress of the run.
•
Pause at and remaining time
The time for the pause when sample well clean up will be performed
(optional) is displayed.
•
The Elapsed time is shown above the graph to the right if using front
detection to stop the electrophoresis run.
If a manually set time has been entered for stopping the electrophoresis
run, Remaining time and when the run will be completed (Ready at) is
displayed instead of Elapsed time.
•
Run status
The status of the run is displayed to the right of the Start button. See
Section 2.9.5 Instrument status panel, on page 76 for information about
the instrument status panel and status messages.
During the run, the message Electrophoresis in progress is displayed.
When the run has finished the status to the right of the Start button is
changed to Electrophoresis completed. The indicator lamp on the Elpho
& scan unit changes to a white square.
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Step
Action
Tip:
The progress of the run can also be viewed in the instrument status panel at
the bottom of the screen. See Section 2.9.5 Instrument status panel, on page 76
for more information.
The name of the experiment, the elapsed time/remaining time and the run
status are displayed.
Note:
To abort a run, select Control:Abort run from the menu bar. When an electrophoresis has been aborted the protocol settings can be changed and the
electrophoresis restarted.
5
To copy a graph (during or after a run), right-click on the graph and select
Copy Graph.
Result: The graph is copied to the clipboard. It can be pasted into another
application, for example Microsoft Excel or Microsoft Word®.
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Step
Action
6
When the electrophoresis has been completed:
•
Gel scanning is automatically started, if this was selected in the Gel
Scanning Protocol area. The scanned gel card images are displayed in
the Gel Scanning area.
or
•
If automatic gel scanning was not included in the the Gel Scanning
Protocol, it is still possible to scan the gel cards by clicking Scan in the
Gel Scanning area.
Note:
To abort an ongoing scanning, select Control:Abort run and click OK in the
displayed dialog. When scanning has been aborted the scanning protocol
can be modified and the scan restarted. The aborted image is included in the
image stack.
See instructions below for more information about the scanned images and
how to re-scan images.
Note:
By default, automatic gel scanning is not included for Easy Western and
Western with endogenous protein normalization experiments because no
pre-labeling of proteins is performed.
For Western experiments where no gel scanning has been performed, see
Section 4.5.3 Procedures after electrophoresis and gel card scanning, on
page 182.
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4.5.2 Run electrophoresis
Overview – Gel image preview
When electrophoresis has been completed, gel scanning is automatically started if this
was selected in the Gel Scanning Protocol area. The scanned gel card images are displayed in the Gel Scanning area.
Information about how to zoom out of the image, adjust contrast and brightness, display
image information, exporting an image and turning annotations on or off are described
in Tool descriptions – Gel Image Preview, on page 178.
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Assess the image quality
Step
Action
1
Check the scanned images.
It is possible to zoom in on the image by holding down the left mouse button
and dragging a rectangle over the gel area of interest.
Saturated signals in the gel images are displayed in red (annotations must
be turned on, see Tool descriptions – Gel Image Preview, on page 178).
•
If you have saturated signals in the areas of interest of your gel images,
consider re-scanning your gels using a lower sensitivity level. It is possible
to calculate volumes, but the volumes of saturated areas should not be
used for quantitative purposes.
•
If you have too weak signals in the areas of interest of your gel images,
consider re-scanning your gel images using a higher sensitivity level.
2
If you need to re-scan your images, see Re-scan of gel images, on page 176
for instructions.
3
If the images look fine, view the information in Section 4.5.3 Procedures after
electrophoresis and gel card scanning, on page 182 and then proceed with
the:
•
EVALUATION workflow step (Electrophoresis experiments)
•
TRANSFER workflow step (Western experiments)
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Re-scan of gel images
Step
Action
1
In the Gel Scanning Protocol area, select the Manual sensitivity radio button
and drag the slider to the appropriate sensitivity level.
Tip:
The sensitivity level used at scanning for the currently displayed gel image
can be viewed by clicking the Image information tool.
176
2
Click Scan to start scanning the gel cards with the new settings.
3
When the scanning has been completed, the latest scanned images are
displayed in the Gel Scanning area.
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Step
Action
4
It is possible to compare the latest scanned gel image with previously
scanned gel images by clicking the Image stack tool.
Result: A window with all scanned images is displayed. For each image, the
Date & Time and Sensitivity level and whether automatic or manual sensitivity was used at scanning are displayed.
5
Choose the best gel image by clicking on the appropriate image.
Result: The selected image is displayed in the Gel Scanning area. This image
will be passed on to the EVALUATION workflow step.
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4.5.2 Run electrophoresis
Step
Action
6
•
Electrophoresis experiments:
Proceed with the EVALUATION workflow step to evaluate your results.
Western experiments:
•
Proceed with the TRANSFER workflow step.
Tool descriptions – Gel Image
Preview
Tool
Description
Image stack tool. Click to display different scans of the same gel image.
•
To remove an image from the image stack, click the Delete symbol
at the top right corner of the image to be removed.
•
To select an image to display in the Gel Image Preview, click the appropriate image.
Note:
Four images per gel can be kept in the image stack at the same time.
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Tool
Description
Contrast and brightness tool. Click to open the contrast and brightness
control.
You can directly modify the brightness and contrast of the display by
dragging the handles on the graph.
•
Moving the handles closer together increases the contrast (and vice
versa) of the pixels within the range.
See Contrast and brightness, on page 180 for more information.
•
To reset any changes, click the
control window.
tool in the contrast and brightness
The change does not alter any raw data or calculations within the software.
It is only a view setting, and optimum values are actually dependent on
the current monitor.
Zoom out tool. This tool is only enabled when an image has been zoomed.
Click to fully zoom out of the image.
Tip:
It is also possible to zoom out by double clicking in the image.
Tip:
Zoom in on an image area by holding down the left mouse button and
dragging a rectangle over the gel area of interest. It is possible to zoom
several times in an image.
Image information tool. Click to to display the Image information dialog.
It shows data about the gel image currently displayed in the Gel Image
Preview.
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4.5.2 Run electrophoresis
Tool
Description
Export image tool.
Select to export the image as:
•
Normal export (.tif), or
•
Compressed export (.jpg)
In the Export Image dialog browse to the appropriate folder, type in a
name for the image, and click Save.
Note:
When exporting to *.tif format, the contrast of the image may need to be
adjusted before export in order to obtain the correct appearance in the
software used (TIFF has over 65000 intensity levels and a normal screen
256).
Tip:
It is also possible to copy a gel image to the clipboard by right-clicking on
the membrane image and selecting Copy (or press Ctrl+C on the keyboard).
The image can then be pasted into another application.
Annotations tool. Click to turn on/off the annotations in the gel images.
If the tool is blue it means that annotations are turned on.
If the tool is white it means that annotations are turned off.
Contrast and brightness
The contrast and brightness control displays the frequency with which each pixel intensity occurs within the image. The peaks on the graph represent the pixel intensities that
occur most frequently within the image.
The left and right handles on the graph show the range of pixel intensities in the image
that will be mapped to a gray scale in the display image. Pixels with intensities below
the left handle will be displayed as completely white in the image. Pixels with intensities
above the right handle will be displayed as completely black in the image. Pixels between
the handles will be displayed in various shades of gray.
The raw image can use up to 65536 intensity levels. The display normally displays 256
levels. The contrast and brightness translate between the wide range raw image and
the display.
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For information about how to change contrast and brightness, see Tool descriptions –
Gel Image Preview, on page 178.
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4.5.3 Procedures after electrophoresis and gel card scanning
4.5.3
Procedures after electrophoresis and gel card scanning
Introduction
This section describes how to remove the gel card and clean the Elpho & scan unit after
electrophoresis.
Remove gel cards
WARNING
After electrophoresis, or after transfer (when the transfer sandwich
has been opened and the PVDF card has been placed in the probing
compartment), dispose of the gel in a safe way. Read the gel card
Safety Data Sheet (SDS/MSDS) for safety instructions regarding the
gel and disposal of the gel.
Note:
If performing a Western experiment, the transfer run should be started within
one hour after the completion of the electrophoresis.
Step
Action
1
When the electrophoresis is ready and the white ready lamp is lit on the instrument panel, press the eject button on the Elpho & scan unit.
Result: The loader is ejected.
2
Open the sealing lid using the latch.
3
Remove the gel card and place it upside down on the bench.
4
Proceed to Clean the Elpho & scan unit, on page 183.
Note:
It is recommended to clean the Elpho & scan unit after each run. However if
performing a Western experiment and you are short of time, proceed to
transfer and clean the unit at a later stage of the experiment.
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4.5 Perform electrophoresis and gel scanning
4.5.3 Procedures after electrophoresis and gel card scanning
Clean the Elpho & scan unit
Step
Action
1
Remove the buffer strip holders from the loader and discard the buffer strips.
2
Wipe off any liquid on the card plate using a lint-free cloth, if needed wetted
with 50% ethanol.
3
Wipe off any liquid and dirt from the protective glass using a lint-free cloth,
if needed wetted with 50% ethanol.
Note:
It is important to keep the protective glass clean in order to obtain a good
result when scanning gel cards and PVDF cards.
4
Close the sealing lid and press the eject button on the Elpho & scan unit.
Result: The loader is inserted.
5
Clean the buffer strip holders using running water to remove salts and buffer.
Leave the buffer strip holders to air dry upside down.
6
Proceed to Continue to transfer, on page 183, if appropriate.
Continue to transfer
Do one of the following, if running a Western experiment:
•
If transfer solutions have been prepared and connected to the Western unit, proceed
with the instructions in Section 4.6.2 Prepare the transfer sandwich, on page 186.
otherwise
•
Proceed with the instructions in Section 4.6.1 Prepare and connect transfer solutions,
on page 185.
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4.6
Perform the Western Blot steps (Western experiments
only)
Introduction
This section describes how to:
•
prepare and connect solutions for transfer and probing
•
assemble the transfer sandwich
•
perform transfer, probing & drying and membrane scanning
•
view the results
In this section
This section contains the following subsections:
Section
184
See page
4.6.1 Prepare and connect transfer solutions
185
4.6.2 Prepare the transfer sandwich
186
4.6.3 Run transfer
200
4.6.4 Procedures after transfer
205
4.6.5 Prepare and connect probing and antibody solutions
208
4.6.6 Run probing
211
4.6.7 Procedures after probing
218
4.6.8 Run drying
222
4.6.9 Scan membrane and view results
224
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4.6 Perform the Western Blot steps (Western experiments only)
4.6.1 Prepare and connect transfer solutions
4.6.1
Prepare and connect transfer solutions
Introduction
This section describes how to prepare and connect buffers and solutions for the transfer.
Transfer solutions can be prepared during the electrophoresis run and must be connected
before starting the transfer.
Prepare transfer solutions
See Transfer solution recipes, on page 103 for information about how to prepare solutions
for the Western blot steps.
Connect tubing to the transfer
buffer and ultra pure water on
the bottle rack
CAUTION
To avoid the splashing of hazardous liquids, use heavy inlet filters
connected to tubing in bottles.
See Section 2.8 Other accessories, on page 61 for descriptions of inlet filters and tubing
holders. See Section Hardware installation in Amersham WB system Operating Instructions
for how to attach the accessories.
Before starting transfer, connect tubing to the transfer buffer and ultra pure water (used
for cleaning the transfer tank) as follows:
Step
Action
1
From the left tubing tower, place the tubing marked T Buffer into a 1000 ml
bottle with transfer buffer.
2
Place the the tubing marked T Water into a 1000 ml bottle with ultra pure
water.
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4.6.2 Prepare the transfer sandwich
4.6.2
Prepare the transfer sandwich
Required materials
The following consumables and accessories are required when preparing one transfer
sandwich:
•
1 transfer holder
•
1 gel card that has been run
•
1 PVDF card
•
2 sponges
•
2 transfer papers
•
1 vessel with transfer buffer for wetting transfer papers
•
1 vessel with at least 96% ethanol for pre-wetting of the PVDF card
•
1 vessel with transfer buffer for equilibration of the PVDF card
Note:
Some ethanols have auto fluorescent properties which will lead to a high
membrane background. Make sure that the ethanol used during transfer is
not auto fluorescent.
Precautions
WARNING
Always wear gloves, protective clothing, and protective glasses
when handling gel cards, PVDF cards and other consumables
supplied with Amersham WB system.
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4.6.2 Prepare the transfer sandwich
Overview illustration of transfer
sandwich assembly
The illustration below shows an overview of the transfer sandwich assembly.
The table below briefly describes the process of preparing a transfer sandwich:
Stage
Description
1
The PVDF card is pre-wetted in ethanol and then equilibrated in transfer
buffer.
2
One sponge is placed on the transfer holder bottom part (black lid).
3
A transfer paper is pre-wetted in transfer buffer and then placed in the
transfer holder.
4
The gel frame including the gel with separated proteins is removed from the
gel frame support and placed in the transfer holder.
5
The PVDF card is placed in the transfer holder.
6
The second transfer paper is pre-wetted in transfer buffer and then placed
in the transfer holder.
7
Air bubbles are removed by using the built in roller in the transfer holder.
8
A second sponge is placed on the transfer paper.
9
The transfer holder is closed.
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4.6.2 Prepare the transfer sandwich
Prepare the PVDF card
The instruction below describes how to prepare to build one transfer sandwich:
Step
Action
1
Take out one PVDF card single package from the PVDF card box.
Note:
Keep the package for the ID of the individual PVDF card and also for later
storage.
2
188
Take out the PVDF card from the package and remove the first blue protective
paper.
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4.6.2 Prepare the transfer sandwich
Step
Action
3
Optional:
•
Before removing the second blue protective paper, write an annotation
(using a pencil) on the PVDF card writing surface.
Tip:
The writing surface can be used to enter which position (A or B) where
the PVDF card is used.
•
Select the TRANSFER workflow step in the software. Put the cursor in
the appropriate Note field and type in the text.
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4.6.2 Prepare the transfer sandwich
Step
Action
4
Remove the second blue protective paper.
Note:
Do not touch the blotting area (marked with a red square in the picture) with
your fingers. Hold the PVDF card using the handles.
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4.6.2 Prepare the transfer sandwich
Step
Action
5
Optional: Enter PVDF card information in the software.
•
Select the TRANSFER workflow step in the software.
•
In the Gel Cards & Membranes area, place the cursor in the appropriate
ID field.
•
Type in the identity number manually or scan the data matrix tag on the
label of the PVDF card single package.
•
To enter a note about the membrane, place the cursor in the Note field
and type in a note.
Tip:
Type in the lot number. This is not included in the data matrix but is
available on the label on the box of PVDF cards.
6
Grip the PVDF card handles and pre-wet the card in ethanol by leaving it in
the tray with ethanol for approximately 20 seconds.
7
Move the PVDF card to the PVDF card transfer buffer vessel and equilibrate
for at least 5 minutes.
Note:
Make sure that the PVDF card is covered with transfer buffer during this time.
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4.6.2 Prepare the transfer sandwich
Start building the transfer
sandwich
Step
1
2
192
Illustration of step
Operator actions
•
Place the transfer holder with
the black side facing downwards.
•
Open the transfer holder by
pressing the latches and lifting
the white lid.
•
Push the lid until the roller pins
reach the two cavities (marked
with orange circles in the image).
•
Remove the white lid by lifting
it through the two cavities.
3
Place the first sponge on the black
lid.
4
Pre-wet one transfer paper in
transfer buffer and place it on the
sponge on the black lid (the transfer paper handle should be positioned between the guiding pins).
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4.6.2 Prepare the transfer sandwich
Overview illustration of the gel
card disassembly
The illustration below shows an exploded view of the gel card parts to be disassembled
after the electrophoresis run.
1
2
3
The table below briefly describes the parts of the gel card to be disassembled.
Stage
Description
1
Protective film.
This film is removed first.
2
Gel frame
The gel frame edges are pre-loosened from the gel frame support (3 in illustration) and then carefully removed.
3
Gel frame support stays on bench.
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4.6.2 Prepare the transfer sandwich
Loosen the gel frame from the
gel frame support and place it in
the transfer holder
Note:
Step
1
194
Do not touch the gel area (marked with red cross) when loosening the gel
frame.
Illustration of step
Operator actions
Hold the gel card with a steady
grip. Remove the protective film
by gripping the end indicated with
an orange arrow and pulling it diagonally in the direction of the
arrow.
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4.6.2 Prepare the transfer sandwich
Step
Illustration of step
Operator actions
2
Place the gel card on the bench
(with the exposed gel facing up)
as illustrated in the image.
3
Grip the corners of the lower gel
frame and loosen the gel frame
between the lower corners as far
as indicated by the dotted line and
the arrows.
Note:
When loosening the gel, continue
to press the gel card towards the
bench with your fingers.
4
Grip the corners of the upper gel
frame and loosen the gel frame as
far as indicated by the dotted line.
Make sure the gel frame is completely loosened from the white
rubber plug (indicated by the upper orange arrow).
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4.6.2 Prepare the transfer sandwich
Step
5
Illustration of step
Operator actions
Continue to carefully loosen the
gel frame from the edges of the
gel card, in the direction towards
the lower end, until the gel frame
is completely loosened.
Note:
When loosening the gel, continue
to press the gel card towards the
bench with your fingers.
Note:
Be careful not to touch the gel.
6
196
Grip the gel frame handles and
carefully lift the gel from the frame
support.
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4.6.2 Prepare the transfer sandwich
Step
Illustration of step
7
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Operator actions
Place the gel frame on the transfer
paper by fitting the gel frame
guiding holes onto the guiding
pins and rolling the gel down on
the transfer paper.
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4.6.2 Prepare the transfer sandwich
Place the PVDF card and finish
building the transfer sandwich
Step
1
Illustration of step
Operator actions
Grip both the PVDF card handles
with your fingers, or with help of
flat tip tweezers. Remove the card
from the transfer buffer tray.
Note:
Do not touch the blotting area of
the PVDF card (marked with a red
square in picture).
2
Place the PVDF card on the gel
card by fitting the PVDF card
guiding holes onto the guiding
pins and rolling the PVDF card
down on the gel.
Note:
Do not adjust the placement of the
PVDF card once placed on the gel
card.
198
3
Pre-wet one transfer paper in
transfer buffer and place it on the
PVDF card (the transfer paper
handle should be positioned between the guiding pins).
4
Remove any air bubbles as follows:
•
Take the white lid and insert it
into the two cavities (left image).
•
Grip the transfer paper handles with your left hand and
drag the roller in the holder
tracks to the other side of the
transfer holder using your
right hand.
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4.6.2 Prepare the transfer sandwich
Step
Illustration of step
Operator actions
5
Place the second sponge on the
transfer paper.
6
Close the transfer holder by
pressing the lid until the latches
snap into place.
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4.6.3 Run transfer
4.6.3
Run transfer
Introduction
This section describes:
•
how to load the transfer holder into the transfer tank
•
how to start and monitor transfer
•
the procedures to be performed after transfer
Before transfer
Make sure that transfer buffer and ultra pure water for the transfer run has been connected. See Connect tubing to the transfer buffer and ultra pure water on the bottle rack,
on page 185 for information.
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4.6.3 Run transfer
Load the transfer sandwiches
Step
Illustration of step
Operator actions
1
Open the transfer tank lid.
2
Insert the transfer holders into the tank. Make
sure that the white arrow is pointing towards
the arrow in the instrument (towards you).
3
Close the transfer tank lid.
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4.6.3 Run transfer
Start and monitor transfer
Step
Action
1
Make sure that:
2
•
the T buffer and T Water tubing are immersed in the transfer buffer and
ultra pure water bottles
•
the prepared transfer sandwiches have been loaded into the transfer
tank in correct positions
In the TRANSFER workflow step in the software, click Start in the Transfer
area.
Result: The transfer is started. The transfer tank indicator lamp on the
Western unit changes to a blue triangle.
Note:
During transfer, it is recommended to prepare and connect the solutions to
be used in the probing step.
See Section 4.6.5 Prepare and connect probing and antibody solutions, on
page 208 for more information.
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4.6.3 Run transfer
Step
Action
3
The progress of the transfer is viewed in the Transfer area and graphs.
•
Graphs
By default, the graph shows the current for the progressing run.
Click a tab (Voltage, Current, Power, Temp) to view the corresponding
graph for that parameter and the progress of the run.
•
Remaining time
The Remaining time for the run and when the run will be completed
(Ready at) is displayed above the graph, to the right.
•
Run status
The status of the run is displayed to the right of the Start button. See
Section 2.9.5 Instrument status panel, on page 76 for information about
the instrument status panel and status messages.
During the run, the message Transfer in progress is displayed.
When the run has finished the status to the right of the Start button is
changed to Transfer completed. The indicator lamp for the transfer tank
on the Western unit changes to a white square.
Tip:
The progress of the run can also be viewed in the instrument status panel at
the bottom of the screen. See Section 2.9.5 Instrument status panel, on page 76
for more information.
The name of the experiment, the remaining time and the run status are displayed.
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4.6.3 Run transfer
Step
Action
Note:
To abort a transfer run, select Control:Abort run in the menu bar. When a
transfer has been aborted the protocol settings can be changed and the
transfer restarted.
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4.6.4 Procedures after transfer
4.6.4
Procedures after transfer
Introduction
This section describes the cleaning procedures to be performed after transfer
Remove the transfer holder(s)
Step
Action
1
Open the transfer tank lid.
2
Remove the transfer holders. Hang them diagonally in the inner front of the
transfer tank, above the liquid.
Note:
To avoid drying of membranes, do not open the transfer holders in this step.
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4.6.4 Procedures after transfer
Clean the transfer flow path
Note:
Before proceeding with cleaning, remove the transfer holder.
Step
Action
1
When the transfer is completed, the Transfer Completed – Clean Transfer
Flow Path dialog opens.
Note:
It is recommended to clean the transfer flow path after a run.
If you choose to skip cleaning of the transfer flow path, click Cancel and
proceed to Continue to probing, on page 207. However, remember to clean
the transfer flow path at a later stage of the experiment. Cleaning can be
performed by selecting Control:Clean Transfer flow path from the menu
bar.
If cleaning has been skipped the transfer flow path needs to be emptied
manually by selecting, Empty Transfer tank in the Control menu.
2
Move the T Buffer tubing to the water bottle containing 1000 ml ultra pure
water (together with the T Water tubing).
3
Click Start clean in the Transfer Completed – Clean Transfer Flow Path dialog.
The cleaning is started and will take approximately 9 minutes.
Note:
Probing can be started while cleaning the transfer flow path, see Continue to
probing, on page 207.
206
4
Discard the solution in the water bottle and place the tubing in an empty
bottle.
5
Wipe off the upper part of the transfer tank interior using a wet lint-free
cloth.
6
Remove any remaining visual particles, fibers and gel pieces using tweezers.
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4.6.4 Procedures after transfer
Clean the transfer holder
WARNING
After electrophoresis, or after transfer (when the transfer sandwich
has been opened and the PVDF card has been placed in the probing
compartment), dispose of the gel in a safe way. Read the gel card
Safety Data Sheet (SDS/MSDS) for safety instructions regarding the
gel and disposal of the gel.
Note:
Perform this step when the transfer sandwich has been opened and the PVDF
card has been placed in the probing chamber.
Step
Action
1
Remove the gel from the transfer sandwich. Dispose of the gel according to
instructions in the SDS/MSDS and local procedures for handling of waste.
2
Remove and discard the sponges and transfer papers.
3
Clean the different parts of the transfer holder using running water.
4
Leave the transfer holder to air dry.
Continue to probing
Do one of the following:
•
If probing and antibody solutions have been prepared and connected to the Western
unit, proceed with the instructions in Section 4.6.6 Run probing, on page 211
else
•
Proceed with Section 4.6.5 Prepare and connect probing and antibody solutions, on
page 208
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4.6.5 Prepare and connect probing and antibody solutions
4.6.5
Prepare and connect probing and antibody solutions
Introduction
This section describes how to prepare and connect buffers and solutions for the probing
run.
Probing and antibody solutions can be prepared during the transfer run and must be
connected before starting the probing run.
Prepare probing and antibody
solutions
See Probing and antibody solution recipes, on page 104 for information about how to
prepare solutions for the Western blot steps.
Connect tubing to the probing
solutions on the bottle rack
CAUTION
To avoid the splashing of hazardous liquids, use heavy inlet filters
connected to tubing in bottles.
See Section 2.8 Other accessories, on page 61 for descriptions of inlet filters and tubing
holders. See Section Hardware installation in Amersham WB system Operating Instructions
for how to attach the accessories.
Before starting probing, connect tubing from the middle and right tubing towers to the
solutions used in the probing run as follows:
Step
Action
1
From the middle tubing tower, place the tubing marked with:
2
208
•
P Water into a 1000 ml bottle with ultra pure water
•
P Block into a 100 ml bottle with blocking solution
From the right tubing tower, place the tubing marked with:
•
P Wash into a 1000 ml bottle with wash solution (PBS-T)
•
P Final Wash into a 500 ml bottle with final wash solution (PBS)
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4.6.5 Prepare and connect probing and antibody solutions
Step
Action
3
Before starting probing, connect the antibody solution tubes in the antibody
compartment (see below for information).
Connect the antibody solution
tubes
Note:
The antibody solutions should be prepared and connected close to the start
of the probing.
Step
Action
1
Open the antibody compartment on the Western unit by pressing the eject
symbol on the antibody compartment lid.
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4.6.5 Prepare and connect probing and antibody solutions
Step
Action
2
Insert each antibody solution tube into the appropriate position, by placing
the tubing in the tube and snapping the tube into position.
The table below describes which antibodies should be placed in which antibody tube position in the antibody compartment.
3
Note:
210
Position
Description
A PRIMARY
Position to be used for primary antibodies directed to membrane in position A in the probing
chamber.
A SECONDARY
Position to be used for secondary antibodies directed to membrane in position A in the probing
chamber.
B PRIMARY
Position to be used for primary antibodies directed to membrane in position B in the probing
chamber.
B SECONDARY
Position to be used for secondary antibodies directed to membrane in position B in the probing
chamber.
Close the antibody compartment lid.
For each membrane there is one antibody tube for the primary antibodies and
one for the secondary antibodies. This means, for example, if two primary
antibodies are selected for labeling of the membrane in Position A, they are
mixed together in the same antibody tube and placed in position A PRIMARY.
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4.6.6 Run probing
4.6.6
Run probing
Introduction
This section describes how to:
•
place the PVDF cards in the Probing chambers
•
start and monitor probing
Precautions
WARNING
After electrophoresis, or after transfer (when the transfer sandwich
has been opened and the PVDF card has been placed in the probing
compartment), dispose of the gel in a safe way. Read the gel card
Safety Data Sheet (SDS/MSDS) for safety instructions regarding the
gel and disposal of the gel.
CAUTION
Pinch hazard. Do not touch the moving probing chamber during
a run.
Before probing
Make sure that buffers, ultra pure water, antibody, blocking and wash solutions are
connected before starting probing.
Note:
Ultra pure water must always be connected, because it is used for rinsing between probing steps. Wash solution is used for rinsing between primary antibodies to position A and B.
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4.6.6 Run probing
Pre-fill the probing chamber and
load the PVDF cards
Step
1
Illustration of step
Operator actions
Pre-fill the probing chamber:
•
Click the PROBING & DRYING
workflow step in the software.
•
Click Pre-Fill in the Probing
area.
Result: The probing chamber
is filled with a few milliliters of
the first solution in the probing
sequence table (by default the
blocking solution).
Note:
After the probing chamber has
been pre-filled:
2
212
•
It is no longer possible to
change the type of the first
step in the probing sequence
table. However, Dur. [min] and
Repeat can be edited.
•
The Pre-Fill button changes to
a Start button and the status
message Ready for Probing is
displayed.
Open the probing compartment
lid and use the latch to open the
probing chamber lid.
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4.6.6 Run probing
Step
Illustration of step
Operator actions
3
Open the transfer holder and remove the sponge and the transfer
paper on top of the PVDF card.
4
•
Remove the PVDF card from
the transfer holder. Hold the
PVDF card handles with your
fingers, or use flat tip tweezers.
•
Place the PVDF card in the
probing chamber, see step 5.
•
For cleaning the transfer
holder and handling of waste,
see Clean the transfer holder,
on page 207.
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4.6.6 Run probing
Step
5
Illustration of step
Operator actions
Place the PVDF card in the prefilled probing chamber by fitting
the PVDF card holes over the
guiding pins (marked with orange
circles) and rolling the PVDF card
down in the probing chamber.
Note:
Take care not to touch the blotting
area of the PVDF card.
6
214
Close the probing chamber lid and
the probing compartment lid.
Make sure that the probing
chamber lid is locked by the latch.
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4.6.6 Run probing
Start and monitor probing
Step
Action
1
Make sure that:
2
•
the probing tubing is immersed in the correct bottles for the probing run
•
the antibody solution tubes are connected in the antibody compartment
Click Start in the Probing area.
Result: Probing is started and the probing sequence table is locked for editing.
The indicator lamp for the probing chamber on the Western unit changes
to a blue triangle.
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4.6.6 Run probing
Step
Action
3
The probing progress is shown in the progress bar.
Completed steps in the probing sequence table are dimmed and the step
currently running is also displayed in the instrument status area.
The Remaining time and when probing will be completed (Ready at) are
displayed in the Probing control area.
When probing has been completed the status to the right of the Start button
changes to Probing completed. The indicator lamp for the probing chamber
on the Western unit changes to a white square.
Tip:
The progress of the run can also be viewed in the instrument status panel at
the bottom of the screen. See Section 2.9.5 Instrument status panel, on page 76
for more information.
The name of the experiment, the remaining time and the run status are displayed.
Note:
To abort a probing run, select Control:Abort run. When probing has been
aborted the protocol settings can be changed and the probing can be
restarted. The probing will be restarted from the first step in the probing sequence.
To re-start probing at the step where it was aborted, remove the completed
probing steps and restart probing.
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4.6.6 Run probing
Step
Action
4
Recovery of antibodies (if included in the setup):
Primary antibodies are automatically collected at the end of probing. When
the Recover Primary Antibody solutions dialog opens:
•
Take out the antibody solution tubes with the recovered primary antibody
solutions.
•
Click OK.
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4.6.7 Procedures after probing
4.6.7
Procedures after probing
Introduction
This section describes how to:
•
place the PVDF card in the drying holder
•
place the drying holder in the drying compartment and start drying
•
clean the probing flow path
Move the PVDF card(s) to the
drying compartment
218
Step
Action
1
Remove one Amersham WB drying holder (drying holder) from the drying
compartment and open it.
2
Grip the PVDF card handles with your fingers, or use flat tip tweezers, and
lift the PVDF card out of the probing chamber.
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4.6.7 Procedures after probing
Step
Action
3
Place the PVDF card in the drying holder by fitting the PDVF card holes over
the three guiding pins.
4
Close the drying holder. Make sure that the drying holder is locked by the
catch.
5
Place the drying holder(s) in the appropriate position in the drying compartment (i.e., PVDF card in probing position A to drying position A).
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4.6.7 Procedures after probing
Clean the probing flow path
Note:
Before proceeding with cleaning, move the PVDF card(s) to the drying compartment (see instructions above).
Step
Action
1
When the probing is completed, the Probing Completed – Clean Probing
Flow Path dialog opens.
Note:
It is recommended to clean the probing flow path after a run.
If you choose to skip cleaning of the probing flow path, click Cancel and
proceed to Section4.6.8 Run drying, on page 222. However, remember to clean
the probing flow path at a later stage of the experiment. Cleaning can be
performed by selecting Control:Clean Probing flow path from the menu bar.
If cleaning has been skipped the Probing flow path needs to be emptied
manually by selecting, Empty Probing chamber in the Control menu.
2
Insert new empty antibody solution tubes in the antibody compartment.
Note:
Always insert four new empty tubes.
3
Wipe off the probing tubing P Block, P Wash and P Final Wash using a wet
tissue and move the tubing to the bottle with ultra pure water (containing
the P Water tubing).
In the software dialog check the amount of ultra pure water needed for
cleaning, make sure that the bottle contain at least that amount of water.
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4.6.7 Procedures after probing
Step
Action
4
Click Start clean in the Probing completed – clean probing system dialog.
The cleaning is started and will take approximately 13 min.
Note:
Drying of membranes can be started while cleaning the probing flow path.
5
When cleaning is completed, discard the solution in the bottle with water,
and discard the waste water in the antibody solution tubes. Place the tubing
in an empty bottle.
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4.6.8 Run drying
4.6.8
Run drying
Introduction
This section describes how to perform drying of PDVF cards. Drying the PVDF cards will
give an even and low background, and stronger singals.
Start and monitor drying
Step
Action
1
Make sure that the drying holders with PVDF cards have been placed in the
drying compartment in the correct positions (i.e., PVDF card in probing position A is placed in drying position A).
2
Click Start in the Drying area.
Result: Drying is started. The indicator lamp for the Drying compartment on
the Western unit changes to a blue triangle.
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4.6.8 Run drying
Step
Action
3
The drying progress is shown in the progress bar and the status message
displays Drying in progress.
The Remaining time is displayed in the Drying area.
Note:
To abort a drying run, select Control:Abort run. The drying can be restarted
after it has been aborted.
4
When the run has finished, the status to the right of the Start button is
changed to Drying completed. The indicator lamp for the Drying compartment on the Western unit changes to a white square.
The card is ready for scanning. See Section 4.6.9 Scan membrane and view
results, on page 224 for information.
Tip:
The drying progress run can also be viewed in the instrument status panel at
the bottom of the screen. The name of the experiment, the remaining time
and the run status is displayed.
Note:
If the membranes are not completely dry, click Start in the Drying area to
perform a new drying run.
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4.6.9 Scan membrane and view results
4.6.9
Scan membrane and view results
Introduction
This section describes how to:
•
place the PVDF card in the Elpho & scan unit
•
start and monitor scanning
•
view the results of the scan
Place PVDF card in the loader
CAUTION
Moving parts. Be careful when opening/closing the loader to avoid
fingers or clothing becoming trapped when the loader is moving.
Never place any bottles or vials in front of the Elpho & scan unit.
They may fall when the loader is opened.
Step
1
Illustration of step
Operator actions
Press the eject button on the Elpho & scan
unit.
Result: The loader is ejected.
2
•
Turn the latch upwards and open the
sealing lid.
•
Wipe off any liquid and dirt from the card
plate protective glass using a lint-free
cloth.
It is important to keep the protective
glass clean in order to obtain a good result when scanning gel cards and PVDF
cards.
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4.6.9 Scan membrane and view results
Step
Illustration of step
3
Operator actions
•
Remove a membrane adapter from the
antibody compartment of the Western
unit.
Note:
Make sure the membrane adapter is dry
and clean.
•
Open the membrane adapter and place
it on the card plate by fitting the guiding
holes in the membrane adapter over the
guiding pins.
Note:
Be careful not to scratch the card plate
with any sharp objects.
4
Open the drying holder.
5
Remove the PVDF card from the drying
holder, and place the card in the membrane
adapter by fitting the guiding holes over the
guiding pins.
Note:
Take care not to touch the blotting area of the
PVDF card.
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4.6.9 Scan membrane and view results
Step
Illustration of step
Operator actions
6
Close the membrane adapter.
7
Close the sealing lid.
8
Press the eject button on the Elpho & scan
unit.
Result: The loader is closed.
Start and monitor membrane
scanning
Step
Action
1
Make sure that the PVDF card(s) is placed in the membrane adapter(s) on
the card plate(s) and the loader is closed.
2
Click Scan in the Membrane Scanning area.
Result: Membrane scanning is started. The indicator lamp on the Elpho &
scan unit changes to a blue triangle.
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4.6.9 Scan membrane and view results
Step
Action
3
Viewing the progressing scan:
•
The progress of the scans are displayed in the Membrane Scanning
area.
•
The status message to the right of the Scan button is changed to Scanning membranes.
•
The Remaining time is displayed in the Membrane Scanning area.
Note:
To abort a scanning, select Control:Abort run. When scanning has been
aborted the scanning protocol can be modified and the scan restarted. The
aborted image is included in the image stack.
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4.6.9 Scan membrane and view results
Step
Action
4
When the scanning has been completed, the membrane images will be
displayed in the Membrane Scanning area.
If two colors (Cy5 and Cy3) were used in the experiment, two images, one
for each color, will be displayed for each position.
The status message changes to Membrane scanning completed. The indicator lamp on the Elpho & scan unit changes to a white square.
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Overview - membrane scanning
result
When membrane scanning has been completed, the scanned membrane images are
displayed in the Membrane Scanning area.
If two colors have been used, one image/color (Cy3 and Cy5 channels) are displayed. If
one color has been used, one image is displayed.
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4.6.9 Scan membrane and view results
For information about how to zoom out of the image, adjust contrast and brightness,
display image information, export an image and turn annotations on or off, see Tool
descriptions – membrane scanning, on page 233.
Assess the image quality
Step
Action
1
Check the scanned images.
It is possible to zoom in on the image by holding down the left mouse button
and dragging a rectangle over the membrane area of interest.
Saturated signals in the membrane images are displayed in red (annotations
must be turned on, see Tool descriptions – membrane scanning, on page 233).
230
•
If you have saturated signals in the areas of interest of your membrane
images, consider re-scanning your membranes using a lower sensitivity
level. It is possible to calculate volumes, but the volumes of saturated
areas should not be used for quantitative purposes.
•
If you have too weak signals in the areas of interest of your membrane
images, consider re-scanning your membrane images using a higher
sensitivity level.
2
If you need to re-scan your images, see Re-scan of membrane images, on
page 231 for instructions.
3
If the images look fine, see Procedures after membrane scanning, on page 235
and then proceed with evaluation of the experiment described in Chapter 5
Evaluate an experiment, on page 237.
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4.6.9 Scan membrane and view results
Re-scan of membrane images
Step
Action
1
In the Scanning Sensitivity area, select the Manual sensitivity radio button.
•
Drag the Cy5 sensitivity slider to the appropriate sensitivity level to
change sensitivity in the Cy5 images scanning.
•
Drag the Cy3 sensitivity slider to the appropriate sensitivity level to
change sensitivity in the Cy3 images scanning.
Note:
When comparing different membranes it is important to use the same sensitivity settings when scanning the membranes.
Tip:
The sensitivity level used at scanning for the currently displayed membrane
image can be viewed by clicking the Image information tool.
If you have several scanned images, the sensitivity level for each image can
also be viewed by clicking the Image stack tool.
2
Click Scan to start scanning the membranes with the new settings.
Note:
To abort a scanning, select Control:Abort run. When scanning has been
aborted the scanning protocol can be modified and the scan restarted. The
aborted image is included in the image stack.
3
When the scanning has been completed, the latest scanned images are
displayed in the Membrane Scanning area.
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4.6.9 Scan membrane and view results
Step
Action
4
It is possible to compare the latest scanned membrane image with previously
scanned membrane images by clicking the Image stack tool. Up to four images can be contained in the stack.
A window with all scanned images is displayed showing the Date and time
and Sensitivity level used at scanning, and if automatic or manual sensitivity was used.
5
Choose the best membrane image by clicking on the appropriate image.
Result: The selected image is displayed in the Membrane Scanning area.
This image will be passed on to the EVALUATION workflow step.
6
Proceed with the EVALUATION workflow step to evaluate your results.
See Chapter 5 Evaluate an experiment, on page 237 for information about
how to evaluate your results.
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Tool descriptions – membrane
scanning
Tool
Description
Image stack tool. Click to display different scans of the same membrane
image.
•
To delete an image from the image stack, click the Delete symbol at
the top right corner of the image to be removed.
•
To select an image to display in the Membrane Image Preview, click
the appropriate image.
Note:
Four images per membrane can be kept in the image stack at the same
time.
Contrast and brightness tool. Click to open the contrast and brightness
control.
You can directly modify the brightness and contrast of the display by
dragging the handles on the graph.
•
Moving the handles closer together increases the contrast (and vice
versa) of the pixels within the range.
See Contrast and brightness, on page 235 for more information.
•
To reset any changes, click the
control window.
tool in the contrast and brightness
The change does not alter any raw data or calculations within the software.
It is only a view setting, and optimum values are actually dependent on
the current monitor.
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Tool
Description
Zoom out tool. This tool is only enabled when an image has been zoomed
in on.
Click to fully zoom out of the image.
Tip:
It is possible to zoom out by double clicking in the image.
Tip:
Zoom in on an image by holding down the left mouse button and dragging
a rectangle over the membrane area of interest. It is possible to zoom in
several times in an image.
Image information tool. Click to display the Image information dialog. It
shows data about the image currently displayed in the Membrane Scanning area.
Export image tool.
Select to export the image as:
•
Normal export (.tif), or
•
Compressed export (.jpg)
In the Export image dialog browse to the appropriate folder, type in a
name for the image and click Save.
Note:
When exporting to *.tif format, the contrast of the image may need to be
adjusted before export in order to obtain the correct appearance in the
software used (TIFF has over 65000 intensity levels and a normal screen
256).
Tip:
It is also possible to copy an image to the clipboard by right-clicking on the
membrane image and selecting Copy (or press the Ctrl+C on the keyboard)
if you do not to save the image as a file. The membrane image can then be
pasted into another application.
Annotations tool. Click to turn on/off the annotations in the membrane
images.
If the tool is blue it means that annotations are turned on.
If the tool is white it means that annotations are turned off.
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Contrast and brightness
The contrast and brightness control displays the frequency with which each pixel intensity occurs within the image. The peaks on the graph represent the pixel intensities that
occur most frequently within the image.
The left and right handles on the graph show the range of pixel intensities in the image
that will be mapped to a gray scale in the display image. Pixels with intensities below
the left handle will be displayed as completely white in the image. Pixels with intensities
above the right handle will be displayed as completely black in the image. Pixels between
the handles will be displayed in various shades of gray.
The raw image can use up to 65536 intensity levels. The display normally displays 256
levels. The contrast and brightness translate between the wide range raw image and
the display.
For information about how to change contrast and brightness, see Tool descriptions –
membrane scanning, on page 233.
Procedures after membrane
scanning
Step
Action
1
Press the eject button on the Elpho & scan unit.
Result: The loader is ejected.
2
Open the sealing lid.
3
Remove the membrane adapter with the PVDF card from the card plate.
4
Remove the PVDF card from the membrane adapter.
Tip:
The PVDF card can be stored in a dried condition between two filter papers
in the original PVDF card single package. Signals on the dried PVDF card are
stable for about 3 months.
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4.6.9 Scan membrane and view results
Step
Action
5
Clean the membrane adapters, using a lint-free cloth, and return the adapters
to the storage space in the antibody compartment.
6
Clean the drying holders using a lint-free cloth, and return the holders to the
drying compartment.
7
Wipe off the card plate, using a lint-free cloth, if needed wetted with 50%
ethanol.
8
Wipe off the protective glass, using a lint-free cloth, if needed wetted with
50% ethanol.
Note:
It is important to keep the protective glass clean on both sides in order to
obtain a good result when scanning gel cards and PVDF cards.
9
Close the sealing lid and press the eject button on the Elpho & scan unit.
Result: The loader is inserted.
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5
Evaluate an experiment
About this chapter
This chapter describes how to evaluate an experiment.
In this chapter
This chapter contains the following sections:
Section
See page
5.1 Introduction
238
5.2 Perform evaluation and check results
239
5.3 Analyze the results of an experiment type
247
5.4 Result views in Amersham WB software
262
5.5 Edit analysis settings
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5 Evaluate an experiment
5.1 Introduction
5.1
Introduction
Introduction
The evaluation of Image analysis data is described in this chapter as a suggested
workflow.
An automatic evaluation is performed, followed by a check of the result and editing of
analysis settings, if necessary. Different analysis approaches depending on the experiment
type are briefly described. Detailed descriptions and instructions for result tabs are found
in a separate section. Finally, there is a section describing how to edit the analysis settings
used if errors were found when results were checked.
Images from the A and B positions in the experiment are evaluated independently.
Workflow overview
Stage
Description
1
Perform evaluation in Amersham WB software.
2
Check the result of the analysis settings used (Lane detection, Band detection,
Band matching and MW calibration)
If necessary, edit analysis settings.
3
Note:
238
Analyze the results for the experiment type and export the results.
The workflow is repeated for both positions A and B if both positions are used
in the experiment. Tabs for results for position A and and B are displayed in
the first display shown.
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5.2 Perform evaluation and check results
5.2
Perform evaluation and check results
Introduction
This section describes:
•
how to evaluate the results of an experiment
•
the default result views for different experiment types
•
how to check that the analysis settings used during evaluation give the appropriate
results
•
how to copy and export experiment results
For information about how to analyze a specific experiment type, see Section 5.3 Analyze
the results of an experiment type, on page 247.
Evaluate an Amersham WB
experiment
Step
Action
1
In Amersham WB software, open the experiment.
2
Click the EVALUATION workflow step in the workflow panel to the left.
Result: Default view (image and result) dependent on the experiment type
is displayed.
Default result views
The table below describes the default result views for the different experiment types.
Experiment type
Default view
Easy Western
•
Membrane image for Primary antibody 1 with detected
and matched protein bands
•
Protein table showing Volume
•
Membrane image Cy3 (target) with detected protein
bands
•
Bar chart showing Normalized ratios
Western with total protein normalization
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5.2 Perform evaluation and check results
Experiment type
Default view
Western with endogenous protein normalization
•
Membrane images overlay with detected protein
bands. Green bands are Cy3 and red bands are Cy5.
•
Bar chart showing Normalized ratios
Easy SDS-PAGE
•
Gel Cy5 image with detected protein bands
•
Lane profile of the first lane set to MW marker, Sample
or Quantity calibrant
•
Gel Cy5 image with used quantity calibrants annotated
•
Quantity calibration curve
•
Membrane image for Primary antibody 1 with used
quantity calibrants annotated
•
Quantity calibration curve
Easy SDS-PAGE with
quantity calibration
Easy Western with
quantity calibration
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Check the results of the analysis
settings used
Step
Action
1
Check lane detection.
Check that all lanes are detected accurately. Lanes are detected individually
for the gel image and for the Cy3/Cy5 membrane images the lane detection
is common.
To edit the lane detection, see Section 5.5.1 Edit lane detection, on page 292.
Note:
By clicking the Default button in Detect lanes tab when in Edit mode, the
experiment is re-evaluated with the current band parameters, that is, the
band detection, matching and molecular weight are also re-calculated.
Therefore, editing of lanes should be performed first and before editing band
detection and bad matching etc.
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5.2 Perform evaluation and check results
Step
Action
2
Check band detection.
Check if band detection is satisfactory. In the displayed gel/membrane image,
detected bands are annotated with purple squares.
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Step
Action
3
Click the Lane profile tab to display the lane profile of a selected lane. Detected bands have numbered boxes above each peak.
A band can be selected by clicking on either the band in the image or the
band number in the lane profile. Selected bands are highlighted both in the
image (yellow box) and in the lane profile (peak number becomes blue).
To edit the band detection, see Section 5.5.2 Edit band detection, on page 297.
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5.2 Perform evaluation and check results
Step
Action
4
Check band matching.
•
Click Protein table tab and check matching of detected bands. Matched
bands are annotated with blue circles connected with lines.
•
The matching of bands is relevant in the Protein table. Matched bands
are placed in the same row in the table.
To edit the band matching, see Section 5.5.3 Edit band matching, on page 304
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Step
Action
5
Check Molecular weight (MW) calibration.
•
Click Edit.
•
Click MW Calibration tab.
Result:
•
Select a lane used for MW calibration and check in the Lane profile that
correct bands have been detected as MW calibrants.
•
Repeat the procedure for all lanes used for MW calibration.
•
Check that the MW calibration curves are OK.
•
Check that the green lines between markers in the image view are horizontal. These are used for MW calibration for the lanes between the MW
marker lanes. For a description of the MW calibration algorithm, see
Description of the molecular weight calibration algorithm, on page 315
Note:
If only one lane is used for MW calibration, all lanes have been MW calibrated using the curve of that lane.
•
If MW calibration has failed, an error message is shown between the
MW calibration curve and the Lane profile
To edit the MW calibration, see Section 5.5.4 Edit molecular weight calibration,
on page 309
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Analyze the results for an
experiment type
For the different experiment types, default views differ and different result formats (tables
and charts) are used. Also, the analysis procedures differ between experiment types.
See Section5.3 Analyze the results of an experiment type, on page247 for more information
about the different analysis procedures.
Copy and export experiment
results
Objective
Action
Copy image views, bar
charts and tables
•
Right-click in the Image view and select Copy image,
or
•
Right-click in a Bar chart and select Copy graph, or
•
Right-click in a table and select Copy table
Note:
When copying a table, only the columns that are currently displayed in the table are copied to the clipboard.
Non-rounded off figures are copied.
Paste the copied object into a document (e.g., Microsoft
Excel or Word).
Export data from a bar
chart or table
•
Right-click in the graph or table and select Export.
•
Browse for a folder, enter a name and click Save. The
format is a text file (.txt).
•
To open the the file in for example, Notepad, doubleclick the file, or
•
To open the file in Microsoft Excel, select the file, rightclick and select Open with. Choose Microsoft Excel.
Note:
When exporting a table all available columns are exported
to the file regardless of if they are currently displayed or
not. Non-rounded off figures are exported.
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5.3 Analyze the results of an experiment type
5.3
Analyze the results of an experiment type
Introduction
For the different experiment types, default result views differ and different result formats
(tables and charts) are used. Also, the analysis procedures differ between experiment
types.
In this section some suggested experiment analysis procedures are described.
For a description of each result tab, independent of the experiment type, see Section 5.4
Result views in Amersham WB software, on page 262
In this section
This section contains the following subsections:
Section
See page
5.3.1 Analyze an Easy Western experiment
248
5.3.2 Analyze a Western experiment with endogenous protein normalization
250
5.3.3 Analyze a Western experiment with total protein normalization
252
5.3.4 Analyze an Easy SDS-PAGE experiment
255
5.3.5 Analyze an Easy SDS-PAGE experiment with quantity calibration
258
5.3.6 Analyze an Easy Western experiment with quantity calibration
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5.3 Analyze the results of an experiment type
5.3.1 Analyze an Easy Western experiment
5.3.1
Analyze an Easy Western experiment
Default result view
•
Membrane image for Primary antibody 1 with detected and matched protein bands.
•
Protein table showing Volume.
Example of result view
Analysis procedure
Objective
Action
Reference for detailed information
Visual analysis
Analyze the displayed membrane view.
See Section 5.4.1
Image view, on
page 263
Detected bands are annotated with a
purple square and matched bands with
circles and connected lines.
Analysis of calculated data
248
Analyze the calculated data in the displayed Protein table. Matched bands are
shown in the same row.
See Section 5.4.6
The Protein table
tab, on page 288
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5.3 Analyze the results of an experiment type
5.3.1 Analyze an Easy Western experiment
Objective
Action
Reference for detailed information
Analysis of Image
view and calculated data for a Primary antibody 2
If a primary antibody 2 has been used in
the experiment, select to display the
other Cy channel. Analyze the displayed
membrane view and calculated data in
the displayed protein table.
See Section 5.4.6
The Protein table
tab, on page 288
Analysis of ratios
of signals for Primary antibody1
and Primary antibody 2
Click the Bar chart tab and select to
show the ratio of Cy signals.
See Section 5.4.2
The Bar chart tab,
on page 272
Copy and export
experiment results
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See Copy and export experiment results, on page 246
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5.3.2 Analyze a Western experiment with endogenous protein normalization
5.3.2
Analyze a Western experiment with endogenous protein
normalization
Default result view
•
View of Membrane Overlay with detected protein bands. Green bands are Cy3 (in
this example Target) and red bands are Cy5 (in this example Control)
•
Bar chart showing Normalized ratio
Example of result view
Analysis procedure
Objective
Action
Reference for detailed information
Visual analysis of
the image view
Analyze the displayed Membrane overlay.
See Section 5.4.1
Image view, on
page 263
Green bands are Cy3 and red bands are
Cy5.
Turquoise dotted lines, are displayed for
Cy3 range and dark-red dotted lines are
displayed for Cy5 range.
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5.3.2 Analyze a Western experiment with endogenous protein normalization
Objective
Action
Reference for detailed information
Define target and
control
Define range and usage of bands for
target and control. See the Target Definition and Control Definition areas below
the Bar chart.
See Section 5.4.2
The Bar chart tab,
on page 272
Note:
Select to show individual membranes
(Control or Target) for a better view.
Analyze normalized ratios in the
bar chart
Copy and export
experiment results
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Click the Bar chart tab.
The normalized ratio is calculated as:
Volume Target/Volume Control , both with
subtracted background.
See Section 5.4.2
The Bar chart tab,
on page 272
See Copy and export experiment results, on page 246
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5.3 Analyze the results of an experiment type
5.3.3 Analyze a Western experiment with total protein normalization
5.3.3
Analyze a Western experiment with total protein normalization
Default result view
•
View of Membrane Cy3 (target) with detected protein band
•
Bar chart showing Normalized ratio
Examples of result views
Membrane Overlay
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5.3.3 Analyze a Western experiment with total protein normalization
Membrane Cy5 (control)
Analysis procedure
Objective
Action
Reference for detailed information
Visual analysis of
target membrane
image
Analyze the displayed Membrane image.
See Section 5.4.1
Image view, on
page 263
Define target
Define range and usage of bands for
target . See the Target Definition area
below the Bar chart.
See Section 5.4.2
The Bar chart tab,
on page 272
Note:
Select to show individual membrane
(Target) for a better view.
Analyze control
membrane image
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Click the Membrane Cy5 (control) tab.
The Volume of the control is calculated
as one band. The background is calculated using a defined rolling ball radius. This
may be edited by the user. See illustration
above, Example: Membrane Cy5 (control)
See Section 5.4.1
Image view, on
page 263
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5.3.3 Analyze a Western experiment with total protein normalization
Objective
Action
Reference for detailed information
Analyze normalized ratios in the
bar chart
Click the Bar chart tab.
See Section 5.4.2
The Bar chart tab,
on page 272
Copy and export
experiment results
254
The normalized ratio is calculated as:
Volume Target/Volume Control , both with
subtracted background.
See Copy and export experiment results, on page 246
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5.3.4 Analyze an Easy SDS-PAGE experiment
5.3.4
Analyze an Easy SDS-PAGE experiment
Default result view
•
Gel Cy5 (visualization of separation of pre-labelled proteins)
•
Lane profile of the first lane set to MW marker, Sample or Quantity calibrant
Examples of result views
Gel view and Lane profile
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5.3.4 Analyze an Easy SDS-PAGE experiment
Gel view and Protein table
Analysis procedure
256
Objective
Action
Reference for detailed information
Visual analysis of
gel view
Perform visual analysis of separated
protein samples.
See Section 5.4.1
Image view, on
page 263
Analysis of data in
Protein table
To display the Protein table, click the
Protein table tab.
See Section 5.4.6
The Protein table
tab, on page 288
Analysis of molecular weights
In the protein table, select to show MW.
SeeSection 5.4.6
The Protein table
tab, on page 288
Purity check of a
sample
By looking at the Band% data in the Protein table for a detected band (corresponding to the protein to be purified)
within a lane, the purity of a sample
containing that protein can be estimated.
See Section 5.4.6
The Protein table
tab, on page 288
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5.3.4 Analyze an Easy SDS-PAGE experiment
Objective
Action
Reference for detailed information
Fraction analysis
By looking at the Volume or Band% data
in the Protein table for a detected band
in different lanes, the concentration or
purity of a sample between fractions can
be followed
See Section 5.4.6
The Protein table
tab, on page 288
Copy and export
experiment results
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See Copy and export experiment results, on page 246
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5.3.5 Analyze an Easy SDS-PAGE experiment with quantity calibration
5.3.5
Analyze an Easy SDS-PAGE experiment with quantity
calibration
Default result view
•
Gel Cy5 (Visualization of separation of pre-labelled proteins)
•
Calibration curve
Examples of result views
Gel view and Calibration curve
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5.3.5 Analyze an Easy SDS-PAGE experiment with quantity calibration
Gel view and Protein table
Analysis procedure
Objective
Action
Reference for detailed information
Visual analysis of
the Calibration
curve
Analyze the curve and the displayed
curve data below the curve (the equation
and the coefficient of regression).
See Section 5.4.5
The Quantity calibration tab, on
page 285
Bands used in the calculation of the Calibration curve are annotated with purple
squares.
Define Quantity
calibrants
Define range and usage of bands. See
the Define Quantity calibrants area below the Quantity calibration curve.
See Section 5.4.5
The Quantity calibration tab, on
page 285
Obtain calibrated
amounts of all detected bands
Click the Protein table tab. Calibrated
amount is also shown in the Band table.
See Section 5.4.6
The Protein table
tab, on page 288
Copy and export
experiment results
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See Copy and export experiment results, on page 246
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5.3.6 Analyze an Easy Western experiment with quantity calibration
5.3.6
Analyze an Easy Western experiment with quantity calibration
Default result view
•
Membrane image for Primary antibody 1 with detected and matched protein bands
•
Calibration curve
Example of result view
Analysis procedure
Objective
Action
Reference for detailed information
Visual analysis of
Calibration curve
Analyze the curve and the displayed
curve data below the curve (the equation
and the coefficient of regression).
See Section 5.4.5
The Quantity calibration tab, on
page 285
Bands used in the calculation of the Calibration curve are annotated with purple
squares.
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5.3.6 Analyze an Easy Western experiment with quantity calibration
Objective
Action
Reference for detailed information
Define Quantity
calibrants
Define range and usage of bands. See
the Define Quantity calibrants area below the Calibration curve.
See Section 5.4.5
The Quantity calibration tab, on
page 285
Obtain calibrated
amounts of all detected bands
Click the Protein table tab. Calibrated
amount is also shown in the Band table.
See Section 5.4.6
The Protein table
tab, on page 288
Copy and export
experiment results
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5.4 Result views in Amersham WB software
5.4
Result views in Amersham WB software
Introduction
The displayed results for an experiment consist of the image view in combination with
the:
•
bar chart
•
quantity calibration curve (where applicable)
•
lane profile
•
band table
•
protein table
This section describes the Image view and the different result tabs.
For the different experiment types, default views differ and different result formats (tables
and charts) are used. Also, the evaluation procedures differ between experiment types.
For information about how to evaluate the results for a specific experiment type, see
Section 5.3 Analyze the results of an experiment type, on page 247.
In this section
This section contains the following subsections:
Section
262
See page
5.4.1 Image view
263
5.4.2 The Bar chart tab
272
5.4.3 The Lane profile tab
278
5.4.4 The Band table tab
281
5.4.5 The Quantity calibration tab
285
5.4.6 The Protein table tab
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5.4.1 Image view
5.4.1
Image view
Introduction
The Image view is displayed for all result tabs in the EVALUATION workflow step. This is
used together with the information on the result tabs to view the results for an experiment.
This section describes the:
•
image view
•
image types that can be displayed in the Image view
•
annotations in the Image view
•
contrast and brightness tool (overview)
•
tools that are used to adjust the appearance of the image view, display image information and export an image.
Image view overview
The image view is displayed for all tabs in the EVALUATION workflow step. It shows the
image selected by choosing one of the tabs above the Image view (Membrane Overlay,
Membrane Cy5/Cy3, Gel Cy5). Image annotations are displayed by default. Below the
image view, tools for adjusting contrast and brightness, zoom out, view image information,
export images and turn on/off annotations are available.
Depending on which experiment type was selected when creating the experiment, different image types are shown by default. See Image types, on page 264 below for more
information about the image types.
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5.4.1 Image view
Image types
The following image types can be displayed for the different experiment types in the
EVALUATION workflow step. For Easy SDS-PAGE experiments, only the gel image is
available. For the Western experiments, depending on the experiment type and setup,
up to four image types are available.
Image type
Description
Membrane Overlay
This image is displayed as default for the experiment type Western with endogeneous protein
normalization.
It shows an overlay of the Cy5 and Cy3 images.
•
Cy3 signals are shown in green. Cy3 band
range definitions are shown as turquoise dotted lines.
•
Cy5 signals are shown in red. Cy5 band range
definitions are shown as dark-red dotted lines.
•
Proteins visible in both channels, such as the
molecular weight markers, are yellow because
the marker proteins are labeled with both Cy3
and Cy5.
Note:
In Western with endogeneous protein normalization experiments, Cy3 and Cy5 are not linked to
target or control. See the EXPERIMENT & SAMPLES
workflow step in the experiment to view the selection of secondary antibodies for the target and for
the control.
In Western with total protein normalization, Cy3
is used to detect the target and Cy5 is used to detect the control.
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5.4.1 Image view
Image type
Description
First membrane image tab
This image is displayed as follows:
Second membrane image
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•
For Easy Western experiments the tab is
named Membrane Cy3 if Cy3 has been selected to detect the first primary antibody and
Membrane Cy5 if Cy5 has been selected to
detect the first primary antibody.
•
For Western with total protein normalization
experiments the tab is displayed as default,
and is named Membrane Cy3 (target).
•
For Western with endogenous protein normalization Membrane Cy3 (target) if Cy3 has been
selected to detect the first primary antibody
and Membrane Cy5 (target) if Cy5 has been
selected to detect the first primary antibody.
This image is displayed as follows:
•
For Easy Western experiments the tab is
named Membrane Cy3 if Cy3 has been selected to detect the second primary antibody and
Membrane Cy5 if Cy5 has been selected to
detect the second primary antibody.
•
For Western with total protein normalization
experiments Membrane Cy5 (control).
•
For Western with endogenous protein normalization Membrane Cy3 (control) if Cy3 has
been selected to detect the second primary
antibody and Membrane Cy5 (control) if Cy5
has been selected to detect the second primary antibody.
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5.4.1 Image view
Image type
Description
Gel Cy5
This image is displayed by default for the experiment type Easy-SDS PAGE.
It shows the Cy5 signals from pre-labeled samples
on the gel image. The wells are included in the
image (not shown).
Annotations
Annotations are displayed in the Image view by default. Annotations can be turned on/off
by clicking the Annotations tool below the Image view.
The table below describes what is annotated in the Image view.
Annotation
Description
Well number
A well number is displayed in a box above each lane representing wells
1-16 in the gel card.
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•
A lane number in a white box indicates a non-selected lane
•
A lane number in a blue box indicates a selected lane
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5.4.1 Image view
Annotation
Description
Lanes
Lines enclosing the lanes show the lane detection.
Bands
•
Purple lines represent non-edited lanes
•
Brown lines represent lanes that have been edited
•
Blue lines and a blue highlight of the lane represent selected lanes
•
White lines represent a lane that has been excluded in the Edit
mode
Detected bands are indicated by a square and a line above (band start)
and a band below (band stop) the black Cy3 or Cy5 signal.
•
Purple square and lines represent a band
•
Yellow square and lines represent any selected band
•
Brown square and lines represent an added or edited band
•
White square and lines represent detected bands that are not used
in the calculation for the currently displayed result
If displaying the overlay image, green color represents Cy3 signals and
red color Cy5 signals. Proteins visible in both channels, such as the
molecular weight markers, are yellow because the marker proteins
are labeled with both Cy3 and Cy5.
Matched bands
Matched bands are visible when displaying the Protein table tab.
Matched bands are surrounded by blue circles. A blue line connecting
the matched bands is also displayed.
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5.4.1 Image view
Annotation
Description
Marker bands used in MW
calibration
Green lines between each corresponding MW marker represent
marker bands which are used for MW calibrating the bands in the
lanes between the lanes with MW calibrants.
Target/control definitions and
quantity calibrant definitions
Dotted black lines across the image view.
If displaying the overlay image, the dotted target definition lines are
turquoise and the dotted control definition lines are dark-red.
Saturated signals
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Saturated signals are shown as red.
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5.4.1 Image view
Tool descriptions
The tools below the Image view are used to adjust the image view display, show data
about the image, and to copy or export the image. The table below describes the available
tools.
Tool
Description
Contrast and brightness tool. Click to open the contrast and brightness
control.
Modify the brightness and contrast of the display by dragging the handles
on the graph.
•
Moving the handles closer together increases the contrast (and vice
versa) of the pixels within the range.
See Contrast and brightness overview, on page271 for more information.
•
To reset any changes, click the
control window.
tool in the contrast and brightness
The change does not alter any raw data or calculations within the software.
It is only a view setting, and optimum values are actually dependent on
the current monitor.
Note:
For the overlay image two contrast and brightness tools are displayed next
to each other. One applies to the Cy3 image and the other to the Cy5 image.
The contrast and brightness is thus adjusted for each of the images independently. The two separate histograms can be used to tune the appearance
of the overlay image.
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5.4.1 Image view
Tool
Description
Zoom out tool. This tool is only enabled when an image has been zoomed.
Click to fully zoom out of the image.
Tip:
Zoom in on an image by holding down the left mouse button and dragging
a rectangle over the gel area of interest. It is possible to zoom in several
times in an image.
Tip:
To zoom out in steps, double-click in the image.
Image information tool. Click to to display the Image information dialog.
It shows data about the image currently displayed in the Image view.
Export image tool.
Select to export the image as:
•
Normal export (.tif), or
•
Compressed export (.jpg)
In the Export Image dialog browse to the appropriate folder, type in a
name for the image, and click Save.
Note:
The export function is not available for Membrane Overlay images.
Note:
When exporting to *.tif format, the contrast of the image may need to be
adjusted before export in order to obtain the correct appearance in the
software used (TIFF has over 65000 intensity levels and a normal screen
256).
Tip:
It is also possible to copy the displayed image to the clipboard by rightclicking on the membrane image and selecting Copy (or press Ctrl+C on
the keyboard). The image can then be pasted into another application.
Annotations tool. Click to turn on/off the annotations in the Image view.
If the tool is blue it means that annotations are turned on.
If the tool is white it means that annotations are turned off.
See Image view overview, on page 263 for more information about annotations.
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5.4.1 Image view
Contrast and brightness
overview
The contrast and brightness control displays the frequency with which each pixel intensity occurs within the image. The peaks on the graph represent the pixel intensities that
occur most frequently within the image.
The left and right handles on the graph show the range of pixel intensities in the image
that will be mapped to a gray scale in the display image. Pixels with intensities below
the left handle will be displayed as completely white in the image. Pixels with intensities
above the right handle will be displayed as completely black in the image. Pixels between
the handles will be displayed in various shades of gray.
The raw image can use up to 65536 intensity levels. The display normally displays 256
levels. The contrast and brightness translate between the wide range raw image and
the display.
For information about how to change contrast and brightness, see Tool descriptions, on
page 269.
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5.4.2 The Bar chart tab
5.4.2
The Bar chart tab
Introduction
The bar chart tab is used to display bars and values of selected options for each lane.
The tab is displayed as default for the following Experiment types where it is used to
display normalized values.
•
Western with endogenous protein normalization, and
•
Western with total protein normalization
Western with normalization
Volumes of a defined target protein have been normalized using the:
272
•
volume for all proteins (Western with total protein normalization). Cy5 pre-labeled
proteins are shown in the Membrane (control) view. All proteins are detected as one
band.
•
volume of a selected control protein (Western with endogenous protein normalization). Bands of the secondary antibody dye, specific to the used primary antibody
bound to the endogenous protein, are shown in the Membrane (control) view.
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5.4.2 The Bar chart tab
Target and control range
definitions
The target and control range definitions are displayed in the images in the Image view
as dotted lines.
If the Membrane overlay is displayed, turquoise horizontal dotted lines, are displayed
for Cy3 and dark-red horizontal dotted lines are displayed for Cy5 in the same image.
The images in the Membrane overlay are green for Cy3 and red for Cy5, on a black
background.
Adjust Target and Control
definitions
The target range definition can be adjusted for all experiment types and the control
range definition can be adjusted for Western with endogenous protein normalization.
The definitions define which bands that will be used in the calculation.
Note:
In Western with total protein normalization, total lane volume is used to
define the control.
Step
Action
1
Select one of the following:
•
Membrane (target) image to adjust the target range definition
•
Membrane (control) image to adjust the control range definition
2
In the Target Definition or Control Definition area, define start and end of
the range with the arrows, or by typing, in the Range start (Rf) and Range
end (Rf) fields.
3
Select which bands to use, most intense or all bands in range. If all bands
are selected in the range, a sum of the volumes of all detected bands within
the range will be used for normalization.
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5.4.2 The Bar chart tab
Relate values to lane
Step
Action
1
Check the box above the Bar chart, Relate values to lane.
2
Select which lane to relate to.
The bar chart will display values divided by the values in the lane that is related to. The lane that is related to will have value 1 in the bar chart.
Copy the Bar chart and paste
into another application
Step
Action
1
Right-click in the graph and select Copy Graph.
2
Paste the bar graph into another application, for example Microsoft Word.
Export Bar chart data to a table
Step
Action
1
Right-click in the graph and select Export.
2
Browse for a folder, enter a name and click Save.
The format is a text file (.txt)
3
•
To open the the file in for example, Notepad, double-click the file.
•
To open the file in Microsoft Excel, select the file, right-click and select
Open with. Choose Microsoft Excel.
Select what data to display in the
Bar chart for different
Experiment types
Select what data to show in the Bar chart by selecting the appropriate option in the
Show drop-down list. One data type at a time can be displayed.
The tables below give a description of the available data types.
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5.4.2 The Bar chart tab
Western with endogeneous protein normalization
Select to show
Description
Normalized ratio
The normalized ratio (Volume Target/Volume Control) is displayed.
The normalized ratio is available for the membrane overlay, membrane target, and membrane control image.
Target Volume
The volumes of the target bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
The target volume is available for the membrane overlay,
and the membrane target image.
Control Volume
The volumes of the control bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band (or bands, if using the option
Use all bands in range) from the original image, divided
by 1000.
The control volume is available for the membrane overlay,
and membrane control image.
Western with total protein normalization
Select to show
Description
Normalized ratio
The normalized ratio (Volume Target/Volume Control) is displayed.
The normalized ratio is available for the membrane overlay, membrane target, and membrane control image.
Target Volume
The volumes of the target bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
The target volume is available for the membrane overlay,
the membrane target, and the Cy5 gel image.
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5.4.2 The Bar chart tab
Select to show
Description
Control Volume
The volumes of the control bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
The control volume is available for the membrane overlay,
and membrane control image.
Easy Western
Select to show
Description
Ratio Cy3/Cy5
The ratio (Volume First primary antibody target/
Volume Second primary antibody target) is displayed.
or
Ratio Cy5/Cy3
If Cy3 has been selected to detect the first primary antibody and Cy5 has been selected to detect the second
primary antibody the ratio will be Ratio Cy3/Cy5, or the
opposite.
This option is only available if two proteins are being targeted. The ratio is then available for the membrane overlay, membrane Cy5, and membrane Cy3 image.
Volume Cy5
The volumes of the Cy5 bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
Volume Cy5 is available for the membrane overlay (if two
proteins are being targeted), and the membrane Cy5 image.
Volume Cy3
The volumes of the Cy3 bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
Volume Cy3 is available for the membrane overlay (if two
proteins are being targeted), and the membrane Cy3 image.
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5.4.2 The Bar chart tab
Easy SDS-PAGE
Select to show
Description
Target Volume
The volumes of the target bands are displayed.
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
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5.4.3 The Lane profile tab
5.4.3
The Lane profile tab
Introduction
The lane profile tab is used to view the lane profile for one or several lanes in the gel or
membrane images in any of the experiment types.
This tab is displayed as default for Easy-SDS PAGE experiments.
Lane profile graph
In the lane profile graph, the detected bands and the background signal for a selected
lane in an image are viewed.
The lane profile graph shows the intensities as a function of pixel positions for one or all
lanes. The intensity for a given profile position is determined as the average intensity for
all pixels in the lane at that position.
By default, the following is shown in the lane profile graph:
•
the lane selected in the Image view
•
intensities for pixel positions (peaks)
•
the background signal (indicated with purple line)
A peak above the background signal with a band number displayed above it corresponds
to a detected band.
The peak with band number 1 corresponds to the detected band with the highest
molecular weight for that lane in the image.
When selecting a detected band in the lane profile graph by clicking on the band number
(highlights the band number in blue) the corresponding band in the Image view is also
selected.
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5.4.3 The Lane profile tab
Tip:
It may sometimes be easier to find bands that have not been detected in the
automatic band detection by looking in the Lane profile graph rather than by
looking in the Image view.
Display options for the lane
profile graph
The table below lists the different display options for the lane profile graph. The options
can be found below the graph.
Option
Description
Display
•
selected lane
Select this radio button to show the selected lane in
the Image view in the Lane profile graph.
•
all lanes
Select this radio button to show all enabled lanes in
the Lane profile graph simultaneously.
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5.4.3 The Lane profile tab
Option
Description
Remove background
The background signal is shown by default in the Lane
profile graph.
Check this box if you want to hide everything below the
background signal in the Lane profile graph.
What can be found when looking
at the Lane profile?
Usually the Lane profile will show all your bands in the image for that lane. Detected
bands have a band number above the peak.
However, by looking at the lane profile, you may find for example:
•
bands that have not been detected in the automatic band detection (peaks above
the background signal that has no band number),
•
that the background signal algorithm parameter (rolling ball circle) needs to be adjusted in order to get the volumes correctly calculated.
If you need to edit the detection of bands or lanes, click the Edit button and select the
Detect bands tab or Detect lanes tab. See Section 5.5 Edit analysis settings, on page 291
for information about how to edit lane or band detection.
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5.4.4 The Band table tab
5.4.4
The Band table tab
Introduction
The Band table tab is used to show selected data for the detected bands in a table format.
By default, the Lane number, Sample Id, Band number, Volume, MW, Calibrated amount,
Band %, and Rf values are shown.
Purity check of a sample
By looking at the Band% data for a detected band (corresponding to the protein to be
purified) within a lane, the purity of a sample containing that protein can be estimated.
Fraction analysis
By looking at the Volume or Band% data for a detected band in different lanes, the
concentration or purity of a sample between fractions can be followed.
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5.4.4 The Band table tab
Select what data to display in the
Band table
Step
Action
1
Click the Select data fields drop-down arrow.
2
Select the data to be displayed in the table by checking/clearing the appropriate boxes.
See Display options for the Band table below for descriptions of the options.
Tip:
To reset the Band table to show the default data fields, check the Default
parameters box at the end of the list.
3
Click the Select data fields drop-down arrow to close the drop-down box.
Display options for the Band
table
Data
Description
Lane number
Shows the lane number in which the detected band(s) is
located.
Only lanes that contain at least one detected band are
displayed.
Tip:
Lanes are expanded by default in the Band table, showing
all band data for all lanes. By clicking the triangle in front
of a lane number, that lane is collapsed.
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Data
Description
Sample Id
Shows the Sample Id for the lane if it was entered in the
Sample layout table in the EXPERIMENT & SAMPLES
workflow step.
Tip:
You can enter and edit a Sample Id in the EXPERIMENT &
SAMPLES workflow step at any time.
Band number
The number of the detected band within each lane.
Number 1 has the highest molecular weight.
Volume
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
MW
Calculated molecular weight using the MW calibration
curves (Mr x 103)
Calibrated amount
Calculated quantity using the Calibration curve.
Band%
A measure of the band's volume divided by the sum of
the volumes of all the bands in the lane.
Rf
Rf (Retardation Factor) is a measurement of position along
the lane, relative to its length. By definition, the first position in each lane has an Rf of 0 and the last has an Rf of
1. There is a linear increase in Rf from start to finish.
Pixel position
The vertical y-position of the center of the band, measured
in pixels.
Volume + background
The band volume before the background intensity has
been removed, divided by 1000.
Peak height
The maximum value of the lane profile of the band, not
including the background.
Peak + background
The maximum value of the lane profile of the band with
the background value added.
Default parameter
Resets the Band table to show the default data fields.
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5.4.4 The Band table tab
Copy the Band table and paste
into another application
Step
Action
1
Right-click in the table and select Copy table.
Note:
Copy will copy only the selected columns.
Export will export all the columns, see instruction below.
2
Paste the table into e.g., a Microsoft Excel sheet.
Export the Band table as a text
file
Step
Action
1
Right-click in the table and select Export.
2
Browse for a folder, enter a name and click Save.
The format is a text file (.txt)
3
•
To open the the file in e.g., Notepad, double-click the file.
•
To open the file in Microsoft Excel, select the file, right-click and select
Open with. Choose Microsoft Excel.
Note:
All available data in the table is exported, not just the columns currently displayed. Included in the table are also experiment information and the settings
used.
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5.4.5 The Quantity calibration tab
5.4.5
The Quantity calibration tab
Introduction
The quantity calibration tab is used to:
•
view the automatically calculated calibration curve,
•
adjust the Rf ranges for the quantity calibrants to be used in the calculation of the
calibration curve.
This tab is displayed as default for Easy-SDS PAGE or Easy Western experiments containing quantity calibrants. The quantity calibrants must have been entered in the
Sample table in the EXPERIMENT & SAMPLES workflow step.
Calibration curve
The calibration curve shows the amount of material as a function of the volume of a
defined protein band, or a group of bands. The curve is calculated using linear regression.
The equation of the curve and obtained coefficient of regression are displayed below
the curve.
The calibration curve is used to calculate the amount of material in all bands in the image
from the band volume (total sum of pixel intensities), based on the quantity calibrants
entered in the EXPERIMENT & SAMPLES workflow step. The calibrated amounts are
found in the Protein table and Band table.
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5.4.5 The Quantity calibration tab
Annotations in the Image view
The detected bands in the lanes that were used in the calculation of the calibration curve
are defined by the quantity calibrants range, marked by the two dotted lines in the Image
view. The bands used in the calculation are annotated with a purple or a brown
(added/edited bands) square.
Detected bands that are not included in the calculation of the curve are annotated with
a white square.
Image display
In Easy SDS-PAGE experiments, the quantity calibrants are visualized in the Gel Cy5
image. The quantity calibrants should have been individually pre-labeled with Cy5.
Samples should have been pre-labeled using the same protocol and conditions.
In Easy Western experiments, the quantity calibrants and sample proteins are visualized
in the membrane image due to the use of a specific primary antibody and labeled secondary antibody.
Define Quantity calibrants
If you have several detected bands in lanes containing your quantity calibrants and
only one, or a group of bands in the lanes that should be used as quantity calibrants in
the calibration curve calculation, adjust the ranges that define your calibrants
In the Define Quantity calibrants area below the graph:
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5.4.5 The Quantity calibration tab
Step
Action
1
Define start and end of the range with the arrows, or by typing, in the Range
start (Rf) and Range end (Rf) fields.
2
•
click the Range start (Rf) arrows, or type in a value, to move the dotted
line defining the start of the quantity calibrants area in the Image view
to the appropriate position
•
click the Range end (Rf) arrows, or type in a value, to move the dotted
line defining the end of the quantity calibrants area in the Image view
to the appropriate position
Select which bands to use, most intense or all bands in range.
If all bands are selected in the range, a sum of the volumes of all detected
bands within the range will be used.
3
To delete a point from the calibration curve, go to EXPERIMENT & SAMPLES
step and set the lane as Blank.
4
To restore default values, click the Default button.
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5.4.6 The Protein table tab
5.4.6
The Protein table tab
Introduction
The Protein table tab shows data for detected bands in selected Membrane or Gel views.
Matched bands are in the same row position.
Purity check of a sample
By looking at the Band% data for a detected band (corresponding to the protein to be
purified) within a lane, the purity of a sample containing that protein can be estimated.
Fraction analysis
By looking at the Volume or Band% data for a detected band in different lanes, the
concentration or purity of a sample between fractions can be followed.
Display options for the Protein
table
Select what data to show in the protein table by selecting the appropriate option in the
Show data in table drop-down list. One data type at a time can be displayed.
The table below gives a description of the available data types.
288
Data
Description
Volume
The volume of a band is the sum of the intensities of all
the pixels within the band from the original image, divided
by 1000.
MW
Calculated molecular weight using the MW calibration
curves (Mr x 103)
Calibrated amount
Calculated quantity using the Calibration curve.
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5.4.6 The Protein table tab
Data
Description
Band%
A measure of the band's Volume divided by the Total Volume of all the bands in the lane.
Rf
Rf (Retardation Factor) is a measurement of position along
the lane, relative to its length. By definition, the first position in each lane has an Rf of 0 and the last has an Rf of
1. There is a linear increase in Rf from start to finish.
Pixel position
The vertical y-position of a band measured in pixels.
Volume + background
The band volume before the background intensity has
been removed, divided by 1000.
Peak height
The maximum value of the lane profile of the band, not
including the background.
Peak + background
The maximum value of the lane profile of the band with
the background value added.
Copy the Protein table and paste
into another application
Step
Action
1
Right-click in the table and select Copy table.
Note:
Copy will copy only the selected columns.
Export: Export only includes the currently selected parameter , see instruction
below.
2
Paste the table into e.g., a Microsoft Excel sheet.
Export the Protein table as a text
file
Step
Action
1
Right-click in the table and select Export.
2
Browse for a folder, enter a name and click Save.
The format is a text file (.txt)
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5.4.6 The Protein table tab
Step
Action
3
•
To open the the file in e.g., Notepad, double-click the file.
•
To open the file in Microsoft Excel, select the file, right-click and select
Open with. Choose Microsoft Excel.
Note:
Included in the table when exported are also experiment information and the
settings used.
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5.5
Edit analysis settings
Introduction
This section describes how to edit the analysis settings used in the evaluation of the results.
The following may be edited:
•
lane detection
•
band detection
•
band matching
•
molecular weight calibration
In this section
This section contains the following subsections:
Section
See page
5.5.1 Edit lane detection
292
5.5.2 Edit band detection
297
5.5.3 Edit band matching
304
5.5.4 Edit molecular weight calibration
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5.5.1 Edit lane detection
5.5.1
Edit lane detection
Introduction
The automatic lane detection calculates and displays the lanes to be fitted on the gel
and membranes. If the lane detection is not correct, or if the algorithm was unable to
detect the lanes, a standard lane grid is shown as a starting point when looking at the
images in the Image view.
The lane detection is common for both membrane images, regardless of which image
is displayed. The gel image has a separate lane detection.
The automatic lane detection can be edited by:
•
moving the lane grid
•
editing the lane start/stop
•
editing the lane width and bending
•
excluding lanes from being used in the calculations
Enter Edit mode for lane
detection
Step
Action
1
In the EVALUATION workflow step, click the Edit button.
Result: The Detect lanes tab is displayed.
Note:
When in Edit mode, an extra set of the Membrane images and the gel image
tabs are displayed to the right of the ordinary tabs (which are dimmed).
The tabs to the right are always used in Edit mode. The performed editing
applies to the tab(s) highlighted blue in Edit mode.
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5.5.1 Edit lane detection
Step
Action
2
Select the image you want to edit and then continue with the editing as
described below.
Move lane grid
The complete lane grid can be moved to fit the actual position of the bands of the separated sample.
Step
Action
1
Click Move lane grid.
2
Click in the grid and move.
Edit lane start/stop
The lane start and stop might need to be edited, for example if the front is uneven, to
improve the band Rf values.
Step
Action
1
Click Edit lane start/stop.
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5.5.1 Edit lane detection
Step
Action
2
Use the purple horizontal lines to set the desired start and stop of the lanes.
3
Use the rectangular handles on the purple horizontal lines to bend the start
and stop of the lanes.
Edit lane width and bending
294
Step
Action
1
Click Edit individual lanes.
2
To re-size the individual lane width:
•
select the lane
•
move the mouse over one of the two rectangular handles (the mouse
pointer changes to a double pointed arrow)
•
drag the handle to re-size the lane width
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5.5.1 Edit lane detection
Step
Action
3
There are four handles that can be used in combination to bend/move the
lane to the appropriate position.
To move or edit the shape of a lane:
4
•
Select the lane.
•
Move the mouse over one of the square handles to adjust the bending.
•
If appropriate, repeat the steps above for another handle.
If appropriate, continue to edit the next lane.
Exclude a lane from calculations
Individual lanes can be excluded from being used in calculations, if for example you
want to compare only a subset of your samples.
Step
Action
1
Click Edit individual lanes.
2
Clear the check box at the lower end of the lane to exclude a lane from the
calculation.
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5.5.1 Edit lane detection
Restore default settings
Step
Action
1
Click Default to restore default lane detection.
Note:
When restoring lane detection to default, the experiment is re-evaluated with
the current band parameters, that is, the band detection, matching and
molecular weight are also re-calculated. Therefore, this can be used to get
back to the original evaluation, if you for example regret the performed editing
of results. However, default values for Rolling Circle, Sensitivity, Match tolerance
etc are not achieved.
2
In the displayed dialog, click OK.
Undo an editing operation
To undo an editing operation, click
Note:
in the lower-right corner of the screen.
Manual changes of lane, band and matches are restored. However, changes
of parameters do not restore default values.
Finish editing
296
•
To exit the Edit mode and apply any changes made, click the Finish button.
•
To edit settings on another tab, click that tab and edit as appropriate. When clicking
Finish, all changes on all tabs will be applied.
•
To exit the Edit mode without applying any changes made, click the Cancel button.
Note:
If you change your mind about result editing, it is possible to perform a new
complete evaluation of the image data for an experiment. In Edit mode, select
the Detect lanes tab and click the Default button. However, default values of
parameters, e.g., Rolling circle, Sensitivity and Match tolerance, are not restored.
Note:
Bands in the molecular weight markers are not affected by the detect band
setting. To edit MW bands go to MW Calibration.
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5.5.2 Edit band detection
5.5.2
Edit band detection
Introduction
The band detection settings can be edited by:
•
changing the parameters for automatic band detection
•
manually adding or deleting bands
•
changing the band width
Enter Edit mode for band
detection
Step
Action
1
In the EVALUATION workflow step, click the Edit button.
Result: The Detect lanes tab is displayed.
Note:
When in Edit mode, an extra set of the Membrane images and the gel image
tabs are displayed to the right of the ordinary tabs (which are dimmed).
The tabs to the right are always used in Edit mode. The performed editing
applies to the tab(s) highlighted in blue in Edit mode.
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5.5.2 Edit band detection
Step
Action
2
To edit the band detection settings or manually add/delete bands, click the
Detect bands tab.
Result: The view for band detection is displayed.
3
To edit the band detection, continue with the instructions below.
Note:
Band detection in MW marker lanes can not be adjusted the in the Detect
bands tab. The MW marker detection is separate and can only be edited in
the MW Calibration tab.
Overview - band detection
display
Image view
The Image view shows the selected Membrane/Gel image with bands.
When showing annotations, detected bands are indicated by a square and a line above
(band start) and a band below (band stop) the black Cy3 or Cy5 signal (depending on the
image being viewed).
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•
Purple square and lines represent a band
•
Yellow square and lines represent any selected band (the corresponding band
number box is highlighted in blue in the lane profile)
•
Brown square and lines represent an edited band
Lane profile
The lane profile of a selected lane is displayed to the right. Detected bands have numbered
boxes above each peak.
Select a lane in the Image view to display the lane profile for that lane.
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5.5.2 Edit band detection
For more information about Lane profiles, see Section 5.4.3 The Lane profile tab, on
page 278
Adjust Automatic band detection
Step
Action
1
To adjust the Automatic band detection, change the settings of the parameters in the Automatic Band Detection area.
Note:
For pre-labeled control in total protein normalization, only background subtraction can be adjusted using the Rolling circle parameter.
2
300
To restore default settings, click Default.
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Band detection parameters
The table below describes the parameters that can be edited for automatic band detection.
Parameter
Description.
Rolling circle
The Rolling circle method requires you to enter a value for
the size of the rolling circle. This method calculates the
background as if a disc, with the radius you have entered,
were rolling underneath the lane profile. The larger the
radius of the disc, the less the background rises with the
profile.
Noise reduction
This parameter represents the degree to which small local
peaks should be ignored on the profile and is designed to
eliminate noise in the image. Noise reduction has no effect
on the profile itself, only the number of peaks detected.
In general, the higher the Noise Reduction value, the
fewer peaks detected.
Sensitivity
This parameter represents how pronounced the band
must be from its surrounding area in the lane. Increase
the value to increase the sensitivity of the band detection.
Note:
None of the parameters above will affect the MW calibration. Edit the calibration
in the MW Calibration tab.
Note:
For pre-labeled control in total protein normalization, only the Rolling circle
background subtraction parameter is applicable.
Manually add or delete bands
Bands can be added/deleted in the Image view or in the Lane profile view.
Note:
Bands in the Cy5 Control image in Total protein normalization experiments
can not be edited.
To start editing of bands:
Step
Action
1
Click in the image view to select a lane.
2
Click the Edit bands button located below the Lane profile in the Manual
Editing area.
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5.5.2 Edit band detection
The table below describes how to add/delete bands using the Lane profile and Image
view:
View
Action
Lane profile view
•
To add a band, place the cursor at the top of a peak
and left-click.
•
To delete a band, place the cursor on the peak number
box and right-click.
•
To add or delete a band, zoom in on the area of interest by holding down the left-mouse-button and create
a box.
•
To add a band, place the cursor on an undetected
band in the image and left-click. The band will be annotated with a brown square indicating that it has
been added manually.
•
To delete a band, place the cursor on the band and
right-click.
Image view
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Tip:
It may sometimes be easier to find bands that have not been detected in the
automatic band detection by looking in the Lane profile graph rather than by
looking in the Image view.
Edit band start/stop
Step
Action
1
Click Edit bands.
2
Click and drag the horizontal lines to set the desired start and stop of the
band.
Undo an editing operation
To undo an editing operation, click
Note:
in the lower-right corner of the screen.
Manual changes of lane, band and matches are restored. However, changes
of parameters do not restore default values.
Finish editing
•
To exit the Edit mode and apply any changes made, click the Finish button.
•
To edit settings on another tab, click that tab and edit as appropriate. When clicking
Finish, all changes on all tabs will be applied.
•
To exit the Edit mode without applying any changes made, click the Cancel button.
Note:
If you change your mind about result editing, it is possible to perform a new
complete evaluation of the image data for an experiment. In Edit mode, select
the Detect lanes tab and click the Default button. However, default values of
parameters, e.g., Rolling circle, Sensitivity and Match tolerance, are not restored.
Note:
Bands in the molecular weight markers are not affected by the detect band
setting. To edit MW bands go to MW Calibration.
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5.5.3 Edit band matching
5.5.3
Edit band matching
Introduction
The band matching shows which bands are matched as the corresponding bands in the
different lanes. Bands are matched if they lie within the area defined by set the match
tolerance value (± Rf-value).
If there are several bands in a lane that can be matched to another band in a nearby
lane (i.e., several bands lie within the defined match tolerance area), the band that has
the most similar Rf value as the band in the nearby lane will be matched.
Note:
Bands in the molecular weight markers are not included in matching.
The band matching is used in the result display in the Protein table tab. Matched bands
are placed in the same row in the table for direct comparison between lanes.
Enter Edit mode for band
matching
Step
Action
1
In the EVALUATION workflow step, click the Edit button.
Result: The Detect lanes tab is displayed.
Note:
When in Edit mode, an extra set of the membrane images and the gel image
tabs are displayed to the right of the ordinary tabs (which are dimmed).
The tabs to the right are always used in Edit mode. The performed editing
applies to the tab(s) highlighted in blue in Edit mode.
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5.5.3 Edit band matching
Step
Action
2
To edit the band matching settings or manually add/delete bands to/from
band matching, click the Match bands tab.
Result: The settings for band matching are displayed on the Match bands
tab. The Image view shows the matched bands.
3
To edit the band matching, continue with the instructions below.
Overview - band matching
display
The Image view shows the selected Membrane/Gel image with bands.
The following band annotation is used:
•
detected bands are annotated with purple squares
•
edited bands are annotated with brown squares
•
matched bands are annotated with blue circles connected with lines
•
a selected band in the Image view is annotated with a yellow square
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5.5.3 Edit band matching
Adjust Automatic band matching
Step
Action
1
Adjust the matching by changing the Match tolerance± value.
2
To remove all matches, click Remove all matches.
Tip:
The Remove all matches function is useful when you only have one protein
of interest in a sample where several proteins are present.
Manual editing of matching
Band matches can be manually created, added to an existing match or removed from
an existing match. To start manual editing of a match:
Step
Action
1
Zoom-in on the area of interest in the image (left-click and draw a box).
2
Proceed with the appropriate instruction below for editing of matches.
Create a match between two
unmatched bands
Step
Action
1
Click Edit matches.
2
Left-click in the lane with the first band.
3
Left-click on the first band.
Result:
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Step
Action
4
Right-click on the second band, which will be added to the match.
Result:
Add a new band to an existing
match
Step
Action
1
Click Edit matches.
2
Left-click in the lane with the last band of a match.
3
Left-click on the last band.
Result:
4
Right-click on the band, which will be added to the match.
Result:
Remove a band from a match
Step
Action
1
Click Edit matches.
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5.5.3 Edit band matching
Step
Action
2
Left-click on one of the bands in the match.
Result:
3
Right-click on the band you want to remove from the match.
Result:
Several bands can be removed from a match by right-click on each of them.
Undo an editing operation
To undo an editing operation, click
Note:
in the lower-right corner of the screen.
Manual changes of lane, band and matches are restored. However, changes
of parameters do not restore default values.
Finish editing
308
•
To exit the Edit mode and apply any changes made, click the Finish button.
•
To edit settings on another tab, click that tab and edit as appropriate. When clicking
Finish, all changes on all tabs will be applied.
•
To exit the Edit mode without applying any changes made, click the Cancel button.
Note:
If you change your mind about result editing, it is possible to perform a new
complete evaluation of the image data for an experiment. In Edit mode, select
the Detect lanes tab and click the Default button. However, default values of
parameters, e.g., Rolling circle, Sensitivity and Match tolerance, are not restored.
Note:
Bands in the molecular weight markers are not affected by the detect band
setting. To edit MW bands go to MW Calibration.
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5.5.4 Edit molecular weight calibration
5.5.4
Edit molecular weight calibration
Introduction
The molecular weight calibration curve is calculated based on the lanes set to Amersham™ WB MW markers in the EXPERIMENT & SAMPLES workflow step.
The molecular weight calibration can be edited by:
•
manually adding/deleting bands in the marker lanes
•
excluding individual marker bands from the calculation
•
changing the width of marker bands
Enter Edit mode for molecular
weight calibration
Step
Action
1
In the EVALUATION workflow step, click the Edit button.
Result: The Detect lanes tab is displayed.
Note:
When in Edit mode, an extra set of the membrane images and the gel image
tabs are displayed to the right of the ordinary tabs (which are dimmed).
The tabs to the right are always used in Edit mode. The performed editing
applies to the tab(s) highlighted in blue in Edit mode.
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5.5.4 Edit molecular weight calibration
Step
Action
2
To edit the molecular weight calibration, click the MW calibration tab.
Result: The following is displayed:
•
Image view
Membrane/Gel image with annotated detected MW marker bands.
3
310
•
MW calibration curves graph
•
Lane profile for a selected lane
•
If MW calibration has failed, an error message is shown between the
MW calibration curve and the Lane profile.
To edit the molecular weight calibration, continue with the instructions below.
Amersham WB system User Manual 29-0214-88 AC
5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Display for molecular weight
calibration
The following is displayed for molecular weight calibration:
Display
Description
Image view
Membrane/Gel image with annotated detected
MW marker bands.
If multiple MW markers are present, green lines
are drawn between each corresponding molecular
weight marker band.
MW marker bands can be edited in this view.
MW calibration curves graph
Shows the molecular weight calibration curves,
one for each marker lane.
To display the curve for a specific lane, click the
lane in the Image view.
Note:
The different curves and points usually overlaps.
The curve for the right most lane is displayed on
top of the other curves.
If MW calibration has failed, a message is displayed that provides an explanation.
Lane profile for a selected lane
Shows the lane profile for a selected lane, or for
all MW marker lanes, in the Image view.
MW marker bands can be edited in this graph.
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5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Check the MW calibration
Step
Action
1
Make sure that the MW marker bands in the marker lanes have been detected correctly. The images below show the correct display of the nine MW
marker bands for gradient (left) and homogeneous (right) gels:
Mr×103
225
97
66
50
225
97
66
50
35
25
35
20
20
14
10
14
25
10
•
If a MW marker band has not been detected, but is visible in the image
view, add it as a detected MW calibration band.
•
If for any reason a band has been detected in the MW marker lane that
is not a MW marker band, delete the band.
See Edit bands in the MW marker lanes, on page 313 for more information.
Tip:
If multiple MW markers are present, green lines are drawn between each
corresponding molecular weight marker band for the marker lanes in the
Image view. If the lines are not horizontal, this indicates that a band may be
missing in one of the molecular weight marker lanes or an extra band may
have been detected.
Tip:
An error message is displayed below the molecular weight calibration curve
if the software detects any errors in the MW calibration.
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5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Step
Action
2
If there is a MW marker band missing from all marker lanes, also after editing
the bands in the marker lanes (for example if the electrophoresis has run
too short or too long or if the marker is not well separated), check that this
band(s) has been excluded in the Select markers drop-down list.
If not, exclude the band from being used in the algorithm, by deselecting it
in the Select markers drop-down list.
See View/edit MW markers in Select markers drop-down list, on page 314 for
information about how to exclude MW marker bands.
Edit bands in the MW marker
lanes
Step
Action
1
Click the Edit bands button located in the Manual Editing area below the
Lane profile.
2
Delete in the Lane profile detected bands which are not MW markers. Place
the cursor on the peak number box and right-click.
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5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Step
Action
3
Add detections (left-click) of bands which are MW markers. Place the cursor
at the top of a peak and left-click.
4
Check that lines between markers are horizontal. These are used for MW
calibration for all sample and quantity calibrant lanes.
For more information about the molecular weight calibration, see below.
Note:
If only one lane is used for MW calibration, all lanes will be MW calibrated using
the curve of that lane.
View/edit MW markers in Select
markers drop-down list
Select in the Amersham WB™ MW Markers scroll list the markers to be included in the
MW calibration curve.
It can be relevant to exclude a MW marker band(s), for example when the electrophoresis
has run too short or too long. In those cases one of the markers may be missing in the
visualized gel image.
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5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Description of the molecular
weight calibration algorithm
Calculated calibration curves are used to calculate the molecular weights. The table
below briefly describes how molecular weights are calculated using calibration curves
determined by interpolation from lanes run with MW markers.
Stage
Description
1
Straight green lines are drawn between each corresponding MW marker
band.
2
The intersection of these lines with the other lanes gives new Rf values.
3
These Rf values are used together with the assigned MW values to generate
a calibration curve for each lane.
4
The bands in each lane are assigned MW values using this calibration curve.
Note:
The calculated calibration curves for the sample lanes are not included in the
displayed MW Calibration curve view.
Note:
If only one lane is used for MW calibration, all lanes will be MW calibrated using
curves created from the rf values of that lane.
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5 Evaluate an experiment
5.5 Edit analysis settings
5.5.4 Edit molecular weight calibration
Undo an editing operation
To undo an editing operation, click
Note:
in the lower-right corner of the screen.
Manual changes of lane, band and matches are restored. However, changes
of parameters do not restore default values.
Finish editing
316
•
To exit the Edit mode and apply any changes made, click the Finish button.
•
To edit settings on another tab, click that tab and edit as appropriate. When clicking
Finish, all changes on all tabs will be applied.
•
To exit the Edit mode without applying any changes made, click the Cancel button.
Note:
If you change your mind about result editing, it is possible to perform a new
complete evaluation of the image data for an experiment. In Edit mode, select
the Detect lanes tab and click the Default button. However, default values of
parameters, e.g., Rolling circle, Sensitivity and Match tolerance, are not restored.
Note:
Bands in the molecular weight markers are not affected by the detect band
setting. To edit MW bands go to MW Calibration.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6
Maintenance
About this chapter
This section lists the periodic maintenance activities that shall be performed by the user
of the Amersham WB analyzer, as well as maintenance activities that should be performed
when required.
Precautions
WARNING
Do not use Amersham WB analyzer if it is not working properly, or
if it has suffered any damage, for example:
•
damage to the power cord or its plug
•
damage caused by dropping the equipment
•
damage to other parts which can affect function
WARNING
Electrical shock hazard. All repairs should be done by service
personnel authorized by GE. Do not open any covers or replace
parts unless specifically stated in the user documentation.
WARNING
Disconnect power. Always disconnect power from the instrument
unit before replacing any component on the instrument unit, unless
stated otherwise in the user documentation.
WARNING
When using hazardous chemicals, avoid spillage and wear protective glasses and other suitable personal protective equipment. For
example NaOH is corrosive and therefore dangerous to health.
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6 Maintenance
WARNING
Only spare parts and accessories that are approved or supplied
by GE may be used for maintaining or servicing the system.
WARNING
When replacing a damaged power cord, use a replacement cord
of the same type and dimensions and in conformance with all applicable local electrical code requirements and approved by GE.
WARNING
Always disconnect the mains supply before replacing the mains
fuse. For continued protection against risk of fire, replace only with
a fuse of the same type and rating as stated on the instrument unit
labels.
CAUTION
When using hazardous chemicals, take all suitable protective
measures, such as wearing protective glasses and gloves resistant
to the chemicals used. Follow local regulations and instructions for
safe operation and maintenance of the system.
In this chapter
This chapter contains the following sections:
Section
318
See page
6.1 Maintenance program
319
6.2 Maintenance instructions
324
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6 Maintenance
6.1 Maintenance program
6.1
Maintenance program
Introduction
This section lists the maintenance activities that should be performed by the user of the
Amersham WB analyzer. Maintenance is divided into:
•
After each run
•
Weekly maintenance
•
Monthly maintenance
•
Annual maintenance
•
Maintenance when required
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6 Maintenance
6.1 Maintenance program
Periodic maintenance program
The following periodic maintenance should be performed by the user of the Amersham
WB analyzer.
Interval
Maintenance action
Instruction
After each run in the Elpho & scan unit
•
Wipe off any liquid on the card plate
•
Wipe off any liquid or dirt from the
protective glass in the sealing lid
•
Inspect the glass of the sealing lid
for scratches or marks and check
that the glass is firmly attached to
the frame
•
Use a lint-free cloth or paper that does
not scratch the protective glass or the
card plate.
Use a lint-free cloth wetted in 50%
ethanol to remove stains.
Contact Service if you need to replace
a part of the sealing lid.
Inspect the sealing lid hatch when
the frame is closed and remove any
dirt
Clean the buffer strip holders
Clean the buffer strip holders using
running water to remove salts and
buffer.
Leave the buffer strip holders to air dry
upside down.
Clean the membrane adapters
320
Clean the membrane adapters, using a
lint-free cloth and place them in the
storage space in the antibody compartment.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.1 Maintenance program
Interval
Maintenance action
Instruction
After each run in the Western unit
Clean the transfer flow path
If the transfer flow path was not
cleaned after transfer was completed,
run the cleaning procedure by clicking
Control:Clean Transfer flow path in the
menu bar.
Clean the probing flow path
If the probing flow path was not
cleaned after probing was completed,
run the cleaning procedure by clicking
Control:Clean Probing flow path in the
menu bar.
Clean the transfer holder
See Clean the transfer holder, on
page 207.
Clean the drying holders
Clean the drying holders, using a lintfree cloth, and place them in the drying
compartment.
Remove any particles in the transfer
tank
Inspect the tank and remove any remains of gel or paper fibers using
tweezers.
Check the transfer tank filter and replace if dirty, see Replace transfer tank
filter, on page 336.
Clean the upper part of the transfer
tank
Amersham WB system User Manual 29-0214-88 AC
Wipe the upper part of the transfer tank
with a wet tissue.
321
6 Maintenance
6.1 Maintenance program
Interval
Maintenance action
Instruction
Weekly (or when the instrument will not be used for a few days)
Maintenance clean of the transfer flow
path
See Section 6.2.1 Weekly cleaning of the
transfer and probing flow paths, on
page 325.
Maintenance clean of the probing flow
path
See Section 6.2.1 Weekly cleaning of the
transfer and probing flow paths, on
page 325.
Inspect, and replace if damaged, the:
See Section 6.2.2 Replacement procedures, on page328 for information about
how to replace pump heads, air filter
and inlet filter.
•
pumps
•
tubing
•
air filter
•
inlet filter
Contact Service if you need to replace
tubing.
Inspect and tighten the tubing connectors
Interval
Maintenance action
Instruction
Replace air filter in dryer module
See Replace air filter, on page 329.
Annually
The air filter may need to be replaced
more frequently if the external environment is more harsh than normal lab
environments with respect to dust in
the air.
322
Replace transfer pump head
See Replace probing or transfer pump
head, on page 331.
Replace probing pump head
See Replace probing or transfer pump
head, on page 331.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.1 Maintenance program
Interval
Maintenance action
Instruction
Clean the drying compartment
Clean the drying compartment from
any dust or particles using a lint-free
cloth wetted with ultra pure water. Let
the compartment dry before use.
Replace transfer electrodes
See Replace transfer electrodes, on
page 334.
Replace buffer strip holders
See Amersham WB system User Manual
for ordering information.
Replace the mains fuse
See Replace the mains fuse, on page337.
Replace damaged power cord
See Precautions in the beginning of this
chapter.
Replace the filter in the transfer tank
Inspect the filter and if dirty or damaged, replace it.
When required
See Replace transfer tank filter, on
page 336.
Replace the inlet filters
Amersham WB system User Manual 29-0214-88 AC
See Replace the inlet filters, on page 336.
323
6 Maintenance
6.2 Maintenance instructions
6.2
Maintenance instructions
Introduction
This section describes the maintenance to be performed on the Amersham WB analyzer.
In this section
This section contains the following subsections:
Section
324
See page
6.2.1 Weekly cleaning of the transfer and probing flow paths
325
6.2.2 Replacement procedures
328
6.2.3 Moving the instrument units
339
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6 Maintenance
6.2 Maintenance instructions
6.2.1 Weekly cleaning of the transfer and probing flow paths
6.2.1
Weekly cleaning of the transfer and probing flow paths
Introduction
Perform maintenance cleaning of the transfer flow path and the probing flow path
weekly, or if the unit will not be used for a couple of days.
Maintenance cleaning of transfer
flow path
The procedure will take about 25 minutes. Probing and drying can be run in parallel.
Note:
Make sure there are no transfer holders left in the tank.
WARNING
When using hazardous chemicals, avoid spillage and wear protective glasses and other suitable personal protective equipment. For
example NaOH is corrosive and therefore dangerous to health.
Step
Action
1
Select in software, Control:Maintenance clean Transfer flow path or click
Maintenance clean Transfer button in the software start screen.
Result: The Maintenance Clean Transfer Flow Path dialog opens.
2
•
Wipe the upper part of the transfer tank and both the transfer tubing
with a wet tissue.
•
Check that the transfer tank filter is intact and clean. If needed, replace
the filter.
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6 Maintenance
6.2 Maintenance instructions
6.2.1 Weekly cleaning of the transfer and probing flow paths
Step
Action
3
Immerse the T Water tubing in a bottle containing 2000 ml of ultra pure
water.
4
Immerse the T Buffer tubing in a bottle containing 1000 ml 0.5 M NaOH.
5
Click the Start clean button in the dialog.
6
When cleaning is finished move the tubing into an empty bottle.
Note:
Discard all solutions after cleaning.
Maintenance cleaning of probing
flow path
The procedure will take approximately 45 minutes. Transfer and drying can be run in
parallel.
Note:
Make sure there are no PVDF cards left in the probing chambers.
WARNING
When using hazardous chemicals, avoid spillage and wear protective glasses and other suitable personal protective equipment. For
example NaOH is corrosive and therefore dangerous to health.
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6 Maintenance
6.2 Maintenance instructions
6.2.1 Weekly cleaning of the transfer and probing flow paths
Step
Action
1
Select in software, Control:Maintenance clean Probing flow path or click
Maintenance clean Probing button in the software start screen.
Result: The Maintenance Clean Probing Flow Path dialog opens.
2
Wipe the probing tubing, and the lid and edges of the probing chamber with
a wet tissue.
3
Immerse the P Water tubing in a bottle containing at least 1000 ml of ultra
pure water.
4
Immerse the P Custom tubing in a bottle containing at least 450 ml 0.5 M
NaOH.
5
Place P Block, P Wash and P Final Wash tubing in an empty waste bottle.
6
Insert and connect four clean empty 15 ml tubes in the antibody compartment.
7
Click Start clean in the dialog.
8
When cleaning is finished move the tubing into an empty bottle.
Note:
Discard all solutions and antibody tubes after cleaning.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
6.2.2
Replacement procedures
Introduction
This section describes how to replace the:
•
air filter
•
transfer and probing pump heads
•
transfer electrodes
•
transfer tank filter
•
inlet filters
•
mains fuse
Maintenance accessories
The following accessories are needed for maintenance of the Amersham WB analyzer:
•
pump head (for transfer pump or probing pump)
•
air filter
•
transfer tank filter
•
transfer electrodes
•
inlet filter set
•
fuse (for correct fuse. see Section 8.1 System specifications, on page 353 )
Precautions
WARNING
Disconnect power. Always disconnect power from the instrument
unit before replacing any component on the instrument unit, unless
stated otherwise in the user documentation.
WARNING
Remove any bottles from the bottle rack before opening the Service
compartment lid.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Replace air filter
The instruction below describes how to replace the air filter.
Step
Action
1
Open the service compartment lid.
2
Open the lid above the compartment where the filter is located by turning
the nut counter-clockwise and removing it.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
330
Step
Action
3
Remove the filter from the frame by pulling it up using the attached holder.
4
Remove the top part of the plastic grid on the holder, where the filter is located.
5
Replace the filter with a new filter and fasten the top part of the plastic grid.
6
Insert the holder with a new filter into the guides in the frame.
7
Put the lid of the filter compartment back into place and fasten the nut by
turning it clockwise.
8
Close the service compartment lid.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Replace probing or transfer
pump head
The instruction below describes how to replace a pump head, using the probing pump
as an example. Replacing the transfer head is similar.
Step
Action
1
Open the service compartment lid to access the probing and transfer pumps.
Note:
The Probing pump is located to the left and the Transfer pump to the right.
2
Disconnect the pump tubing on the left.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
332
Step
Action
3
Disconnect the pump tubing on the right.
4
Unlock the catch that keeps the pump head in position.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Step
Action
5
Turn the pump head counterclockwise.
6
Lift up the pump head out from the service compartment.
Note:
When removing the head be careful not to damage or bend any of the tubing
in the Western unit. If any tubing is damaged or bent it needs to be replaced
with new tubing. Contact Service for help.
7
Unpack a new pump head.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Step
Action
8
Place the new pump head into the correct position and turn clockwise.
Note:
Make sure the corresponding wheel of the pump head is in the correct position
to fit the drive shaft of the pump motor.
9
Lock the catch to keep the pump head in the correct position.
10
Connect the pump tubing on the right to the right connector of the pump
head.
11
Connect the pump tubing on the left to the left connector of the pump head.
12
Close the service compartment lid.
Replace transfer electrodes
If the transfer procedure fails, the reason could be defective transfer electrodes. It is
recommended to replace both the electrodes. The instruction below describes how to
replace the transfer electrodes.
334
Step
Action
1
Open the transfer tank lid. The electrodes are located on each side.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Step
Action
2
Pull up the electrode.
3
Insert the new electrode and press down.
4
Repeat the procedure in the same way with the right side electrode.
5
Close the transfer tank lid.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Replace transfer tank filter
Note:
If the transfer filter is dirty, it is not possible to remove, clean and put it back
again. The filter must be replaced.
The instruction below describes how to replace the transfer tank filter.
Step
Action
1
Open the lid of the transfer tank. The filter is located in the bottom of the
transfer tank.
2
Pierce through the middle of the filter using tweezers.
Note:
Do not remove the filter by gripping its edges, as this might damage the filter
seal.
3
Use the hole to grip and remove the filter.
4
Place the new filter and push it gently, onto the filter seal.
Replace the inlet filters
Replace the inlet filter when required, for example when the filters become clogged.
Required material: Inlet filter set.
336
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Follow the instructions below to replace an inlet filter and a support net.
Step
Action
1
Pull off the inlet filter and the support net from the inlet filter holder.
2
Fit the new support net and inlet filter on the inlet filter holder, and press the
filter into position.
Replace the mains fuse
WARNING
Always disconnect the mains supply before replacing the mains
fuse. For continued protection against risk of fire, replace only with
a fuse of the same type and rating as stated on the instrument unit
labels.
Step
Action
1
Turn off the power to the Amersham WB analyzer by setting the mains
power buttons on the rear sides of the Elpho & scan and Western units to
the off (0) position.
2
Disconnect the mains cords from the mains power inlets on the Elpho &
scan and Western units.
3
Locate the the fuse drawer in the connector panel on the appropriate unit.
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6 Maintenance
6.2 Maintenance instructions
6.2.2 Replacement procedures
Step
Action
4
Insert a small screwdriver into the notch next to the fuse drawer.
5
Twist the screwdriver to open the fuse drawer.
6
Replace the fuses.
For fuse data, see the instrument unit labels on the rear panels.
7
338
Insert the fuse drawer into its receptacle on the connector panel.
Amersham WB system User Manual 29-0214-88 AC
6 Maintenance
6.2 Maintenance instructions
6.2.3 Moving the instrument units
6.2.3
Moving the instrument units
Precautions
CAUTION
Personal Protective Equipment (PPE). Whenever packing, unpacking, transporting or moving the system, wear:
•
Protective footwear, preferably with steel lining
•
Working gloves, protecting against sharp edges
•
Protective glasses
CAUTION
Heavy object. Two people are required to lift the instrument units
safely.
CAUTION
Never move the Western unit with bottles standing on the unit.
NOTICE
Disconnect cables. To prevent equipment damage, always disconnect cables before an instrument unit is moved.
Lifting instruction
Step
Action
1
Disconnect all cords and cables from the instrument units and remove any
bottles on the units.
2
Two people are required. To lift a unit, grip with both hands on each side of
the unit and lift.
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7 Troubleshooting
7
Troubleshooting
Introduction
This chapter provides general advice for troubleshooting for the Amersham WB system.
For advice regarding electrophoresis and Western blotting in general, please consult
the handbook Western Blotting – Principles and Methods 28-9998-97.
General
Problem
Possible cause and action
Red indicator is lit.
•
An error has caused the red indicator to be lit.
Open the software and read the instructions on the
screen.
Loader cannot be
closed.
•
Spots or clouds in the
image
•
The sealing lid is not closed properly.
Make sure that the sealing lid is closed.
Contaminations
Always use clean powder-free gloves and only touch
the frame when handling the gel card and PVDF card.
Load the buffer strip by pushing it out from the package directly into the buffer strip holder.
Make sure to use clean incubation trays that have not
previously contained stains, such as Coomassie or
fluorescent stains.
Make sure that all equipment and components are
clean and free of residues from a previous run.
Make sure that recommended cleaning procedures
have been performed, and in a correct way.
No contact with instrument
•
No connection
Check the USB cable and that the power is on for both
the Elpho & scan unit and the Western unit. Unplug
the USB cable and wait for 10 s until you reconnect
the cable. This will restart the communication.
If this does not work close the Amersham WB software
and restart to get communication.
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7 Troubleshooting
Pre-labeling
Problem
Possible cause and action
White precipitation in
Labeling buffer.
•
SDS precipitates at low temperature.
Equilibrate the vials to room temperature and vortex.
White/orange precipitation in Loading buffer.
The protein precipitates in Labeling buffer
during sample preparation.
•
SDS is included in the Labeling buffer. Some proteins
may precipitate when they come in contact with
SDS.
Heat the sample before pre-labeling as described in
the pre-labeling protocols.
Electrophoresis
Problem
Possible cause and action
Air between gel and
cassette before run
(visual appearance)
•
Electrophoresis is not
started due to no current through the gel.
•
The electrophoresis
does not stop as expected. (Easy Western or
Western with Endogenous protein normalization)
•
Electrophoresis is not
possible to re-start after power failure during a run.
•
Amersham WB system User Manual 29-0214-88 AC
Expected behavior
The over pressure applied in the instrument will ensure
all air is removed during the electrophoresis step.
Performance is not affected.
Missing one or both buffer strips.
Remove the gel card and insert the missing buffer
strip(s). Place a new gel card and reload samples. A
gel card with the well lid removed cannot be reused.
The front detection has not worked due to a weak
front, when using no pre-labeled samples and no
or too diluted MW markers.
Stop electrophoresis on time when using MW markers
diluted higher than 20 fold.
The over-pressure has not been turned on.
Open the loader. Manually press down the sealing lid
and then open and close one of the sealing lid latches.
Close the loader and re-start the electrophoresis from
the software.
341
7 Troubleshooting
Transfer
Problem
Possible cause and action
Transfer is not started
•
The transfer tank lid is not completely closed.
Make sure that the transfer tank lid is completely
closed.
An error message during transfer: Too high
resistance in transfer
tank.
•
Mix up of tubing from transfer buffer and water.
Check buffer inlet. Empty the transfer tank and start
a transfer with correct transfer buffer inlet.
•
Transfer electrode malfunction
Remove the electrodes and check for damage. If
damaged, see Maintenance chapter how to replace
the electrodes.
Transfer tank is not
emptied or filled in a
correct way.
•
Clogged inlet filters of the transfer tubing
Clean or replace inlet filters, see Maintenance chapter
regarding replacement.
•
Clogged transfer filter in the bottom of the tank.
Carefully remove visual particles with tweezers after
every run. A clogged filter must be replaced. To replace
the filter, see Maintenance chapter.
Prompt for missing liquid even though the
bottle is not empty.
•
Transfer pump malfunction
Replace the pump head. See Maintenance chapter.
•
Leaking tubing connectors
Check all tubing connections in the flow path inside
the Western unit.
Probing and drying
Problem
Possible cause and action
Antibody tubes are not
emptied completely
during probing.
•
Probing pump malfunction
Replace the pump head. See Maintenance chapter.
•
Leaking tubing connectors
Check all tubing connections in the flow path inside
the Western unit.
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7 Troubleshooting
Problem
Possible cause and action
Antibody compartment
is wet after cleaning of
the probing flow path.
•
No empty antibody tubes connected
Always connect four empty tubes before cleaning is
started.
Membrane is not dry
after the drying procedure.
•
High humidity in lab
Repeat drying procedure.
•
Air filter is dirty.
Replace the air filter, see Maintenance chapter
•
Ventilation is blocked.
Check ventilation. Make sure that inlet and outlet
ventilations are not blocked.
Scanning
Problem
Possible cause and action
Weak signals in gel or
membrane image.
•
The scanning sensitivity has been automatically set
too low because there is some spot/part with
stronger signals in the image, or in the other position (A/B). The automatic scanning sensitivity always
set the same scanning sensitivity for both positions.
Re-scan the membrane, or gel, using a higher scanning sensitivity (manually).
Gel and membrane images
Problem
Possible cause and action
Fluorescent spots in
the gel image
•
Lighter areas in the gel
image
•
Amersham WB system User Manual 29-0214-88 AC
Dirty protective glass in the Elpho & scan unit.
Clean the glass, see Clean the Elpho & scan unit, on
page 183
Card plate not dry in the Elpho & scan unit
Remove the gel, wipe the plate dry with a lint-free
cloth and then re-scan the gel.
343
7 Troubleshooting
Problem
Possible cause and action
Unclear MW marker
bands or double bands
•
MW markers degradation. The markers are not
stable over long time in room temperature. Double
bands occur and others become wider. See illustration below.
Always use fresh MW marker solution and store at
-20°C.
-20ºC 37ºC
Mr 10 000 or even the
14 000 band is missing
in the MW marker lane.
344
•
The gel has run for too long time.
It is still possible to do a MW calibration with the remaining bands. Remove the missing band(s) in the
Amersham WB MW markers scroll list, see Section5.5.4 Edit molecular weight calibration, on page309.
Amersham WB system User Manual 29-0214-88 AC
7 Troubleshooting
Problem
Possible cause and action
Diffuse bands, or poor
band resolution
•
Too large sample volumes or too high protein concentration when loading on gel.
Follow the recommended loading 20 µl and
max 20 µg.
•
Loading buffer has not been used.
Use Loading buffer and prepare the sample according
to recommendations. See Section 4.4.2 Prepare unlabeled samples, on page 161.
•
Too high concentration of DTT
Decrease the DTT concentration to 20 mM (final).
•
Loading buffer too old.
Prepare fresh solutions.
Note:
See also the Troubleshooting chapter in the handbook
Western Blotting – Principles and Methods 28-9998-97
for examples and solutions.
Vertical streaks in
lanes
•
Streaks in lower part of gel due to sample wells not
cleaned
Select the option Pause for sample well cleanup before starting electrophoresis and use a paper comb
to remove excess Cy5 dye reagent.
•
Too high concentration of DTT
Decrease the DTT concentration to 20 mM (final)
Precipitations in the
sample well or stacking
Amersham WB system User Manual 29-0214-88 AC
•
Protein samples with precipitation
During protein sample preparation, the samples should
be mixed by vortexing and centrifuged before and
after the heating step, prior to loading for best resolution.
345
7 Troubleshooting
Problem
Possible cause and action
Smeared bands
•
Samples are not fully reduced.
Add DTT to the Loading buffer according to recommendations (40mM).
•
High salt concentrations.
Dialyze the sample, precipitate the protein with TCA
or use desalting columns.
•
Concentration of protein is too high when loading
on gel.
Follow the recommendations in manual. Load no more
than 20 μg per well.
No distinct lanes
•
Leakage between the gel card wells due to the
sample well cover have been removed before the
gel card was placed in the loader, or the sealing lid
have been opened after the loading of samples.
It is important to close the sealing lid before removing
the sample well cover.
Lanes are wider in the
low molecular weight
region.
346
•
All wells are not filled, causing smaller proteins in
the sample wells to diffuse during run.
Fill unused wells with Loading buffer, diluted with an
equal volume of ultra pure water.
Amersham WB system User Manual 29-0214-88 AC
7 Troubleshooting
Problem
Possible cause and action
No bands on the membrane
•
Transfer did not work.
Make sure that the foil is removed from the gel before
transfer and that the gel is placed in the transfer
holder before the PVDF card.
Sandwich order from bottom: Sponge, Transfer paper,
Gel, PVDF card, Transfer paper and Sponge.
•
No antibody binding
Make sure to place the antibody tubes in correct positions in the antibody compartment.
Do not use primary antibody species other than mouse
or rabbit, and make sure the secondary antibodies
are directed against the species in which the primary
antibodies were raised.
•
Insufficient membrane equilibration procedure
It is important to follow the recommendations in the
manual. Be aware that the membrane shall never
partly dry. Keep the membrane completely wet all the
time to avoid drying before transfer and probing.
•
Target protein not present at detectable levels.
Use positive control to test the blotting procedure.
Note:
See also the Troubleshooting chapter in the handbook
Western Blotting – Principles and Methods 28-9998-97
for examples and solutions.
See also troubleshooting for weak bands below.
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7 Troubleshooting
Problem
Possible cause and action
Week bands on the
membrane (general)
•
Wrong blocking agent: the blocking agent may have
strong affinity for the protein of interest.
Try different blocking solutions and concentrations.
•
Insufficient primary antibody incubation
Optimize primary antibody incubation time.
•
Too low antibody concentration
Optimize antibody concentration.
•
Weak or inactive antibody
Use a specific primary antibody with high affinity for
the target protein, validated for Western blotting.
•
Too low amount of target protein in the sample.
Concentrate the protein sample, but follow the recommended maximum protein load on the gel, 20 μg per
well.
Note:
See also the Troubleshooting chapter in the handbook
Western Blotting – Principles and Methods 28-9998-97
for examples and solutions.
Weak bands (poor
transfer) for small proteins
•
Insufficient protein retention.
Optimize transfer time.
Use a gradient gel to help retain small proteins during
transfer.
•
Too low ethanol/methanol concentration in transfer
buffer to remove SDS. SDS can interfere with the
binding of small molecular weight proteins to
membranes.
Use a higher percentage of ethanol in transfer buffer
(max. 40%).
Do not use SDS in transfer buffer.
Weak band (poor
transfer) for large proteins
•
Insufficient transfer time.
Increase transfer time to increase binding.
•
Ethanol/Methanol concentration is too high.
Reduce ethanol concentration.
348
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7 Troubleshooting
Problem
Possible cause and action
High background on
the membrane
•
Insufficient quality of chemicals used in transfer
and probing
Always use high quality chemicals.
•
Ethanol with high auto fluorescence used in transfer
Some ethanol grades will give rise to a high background especially in Cy3. Make sure that the ethanol
used during transfer is not auto fluorescent.
•
Wrong detergent or incorrect concentrations are
used in buffers.
Check that the correct detergent and concentrations
are used
•
Insufficient blocking
Make sure that appropriate blocking conditions are
used.
Use freshly prepared blocking agent that is fully dissolved.
•
Insufficient washes
Increase the number of washing steps, volume or duration of the washing steps.
Note:
See also the Troubleshooting chapter in the handbook
Western Blotting – Principles and Methods 28-9998-97
for examples and solutions.
Uneven background on
the membrane
•
Membrane not completely dry
Dry the membrane again and re-scan.
•
A felt pen or a pen has been used when marking
consumables.
Always use a pencil when marking buffer strip packages, reagent packages, PVDF cards, gel cards, etc.
Note:
See also the Troubleshooting chapter in the handbook
Western Blotting – Principles and Methods 28-9998-97
for examples and solutions.
See also troubleshooting for spots or clouds in the image.
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7 Troubleshooting
Problem
Possible cause and action
Uneven band intensity
across membrane
•
Probing liquids do not cover the complete membrane during probing.
Western unit does not stand horizontally.
Adjust the feet of the Western unit.
•
Insufficient volume of antibody solutions
Increase the volumes. The recommended minimum
volume of antibody solutions is 5 ml.
•
Partly dry membrane before transfer or probing
It is important to follow the recommendations in the
manual. Be aware that the membrane shall never
partly dry. Keep the membrane completely wet all the
time to avoid drying before transfer and probing.
•
The antibody has not been pumped correctly.
See the problem "Antibody tubes are not emptied
completely during probing" in the Probing section
above.
Clouded bands, bands
spread out into swirls
or white spots on the
membrane
•
Black fluorescent spots
on the membrane /
Speckled background
•
Insufficient contact between membrane and gel
during transfer
Make sure the transfer sandwich is assembled correctly according to the instructions.
Dirty protective glass
Clean the glass with a lint-free cloth.
•
Dirty membrane adapter
Clean the membrane adapter, using a lint-free cloth.
•
Aggregates in the blocking agent
Make sure the blocking agent is completely dissolved
in the buffer.
Note:
See also troubleshooting for spots or clouds in the image.
The membrane overlay
image displays bad
alignment between the
two images (Cy3 and
Cy5 scans).
350
•
The membrane has been scanned for Cy3 and Cy5
at different occasions. Slightly different positions
of membranes during scanning.
Always scan both channels at the same time.
Amersham WB system User Manual 29-0214-88 AC
7 Troubleshooting
Problem
Possible cause and action
Multiple bands of small
proteins using the SDSPAGE pre-labeling protocol
•
Too many dye molecules per labeled protein
molecule can give rise to multiple bands for small
proteins. The extra bands appear with higher Mw
and weaker intensity compared to the main band.
Use less dye in the SDS-PAGE pre-labeling reaction.
This can be achieved by decreasing the volume of dye
reagent or diluting the dye in DMSO, e.g. by a factor
in the range 2-5. An other option is to scale up the reaction and keep the amount of dye constant.
Evaluation
Problem
Possible cause and action
Some options in Evaluation are disabled or
unavailable, for example Quantity calibration.
•
Incorrect Experiment type in the start screen or incorrect Sample types in the experimental setup have
been chosen.
Sample types can be changed after the run.
If wrong Experiment type, create a new experiment
of correct type, re-scan the gel and/or membranes
and perform evaluation.
Multiple images using
different sensitivities
have been scanned but
only one of them is visible in Evaluation.
•
The Normalized ratios
for Quantitative Western blotting varies significantly from run to
run.
•
Amersham WB system User Manual 29-0214-88 AC
The different images are visible in the image stack
in the scanning screens. The image that is selected
is the one that is used in Evaluation.
Select the preferred image in the scanning screens in
order to use it in Evaluation.
Automatic scanning sensitivity may result in different sensitivity settings between runs. Different
sensitivity settings will directly affect the ratio between target and control signals.
Only compare normalized ratios within the same run
using the same sensitivity settings. Use manual sensitivity setting when scanning.
351
8 Reference information
8
Reference information
About this chapter
This chapter lists the technical specifications of the Amersham WB system. The chapter
also includes a chemical resistance guide and a decontamination report that must be
used to record decontamination details before a service.
In this chapter
This chapter contains the following sections:
Section
352
See page
8.1 System specifications
353
8.2 Chemical resistance guide
358
Amersham WB system User Manual 29-0214-88 AC
8 Reference information
8.1 System specifications
8.1
System specifications
Introduction
This section lists the system specification data of the Amersham WB analyzer.
Environmental ranges
Parameter
Data
Storage and transport temperature range
-25°C to +60°C
Chemical environment
See Section8.2 Chemical resistance guide,
on page 358.
Operating range
Parameter
Limits
Operating temperature range
15°C to 32°C
For full performance: 16°C to 28°C
Relative humidity
20% to 80%, non-condensing
For full performance: 20% to 70%, noncondensing
Altitude
Maximum 2000 m
Pollution degree
2
Transient level
Overvoltage category II
Environment
Indoor use only
EMC
EN 61326-1, IEC61326-1 and FCC
Part15B.
(Emission according to CISPR 11, Group
1, class B)
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8 Reference information
8.1 System specifications
System specifications Amersham
WB analyzer
Parameter
Data
System configuration
Benchtop system consisting of external
computer and two units:
Elpho & scan unit and Western unit
The computer is not included in the delivery.
Controlling computer operating system
PC with Windows 7
Control software
Amersham WB software
Connection between Elpho & scan and
Western units
Ethernet cable
Connection between PC and Elpho & scan
unit
USB cable (Type A to Type B)
Pollution degree
2
Sound level
Below 80 dB(A)
System specifications Elpho &
scan unit
Parameter
Data
Dimensions (W x D x H)
47 x 51 x 27 cm
Weight (excluding computer)
25 kg
Power supply
Voltage: 100-240 V~
Frequency: 50-60 Hz
354
Power consumption
Max Power: 300 VA
Fuse
2x T4AH 250 V
Amersham WB system User Manual 29-0214-88 AC
8 Reference information
8.1 System specifications
Scanner specifications
Parameter
Data
Image sensor
Silicon Photodiode
Warm up time
At least 1 minute
Note:
The warm up is included in the automatic
sensitivity mode.
Lens
F1.0/13 mm
Light source
Cy5:
Laser diode module, 635 nm, 10 mW
Cy3:
Laser diode module, 532 nm, 10 mW.
Operation
Fully automated (auto exposure, no focus
or other adjustment or calibrations
needed)
Maximum sample size
2 samples of approximately 80 x 65 mm2
Gray scale
65 536 levels (16 bit)
Dynamic range
4.6 orders of magnitude
Image output
Gray scale 16 bit (tif)
Separation specifications
1
Parameter
Description
Voltage
250-600 V 1
Current
20-50 mA1
Maximum power is 20 W/gel card. The maximum values for the parameters can not be reached simultaneously.
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355
8 Reference information
8.1 System specifications
System specifications Western
unit
Parameter
Data
Dimensions (W x D x H)
43 x 53 x 39 cm
Weight
20 kg
Power supply
Voltage: 100-240 V~
Frequency: 50-60 Hz
Power consumption
Max Power: 400 VA
Fuse
2x T4AH 250 V
Transfer tubing and connectors
Tubing material: FEP, ID 1/8"
Ferrule blue
Tubing connector: Nut 5/16"-24UNF 2-A
Probing tubing and connectors
Tubing material: FEP, ID 0.063"
Ferrule yellow
Tubing connector: Nut 1/4"-28UNF 2-B
Transfer specifications
1
Parameter
Description
Voltage
10-100 V 1
Maximum power is 40 W. Maximum current is 400 mA.
Probing specifications
356
Parameter
Description
Volumes, antibody probing
5-12 ml
Amersham WB system User Manual 29-0214-88 AC
8 Reference information
8.1 System specifications
Drying specifications
Parameter
Description
Temperature
Maximum 45°C
Drying time
10 minutes
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357
8 Reference information
8.2 Chemical resistance guide
8.2
Chemical resistance guide
Introduction
This section specifies the chemical resistance of Amersham WB analyzer to some of the
most commonly used chemicals in electrophoresis and Western blotting.
Assumptions made
The ratings are based on the following assumptions:
•
Synergy effects of chemical mixtures have not been taken into account.
•
Room temperature and limited overpressure is assumed.
Note:
Chemical influences are time and pressure dependent. Unless otherwise stated,
all concentrations are 100%.
List of chemicals
For a list of chemicals used in the gel cards and buffer strips, see the Safety Data Sheet
(SDS/MSDS).
Usage
Chemical
Concentration
CAS no and
EC no
General
Aqueous buffers pH 4-10 (e.g., Tris,
Glycine, Phosphate)
0-0.2 M
N/A
Transfer
Ethanol
40%
75-08-1/200-837-3
Methanol
40%
67-56-1/200-659-6
Sodium Chloride
0.2 M
7647-14-5/231-598-3
Potassium Chloride
50 mM
7447-40-7/231-211-8
Tween
1%
9005-64-5/500-018-3
Cleaning of flow
paths
Sodium Hydroxide
0.5 M
1310-73-2/215-185-5
Sodium Hypochlorite
5%
7681-52-9/231-668-3
Cleaning of card
plate
Ethanol
50%
75-08-1/200-837-3
Transfer & Probing
358
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8 Reference information
8.2 Chemical resistance guide
Usage
Chemical
Concentration
CAS no and
EC no
Cleaning of surfaces
Ethanol
96%
75-08-1/200-837-3
Mild detergents
N/A
N/A
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9 Ordering information
9
Ordering information
Introduction
This chapter lists the ordering information for consumables, accessories, spare parts for
user maintenance etc. For the most recent information, refer to www.gelifesciences.com.
Consumables
The table below lists the different consumables that can be ordered. Depending on the
experiments to be performed, different combinations of consumables are required. A
selection guide for putting a kit of consumables together is available at
www.gelifesciences.com.
360
Consumable
Product code
Amersham WB Cy5
29-0307-31
Amersham WB labeling buffer
29-0307-32
Amersham WB loading buffer
29-0307-33
Amersham WB molecular weight markers
29-0307-35
Amersham WB gel card 14, 8-18%
29-0225-65
Amersham WB gel card 14, 13.5%
29-0225-64
Amersham WB buffer strip
29-0225-70
Amersham WB PVDF card
29-0225-66
Amersham WB transfer paper
29-0639-02
Amersham WB goat anti-mouse Cy3
29-0382-75
Amersham WB goat anti-rabbit Cy3
29-0382-76
Amersham WB goat anti-mouse Cy5
29-0382-77
Amersham WB goat anti-rabbit Cy5
29-0382-78
Amersham WB paper comb
29-0562-86
Amersham WB system User Manual 29-0214-88 AC
9 Ordering information
Accessories
Accessory
Product code
Amersham WB buffer strip holder
29-0479-61
Amersham WB transfer holder
29-0384-64
Amersham WB sponge
29-0341-13
Amersham WB drying holder
29-0993-46
Amersham WB membrane adapter
29-0384-66
Barcode scanner 2-D with USB
28-9564-52
Tubing holder
29-0562-62
Inlet filter holding kit:
11-0004-07
•
1 x Filter holder
•
1 x Filter
•
1 x Support screen
Inlet filter set:
•
5 x Filter
•
5 x Support screen
11-0004-14
Spare parts for user
maintenance
Spare part
Product code
Transfer electrode
29-0384-65
Air filter (dryer)
29-0341-15
Transfer tank filter
29-0454-13
Pump head (same head for transfer and
probing pump)
29-0341-14
Fuse:
22-0659-27
2x T4AH 250 V
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361
9 Ordering information
Product recommended for buffer
exchange
Buffer exchange product
Product code
Amersham WB MiniTrap kit
29-0222-21
Handbook
Product code
Western Blotting –
Principles and Methods
28-9998-97
Product
Product code
Amersham WB analyzer
29-0320-30
Handbook
Instrument
362
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A The Amersham WB watch app
Appendix A The Amersham WB watch
app
Introduction
The instrument status and the progress of runs can be remotely monitored through the
Amersham WB watch app. The app can alert users when the instrument requires manual intervention or when runs are completed. Optionally snapshots of the images from
the last run can be previewed. No detailed run information like e.g., file names, sample
names and notes will be possible to view remotely.
It is also possible to select whether to upload service-related data to the cloud for service
and maintenance purposes.
To establish connection between an instrument and a registered user account in the
mobile device, follow the steps below:
•
install the app and register a user account
•
activate an instrument for remote access
•
add the instrument to the app by entering an access code in the app (the access
code is obtained from the software connected to the instrument)
Note:
In order for the Amersham WB watch app status updates to work, the computer
on which the Amersham WB software is installed:
•
must be connected to the instrument and have Internet access
•
may not be in power save mode (sleep or hibernate)
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363
A The Amersham WB watch app
Install Amersham WB watch and
register an account
Step
Action
1
Download Amersham WB watch from Apple™ AppStore or Google Play™
and install it.
2
Select Register new account in the app, fill out the registration form and
click the Register new account button.
Result: The user account is registered.
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A The Amersham WB watch app
Activate instrument remote
access
Step
Action
1
Select Remote:Activate remote access in the menu bar in Amersham WB
software to enable remote access to Amersham WB analyzer.
Note:
The Remote menu is only available when connected to an instrument.
Result: If it is the first time that the connection is established to the instrument, the Remote access settings dialog opens.
2
If appropriate, edit the alias for the instrument in the System name field
(default is the serial number of the instrument).
This name will appear in the app for users with remote access to the instrument.
3
Check the Allow listed WB watch users to view image snapshots box to
allow snapshots of the last scanned images to be uploaded to the cloud. All
users connected to the system will be able to see the images.
4
Check the Allow GE to review service related data for improved service
box to allow service-related data to be uploaded to the cloud for service
and maintenance purposes.
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A The Amersham WB watch app
Add a WB watch user
To add a WB watch user who will be able to monitor an instrument activated for remote
access:
Step
Action
1
Select Remote:Add WB watch user in the menu bar of the software connected to the activated instrument.
Note:
This menu option is only available when connected to an instrument with
remote access activated.
Result: The Add WB Watch User dialog opens displaying an access code for
the user to enter in the Amersham WB watch app to establish the remote
connection.
Note:
The access code can only be used once.
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A The Amersham WB watch app
Step
Action
2
Select Add new system in the Amersham WB watch app.
Result: The Add System page is displayed.
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367
A The Amersham WB watch app
Step
Action
3
Enter the access code from Add WB Watch User dialog (in the Amersham
WB software) in the Access Code text field and select Add.
Result: The added instrument appears in the app and the Add WB Watch
User dialog in the software displays the e-mail address of the added user.
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A The Amersham WB watch app
Remove a user
To remove a user from being able to remotely monitor an instrument:
Step
Action
1
Select Remote:List of WB watch users in the menu bar.
Result: The List Of WB Watch Users dialog opens.
2
Select the name of the user to be removed.
3
Click the Remove user button.
4
Click OK to close the dialog.
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A The Amersham WB watch app
Edit remote access settings
To edit the system name or change the type of data to be uploaded to the cloud:
Step
Action
1
Select Remote:Remote access settings in the menu bar.
Result: The Remote access settings dialog opens.
2
The following can be edited:
•
the alias for the system in the System name field (visible in the app).
•
check/clear the Allow listed WB watch users to view image snapshots
box.
When checked, snapshots of the last scanned images are uploaded to
the cloud and are available for connected users.
Note:
Status data for the run will be shown to all WB watch users regardless of
these options. To stop a user from viewing status, remove the user. See
Remove a user, on page 369 above.
•
check/clear the Allow GE to review service related data for improved
service box.
When checked, service related data is uploaded to the cloud for service
and maintenance purposes.
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Index
Index
Description, 48
Place in Elpho & scan
unit, 165
A
Accessories
Ordering information, 361
Accessories for user maintenance
Ordering information, 361
Air filter
Replace air filter, 329
Antibody
Optimization, 102
Antibody (secondary)
Conjugated CyDyes, 57
Description, 57
Dilution, 102
Select in software, 126
Selection, 99
Storage of lyophilized antibodies, 38
Storage of reconstituted
antibodies, 39
Antibody compartment
Connect antibody solutions, 209
Description, 29
B
Buffers and solutions
Antibody solution, probing, 104
Blocking solution, 104
Compatible buffer substances, 86
Final wash buffer, probing, 104
Lysis buffers, 88
Transfer buffer, 103
Ultra pure water, cleaning, 103–104
Wash buffer, probing, 104
Buffer strip
Description, 48
Place in buffer strip holder, 164
Buffer strip holder
Clean, 183, 320
Amersham WB system User Manual 29-0214-88 AC
C
Clean
Buffer strip holder, 183, 320
Drying compartment, 323
Drying holder, 236, 321
Elpho & scan unit, 183
Membrane adapter, 236,
320
Probing flow path, 220, 321
Transfer flow path, 206, 321
Transfer holder, 207
Transfer tank, 321
Consumables
Order, 37
Ordering information, 360
Pre-labeling reagents, 88
Storage, 37
Copy and export
Evaluation results, 246
CyDye
Description, 84
Emission wavelength, 57
Excitation wavelength, 57
D
Documentation
Data files and application
notes, 13
Method handbook, 13
User documentation, 12
Drying
Start and monitor, 222
Drying compartment
Clean, 323
Description, 28
Drying holder, 59
Clean, 236, 321
E
Easy SDS-PAGE
Analyze results, 255
Description, 81
371
Index
Easy SDS-PAGE with quantity
calibration
Analyze results, 258
Description, 92
Easy Western
Analyze results, 248
Description, 81
Easy Western with quantity
calibration
Analyze results, 260
Description, 124
Electrophoresis
Load samples, 168
Place buffer strip holders
Elpho & scan unit, 165
Place buffer strips in buffer
strip holders, 164
Pre-labeling reagents, 90
Prepare, 164
Remove gel card, 182
Electrophoresis experiment
Create in software, 113
Description, 81
Edit protocol, 132
Overview, 82, 91, 107
Run, 169
Sample preparation, 161
Elpho & scan loader, 20
Elpho & scan unit, 18
Clean, 183
Close, 168
Open, 165
Start, 108
Evaluation
Fraction analysis, 281, 288
Purity check of a sample, 281, 288
Workflow overview, 238
Evaluation: Editing of analysis
settings
Edit band detection, 297
Edit band matching, 304
Edit lane detection, 292
Edit MW calibration, 309
Evaluation and analysis of results
Easy SDS-PAGE, 255
Easy SDS-PAGE with quantity calibration, 258
Easy Western, 248
372
Easy Western with quantity
calibration, 260
Western experiment with
total protein normalization, 252
Western with endogenous
protein normalization, 250
Evaluation and check results
Check band detection, 242
Check band matching, 244
Check lane detection, 241
Check MW calibration, 245
Evaluation and result views
Band table, 281
Bar chart, 272
Image view, 263
Lane profile, 278
Protein table, 288
Quantity calibration, 285
Evaluation default views
Easy SDS-PAGE, 240
Easy SDS-PAGE with quantity calibration, 240
Easy Western, 239
Easy Western with quantity
calibration, 240
Western with endogenous
protein normalization, 240
Western with total protein
normalization, 239
Evaluation results
Copy and export, 246
Experiment
Electrophoresis experiments, 81
Save, 152
Western experiments, 81
Experiment information
View and enter information, 147
Experiment log
View, 150
Experiment type
Electrophoresis experiment, 91
Western experiments, 101
Export
Evaluation results, 246
Amersham WB system User Manual 29-0214-88 AC
Index
F
Fraction analysis
Evaluation, 281, 288
G
Gel card
Composition, 45
Dissassembly overview, 193
Loosen gel frame from gel
support, 194
Place on card plate, 167
Protein separation resolution, 45
Remove protective films before electrophoresis, 166
Select in software, 120
Types, 45
Gel scanning
Edit protocol, 134
Images, 175
Re-scan, 176
Run, 173
I
Indicators, 17
Inlet filter
Inlet filter holder, 61
Replace inlet filter, 336
Inlet filter holder
Description, 61
Instrument
Elpho & scan loader, 20
Elpho & scan unit, 18
Indicators, 17
Western unit, 22
L
Maintenance clean of
transfer flow path, 325
Maintenance program, 317
Replace air filter, 329
Replace inlet filter, 336
Replace mains fuse, 337
Replace probing or transfer
pump head, 331
Replace transfer electrodes, 334
Replace transfer tank filter, 336
Matrix tag reader
Description, 61
Membrane adapter
Clean, 236, 320
Description, 60
Place on card plate, 225
Membrane scanning
Images, 229
Start and monitor, 226
Multiplex detection
Principle Cy5 total protein
labeling and Cy3 secondary
antibody, 95
Multplex detection
Principle Cy3 and Cy5 secondary antibodies, 94
MW markers
Dilution in Western experiments, 98
Electrophoresis experiment, 91
Illustration, 43
Proteins, 44
N
Loading capacity
Sample loading capacity, 161
Load samples, 168
Normalization
Endogenous protein, 97
quantitation, 96
Total protein labeling, 96
Notes and tips, 10
M
O
Mains fuse
Replace the mains fuse, 337
Maintenance
Accessories, 328
Maintenance clean of probing flow path, 326
Ordering information
Accessories, 361
Accessories for user maintenance, 361
Buffer exchange, 362
Consumables, 360
Amersham WB system User Manual 29-0214-88 AC
373
Index
Handbook, 362
Instrument, 362
Order consumables, 37
P
Paper comb
Description, 50
Pre-labeling, 154
Compatible lysis buffers, 88
Description, 84
Illustration of reaction, 85
Interfering substances, 87
Preparations, 156
Protocols, 89
Quantity calibrants, 156
Quick SDS-PAGE pre-labeling protocol, 160
Reagents and solutions, 88
Required solutions and materials, 155
Sample concentration, 86
Sample loading capacity, 89
Sample types, 86
SDS-PAGE pre-labeling protocol, 157
Western pre-labeling protocol, 159
Probing
Basic principle of probing
process, 34
Clean flow path, 220, 321
Connect antibody solutions, 209
Connect probing solutions, 208
Edit protocol in software, 141
Liquid flow path, 33
Maintenance clean of flow
path, 326
Pre-fill probing chamber, 212
Prepare probing and antibody solutions, 104
Print protocol, 144
Probing time, 100
Replace probing pump
head, 331
Start and monitor, 215
Probing compartment
374
Description, 27
Protocols
Pre-labeling, 89
Pump head
Replace probing or transfer
pump head, 331
Purity check of a sample
Evaluation, 281, 288
Purpose of this document, 8
PVDF card
Description, 54
Move to Drying compartment, 218
Place in Elpho & scan
unit, 224
Place in probing chamber, 214
Prepare, 188
Q
Quantity calibrants
Analyze results, 258
Pre-labeling, 156
Quick SDS-PAGE pre-labeling
protoco, 160
R
Recipes
Antibody solutions, 104
Probing solutions, 104
Transfer solutions, 103
Remove sample well cover, 167
S
Safety notices, 10
Safety switches, 15
Sample
Loading capacity, 161
Prepare sample, 161
Sample types in software, 124
Set up in software, 121
Sample table
Copy and paste, 125
Print, 129
Sample types, 124
Scanning
Edit gel scanning protocol, 134
Amersham WB system User Manual 29-0214-88 AC
Index
Edit scanning protocol in
software, 145
Membrane images, 229
Preparations before, 224
Procedures after, 235
PVDF card, 224
Re-scan gel images, 176
Run gel scanning, 173
Sensitivity, 146
Start and monitor membrane scanning, 226
SDS-PAGE pre-labeling protocol, 157
Secondary antibodies
Dilution, 102
Select in software, 126
Selection, 99
Sensitivity
In scanning, 146
Service compartment
Description, 30
Replace air filter, 329
Replace pump heads, 331
Software
Overview, 63
Start, 111
Solutions
Antibody, 104
Blocking, 104
Connect antibody solutions, 209
Connect probing solutions, 208
Connect transfer solutions, 185
Probing, 104
Transfer, 103
Sponge
Description, 56
Place in transfer holder, 192
T
Transfer
Basic principle of transfer
process, 32
Clean transfer flow
path, 321
Connect solutions, 185
Edit protocol, 137
Liquid flow path, 31
Amersham WB system User Manual 29-0214-88 AC
Maintenance clean of flow
path, 325
Prepare and connect solutions, 185
Replace transfer electrodes, 334
Replace transfer pump
head, 331
Replace transfer tank filter, 336
Solutions in software, 138
Start and monitor, 202
Transfer electrodes
Replace transfer electrodes, 334
Transfer holder
Clean, 207
Description, 52
Remove after run, 205
Transfer paper
Description, 55
Transfer sandwich
Assembly overview, 187
Load into Transfer tank, 201
Materials, 186
Prepare, 186
Transfer tank
Clean, 321
Description, 26
Load transfer sandwich, 201
Transfer tank filter
Replace transfer tank filter, 336
Troubleshooting
Electrophoresis, 341
Evaluation, 351
Gel and membrane image, 341
General, 340
Membrane image, 347
Pre-labeling, 341
Probing and drying, 342
Scanning, 343
Transfer, 342
Tubing holder
Description, 62
Typographical conventions, 8
W
Western experiment
375
Index
Create in software, 115
Description, 81
Experiment type, 101
Multiplex detection, 94
MW markers, 98
Normalization, 96
Overview, 82, 107
Western experiment with total
protein normalization
Analyze results, 252
Description, 96
Western pre-labeling protocol, 159
Western unit, 22
376
Antibody compartment, 29
Drying compartment, 28
Probing compartment, 27
Service compartment, 30
Start, 109
Transfer tank, 26
Western with endogenous
protein normalization
Analyze results, 250
Description, 97
Workflow overview
General, 82, 107
Work flow overview
Evaluation, 238
Amersham WB system User Manual 29-0214-88 AC
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© 2014 General Electric Company – All rights reserved.
First published Mar. 2014
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29-0214-88 AC 03/2014 a1681
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