E.2 - University of Alberta

E.2 - University of Alberta
user manual
proteomics
Ettan DIGE System
User Manual
um 18-1173-17 Edition AA
Terms and Conditions of Sale
Unless otherwise agreed in writing, all goods and
services are sold subject to the terms and conditions of
sale of the company within the Amersham Biosciences
group which supplies them. A copy of these terms and
conditions is available on request.
Trademarks
Office Addresses
Amersham Biosciences AB
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SE-751 84 Uppsala
Sweden
Amersham Biosciences UK Limited
Cy, CyDye, DeCyder, Destreak, Ettan, Hoefer,
ImageQuant, Immobiline, IPGphor, Multiphor,
MultiTemp, Pharmalyte, PlusOne, and Typhoon are
trademarks of Amersham Biosciences Limited.
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Amersham and Amersham Biosciences are trademarks
of Amersham plc.
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SYPRO is a trademark of Molecular Probes Inc.
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Patents and Licences
CyDye: 2-D Fluorescence Difference Gel
Electrophoresis (2-D DIGE) technology is covered by
US Patent Numbers 6,043,025, 6,127,134, and
6,426,190 and foreign equivalents and exclusively
licensed from Carnegie Mellon University.
CyDye: this product or portions thereof is
manufactured under licence from Carnegie Mellon
University under US Patent Number 5,268,486 and US
and foreign equivalents.
The purchase of CyDye fluors includes a limited license
to use the CyDye fluors for internal research and
development, but not for any commercial purposes. A
license to use the CyDye fluors for commercial purposes
is subject to a separate license agreement with
Amersham Biosciences.
Amersham Biosciences has patent applications pending
relating to its DeCyder software technology, European
patent application number EP1,234,280.
©Amersham Biosciences AB 2003
-All rights reserved
Contents
1 Introduction to Ettan DIGE system
1.1 Description of Ettan DIGE system ............................................... 11
1.2 The chemistry of labelling proteins with CyDye DIGE
Fluor minimal dyes .................................................................... 12
1.3 Spot picking .............................................................................. 13
1.4 Identifying proteins of interest .................................................... 14
2 Experimental design
2.1 Introduction ............................................................................... 15
2.2 Designing a 2-D DIGE experiment .............................................. 18
2.2.1
The importance of an internal standard ................................ 18
2.2.2
DeCyder Differential Analysis Software co-detection and
matching using the internal standard ................................... 21
2.3 Examples of experimental design ............................................... 23
2.4 Summary ................................................................................... 29
3 Sample preparation and labelling
3.1 Overview .................................................................................... 31
3.2 Sample preparation ................................................................... 31
3.2.1
Requirements for a cell wash buffer ..................................... 32
3.2.2
Requirements for a cell lysis buffer....................................... 32
3.2.3
Preparing a cell lysate compatible with CyDye DIGE Fluor
minimal dye labelling ........................................................... 32
3.2.4
How to determine the concentration of a protein sample....... 34
3.2.5
How to adjust the pH of the protein sample .......................... 34
3.2.6
Checklist.............................................................................. 34
3.3 Preparation of CyDye DIGE Fluor minimal dyes for protein
labelling ..................................................................................... 35
3.3.1
Introduction ......................................................................... 35
3.3.2
Reconstituting the stock CyDye DIGE Fluor minimal dye in
dimethylformamide (DMF) ................................................... 35
3.4 Calculating the amount of CyDye DIGE Fluor minimal dye
required to label a protein lysate ................................................ 36
3.4.1
Checklist.............................................................................. 37
3.5 Protein sample labelling ............................................................. 37
3.5.1
Preparation of an internal standard ...................................... 38
3.5.2
Protein labelling with the CyDye DIGE Fluor minimal dyes..... 38
3.6 Preparing labelled protein samples for the
first dimension ........................................................................... 38
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4 Focusing using the Ettan IPGphor isoelectric
focusing system
4.1 Overview ................................................................................... 41
4.2 Immobiline DryStrip rehydration ................................................ 42
4.2.1
Calculating the volume of buffer required to rehydrate an
Immobiline DryStrip............................................................. 42
4.3 Protocol 1 – Rehydration of Immobiline DryStrips in the
absence of protein samples ....................................................... 43
4.3.1
Cup loading the labelled protein sample onto the
Immobiline DryStrip............................................................. 44
4.4 Protocol 2 – Rehydration of Immobiline DryStrips in the
presence of protein sample ....................................................... 47
4.4.1
Loading IPGphor Cup Loading Strip Holders onto the
Ettan IPGphor IEF unit......................................................... 47
4.4.2
Recommended isoelectric focusing parameters ................... 48
4.5 How to store Immobiline DryStrips after the proteins have been
focused ..................................................................................... 48
5 Focusing using the Multiphor II isoelectric
focusing system
5.1 Overview ................................................................................... 49
5.2 Protocol 1 - Rehydration of Immobiline DryStrips in the
absence of protein sample ......................................................... 50
5.3 Preparing the Immobiline DryStrip Kit ........................................ 52
5.3.1
Preparing the Immobiline DryStrip Kit .................................. 52
5.4 Application of sample after gel rehydration ................................. 54
5.5 Protocol 2 - Rehydration of Immobiline DryStrips in the
presence of protein sample ....................................................... 56
6 2–D electrophoresis using Ettan DALT
electrophoresis system
6.1 Overview ................................................................................... 59
6.2 Casting homogeneous Ettan DALT gels ...................................... 59
6.2.1
Casting homogeneous 2–D gels ........................................... 60
6.2.2
Checklist ............................................................................. 62
6.3 2–D electrophoresis using Ettan DALT electrophoresis system .... 62
6.3.1
Equilibration of focused Immobiline DryStrips ...................... 62
6.3.2
Loading of focused Immobiline DryStrips ............................. 63
6.3.3
Inserting gels into the Ettan DALT electrophoresis
buffer tank .......................................................................... 64
6.4 Recommended running conditions ............................................ 65
6.5 Checklist ................................................................................... 65
6.6 Preparing Ettan DALT gels for use with the Ettan Spot Picker ..... 66
6.6.1
Gel preparation.................................................................... 66
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6.6.2
6.6.3
6.6.4
6.6.5
Cleaning and Bind-Silane treating glass plates...................... 66
Reference markers .............................................................. 67
Positioning the reference markers ........................................ 67
Loading Immobiline DryStrips onto a picking gel................... 68
7 Using Typhoon Variable Mode Imager with Ettan
DIGE system
7.1 Overview .................................................................................... 69
7.2 Scanning gels using Typhoon Variable Mode Imager .................. 70
7.3 Turning on and warming up Typhoon Variable Mode
Imager ....................................................................................... 71
7.4 Fluorescence scanning software workflow .................................. 72
7.5 Placing an assembled Ettan DALT gel or SE 600 Ruby gel
on the platen ............................................................................. 72
7.6 Selection of fluorescence acquisition mode ................................ 75
7.7 Selection of tray options ............................................................. 77
7.7.1
Option 1 - Predefined Tray area, e.g. DIGE Ettan DALT or
DIGE SE 600........................................................................ 78
7.7.2
Option 2 - User Select.......................................................... 79
7.8 Setting gel orientation and scan resolution .................................. 79
7.9 Starting a scan ........................................................................... 81
7.9.1
DIGE file naming format ....................................................... 82
7.9.2
Tray setting with "DIGE Ettan DALT" or "DIGE SE 600"
options ................................................................................ 83
7.9.3
Standard file naming format ................................................. 84
7.10 Monitoring the scan progress ..................................................... 85
7.11 Image file output and cropping nonessential
information ................................................................................ 85
7.11.1 File output ........................................................................... 85
7.11.2 Image cropping.................................................................... 85
7.12 Creating and using templates ..................................................... 87
7.13 Shut-down procedure. ............................................................... 87
8 Recipes
8.1 Sample preparation and labelling ............................................... 89
8.1.1
Standard cell wash buffer..................................................... 89
8.1.2
How to make the standard cell lysis buffer............................ 89
8.1.3
Standard cell lysis buffer (option 1) - contains thiourea......... 89
8.1.4
Standard cell lysis buffer (option 2) ...................................... 90
8.1.5
10 mM Lysine...................................................................... 90
8.1.6
1 M Magnesium acetate....................................................... 90
8.2 Gel preparation and running ...................................................... 90
8.2.1
2× Gel loading buffer .......................................................... 90
8.2.2
12.5% 1-D PAGE gel composition (for SE 600 Ruby)............ 91
8.2.3
1% (w/v) Agarose gel sealant ............................................... 91
8.2.4
1.5 M Tris, pH 8.8 ............................................................... 91
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8.2.5
10% (w/v) SDS .................................................................... 91
8.2.6
10% (w/v) APS .................................................................... 91
8.2.7
1× SDS electrophoresis running buffer................................. 92
8.2.8
1.0 M Tris, pH 8.0............................................................... 92
8.2.9
Water saturated butanol....................................................... 92
8.2.10 2× sample buffer ................................................................. 92
8.2.11 40% (w/v) CHAPS ............................................................... 93
8.3 First dimension IEF ................................................................... 94
8.3.1
Rehydration buffer............................................................... 94
8.3.2
SDS Equilibration buffer stock solution ................................. 95
8.3.3
Equilibration solution 1 ........................................................ 95
8.3.4
Equilibration solution 2 ........................................................ 95
8.4 Loading and running 2–D gels ................................................... 96
8.4.1
10% (v/v) TEMED................................................................ 96
8.4.2
12.5% 2–D PAGE gel composition for Ettan DALT................ 96
8.4.3
Displacing solution .............................................................. 96
8.4.4
SDS electrophoresis running buffer for Ettan DALT............... 96
8.4.5
0.5% (w/v) Agarose overlay solution ..................................... 97
8.5 Post staining gels ...................................................................... 97
8.5.1
SYPRO Ruby gel fix ............................................................. 97
8.5.2
SYPRO Ruby gel destain...................................................... 97
9 Introduction to DeCyder Differential Analysis
Software
9.1 Introduction .............................................................................. 99
9.2 Integration of DeCyder Differential Analysis Software within
Ettan DIGE system ..................................................................... 99
9.2.1
Overview of Ettan DIGE system and experimental design ...... 99
9.2.2
Advantages of using DeCyder Differential Analysis Software
with Ettan DIGE system...................................................... 100
9.3 Structure of DeCyder Differential Analysis Software .................. 101
9.3.1
Introduction....................................................................... 101
9.3.2
DIA (Differential In-gel Analysis)......................................... 102
9.3.3
BVA (Biological Variation Analysis) ..................................... 103
9.3.4
Batch Processor ................................................................ 104
9.3.5
XML Toolbox ..................................................................... 104
Appendices
Appendix A: How to sonicate cells .................................................. 105
Appendix B: How to prepare and run a 1-D PAGE gel on the
Hoefer SE 600 Ruby Standard Vertical
Electrophoresis gel system .......................................... 107
Appendix C: Testing a new protein lysate for successful labelling ..... 111
Appendix D: Scanning and staining protocols for spot picking ......... 119
Appendix E: Recommended experimental conditions ...................... 123
Appendix F: Typhoon Variable Mode Imager ................................... 155
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Appendix G: Trouble shooting guide ................................................ 167
Appendix H: Related products and consumables ............................. 175
Appendix I: Glossary ...................................................................... 179
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Introduction to Ettan DIGE system
1 Introduction to Ettan DIGE system
1.1 Description of Ettan DIGE system
Ettan™ DIGE system is based on the technique of two-dimensional
difference gel electrophoresis (2–D DIGE).
• The system is based upon the specific properties of the three
CyDye™ DIGE Fluor minimal dyes. These enable multiplexing of
up to three separate protein mixtures on the same 2–D gel.
• The key benefit of Ettan DIGE system is that multiplexing enables
the incorporation of the same internal standard on every 2–D gel.
• Ettan DIGE system enables the production of quantitative data of
unparalleled accuracy, supported by statistical tests. This gives
confidence that the results achieved reflect true biological outcomes
and are not due to the system i.e., experimental variation.
• Ettan DIGE system comprises CyDye DIGE Fluor minimal dyes,
Typhoon™ Variable Mode Imager and DeCyder™ Differential
Analysis Software.
The multiplexing capability of the 2-D DIGE methodology enables the
incorporation of the same internal standard on every 2–D gel. The
internal standard is a pool of all the samples within the experiment, and
therefore contains every protein from every sample. The internal
standard is used to match the protein patterns across gels thereby
negating the problem of inter-gel variation, a common problem in
standard “one sample per gel” 2-D electrophoresis experiments. This
allows accurate quantitation of differences between samples, with an
associated statistical significance. The 2-D DIGE methodology is the
only technique to enable accurate standardized quantitation.
The CyDye DIGE Fluor minimal dyes are three spectrally resolvable
dyes (Cy™2, Cy3 and Cy5) matched for mass and charge. This means
that the same protein labelled with any of the CyDye DIGE Fluor
minimal dyes, will migrate to the same position on the 2–D gel. This
multiplexing capability eliminates intra-gel variation. The dyes afford
great sensitivity with detection down to 125 pg of a single protein, and
a linear response to protein concentration up to five orders of
magnitude (105). In comparison, silver stain detects 1–60 ng of protein
with a dynamic range of less than two orders of magnitude.
To capitalize on this ability to multiplex, DeCyder Differential Analysis
Software has been specifically designed for the Ettan DIGE system.
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Introduction to Ettan DIGE system
DeCyder Differential Analysis Software contains proprietary
algorithms that perform co-detection of differently labelled samples
within the same gel. DeCyder Differential Analysis Software also
permits automated detection, background subtraction, quantitation,
normalization, internal standardization and inter-gel matching. The
benefits are low user interaction, high throughput and low
experimental variation.
For a brief introduction to DeCyder Differential Analysis Software,
please refer to Chapter 9 of this manual. For a more detailed guide,
please refer to the DeCyder Differential Analysis Software User Manual
(code no. 18-1173-16).
Fig 1-1. Outline of Ettan DIGE system (when used with three CyDye DIGE
Fluor minimal dyes separated in a single gel)
1.2 The chemistry of labelling proteins with CyDye DIGE
Fluor minimal dyes
There are three CyDye DIGE Fluor minimal dyes available; Cy2, Cy3
and Cy5. These have been designed to be matched for charge and
molecular weight. Consequently the same protein labelled with any of
the CyDye DIGE Fluor minimal dyes, will migrate to the same position
on a 2–D gel.
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Introduction to Ettan DIGE system
CyDye DIGE Fluor minimal dyes have an NHS ester reactive group,
and are designed to form a covalent bond with the epsilon amino group
of lysine in proteins via an amide linkage. The dye is added to the
protein such that the amount of dye is limiting within the labelling
reaction. The ratio used ensures that the dyes label approximately
1–2% of lysine residues so each labelled protein carries only one dye
label and is visualised as a single protein spot. The CyDye DIGE Fluor
minimal dyes therefore only label a small proportion of the total
protein in a sample. For that reason, this type of labelling has been
called “minimal” labelling.
The lysine amino acid in proteins carries an intrinsic +1 charge at
neutral or acidic pH. CyDye DIGE Fluor minimal dyes also carry a
+1 charge which, when coupled to the lysine, replaces the lysine’s
+1 charge with its own, ensuring that the pI of the protein does not
significantly alter.
Each CyDye DIGE Fluor minimal dye, when coupled to a protein, will
add approximately 500 Da to the mass of the protein. This mass shift
does not effect the pattern visible on a 2-D gel.
Fig 1-2. Schematic of the minimal labelling reaction. CyDye DIGE Fluor minimal
dye containing NHS ester active group covalently binds to the lysine residue of a
protein via an amide linkage.
1.3 Spot picking
The nature of the minimal labelling method results in populations of
labelled and unlabelled species for each protein in a lysate. For each
protein spot on a 2-D gel, the labelled species will be slightly shifted
from the unlabelled species due to the addition of a single dye molecule.
This effect is more marked for lower molecular weight proteins. If a
protein was picked using the centre of the spot detected from the CyDye
DIGE Fluor fluorescent image (i.e. labelled protein), this may not
correspond to the area of highest protein concentration. To circumvent
this problem, the total protein should be visualized using a poststaining method and the position of spots for picking based on this new
image. This maximizes the amount of protein available for mass
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Introduction to Ettan DIGE system
spectrometry identification. The standard post-stain used for this step
is SYPRO™ Ruby. Other post-staining methods, such as Coomassie™
and silver staining can be used, but DeCyder Differential Analysis
Software is optimized for a fluorescent signal output so these stains
require more complex analysis.
An analytical gel can be post-stained and used directly for spot picking.
The SYPRO Ruby and CyDye DIGE Fluor minimal dye images from
this gel are matched, locating spots for picking on the SYPRO Ruby
image. More commonly, a separate preparative gel is generated, using
a high loading of unlabelled protein. This gel is post-stained and then
matched back to the analytical set of gels. This allows the spots selected
for picking to be linked between the analytical data and the poststained gel image.
For a pH 3-10 NL 24 cm Immobiline™ DryStrip, it is recommended
that 500 µg of protein is loaded for a preparative gel. The loading
should be optimized for different strip lengths and pH ranges.
1.4 Identifying proteins of interest
Protein identification by mass spectrometry is usually performed on
unlabelled protein, visualized on the 2-D gel with a post-electrophoresis
stain, such as SYPRO Ruby. Some applications may require direct spot
picking from a 2-D gel containing protein labelled with CyDye DIGE
Fluor minimal dye. The nature of the minimal labelling approach
results in the majority of the protein (and peptide) population
remaining unlabelled. The proteins are identified from unlabelled
peptides giving equivalent levels of sequence coverage compared to
direct identification from unlabelled proteins.
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Experimental design
2 Experimental design
2.1 Introduction
Prior to commencing practical work, experimental design needs to be
carefully considered. The main steps in Ettan DIGE system workflow
are outlined below.
Fig 2-1. Workflow for differential abundance analysis and protein
identification using Ettan DIGE system.
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Experimental design
This section will describe the concept of experimental design and its
implications for subsequent data analysis using DeCyder Differential
Analysis Software.
2-D analysis experiences variation which must be differentiated from
the induced biological change (the differences that are caused by a
disease state/drug treatment/life-cycle stage etc.) being measured in the
2-D electrophoresis experiment. This variation arises from two main
sources.
1
System variation:
System variation may arise from two areas. Firstly, gel-to-gel
variation can result from differences in electrophoretic conditions
between first dimension strips or second dimension gels, gel
distortions and user-to-user variation. The second source of system
variation is due to user-specific editing and interpretation when
using the data analysis software. System variation cannot be
overcome when using conventional 1-color 2-D electrophoresis.
Ettan DIGE system is able to minimize gel-to-gel variation by
allowing the inclusion of an internal standard within each gel.
Software-originated variation is minimized using DeCyder
Differential Analysis Software. This provides automated codetection, background subtraction, quantitation, normalization
and inter-gel matching, which limits user intervention and
subjective editing, generating consistent data.
2
Inherent biological variation:
Inherent biological variation arises from intrinsic differences that
occur within populations. For example, differences from animal-toanimal, plant-to-plant or culture-to-culture which have been
subjected to identical conditions. This type of variation cannot be
removed from any 2-D electrophoresis experiments. However,
Ettan DIGE system allows it to be effectively differentiated from
induced biological changes using appropriate experimental design
and statistical analysis.
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Experimental design
When designing 2-D DIGE experiments, the following
recommendations should be considered:
1
Inclusion of an internal standard sample on each gel;
2
The requirement for biological replicates such as multiple cultures,
tissue etc.;
3
Randomization of samples to produce unbiased results, thus
conforming with best experimental practice.
It is strongly advised that biological replicates are included in every
group. This will enable accurate measurement of the change due to a
treatment/disease that is significant above a baseline of inherent
biological variation. The more biological replicates, the more that
inherent biological variation is accounted for and therefore, the more
meaningful the results. Without biological replicates, results are not
biologically relevant and it is only possible to conclude that differences
are above system variation. Ettan DIGE system variation is so low due
to the internal standard and method of analysis, that gel replicates are
not needed - any system variation should be far outweighed by the
inherent biological variation. Gel replicates can be included if the user
wishes.
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Experimental design
2.2 Designing a 2-D DIGE experiment
The preparation of a protein lysate that can be successfully labelled
with CyDye DIGE Fluor minimal dyes is described in Chapter 3.
When a protein lysate is prepared for the first time, it is recommended
that the labelling is checked by 1-D PAGE analysis - see Appendix C.1,
Testing a new protein lysate for successful labelling.
2.2.1 The importance of an internal standard
The recommended protocol suggests an internal standard should be run
on all gels within an experiment, which is then analyzed using the
DeCyder Differential Analysis Software. The use of spectrally
resolvable CyDye DIGE Fluor minimal dyes that are matched for both
mass and charge enables up to three differently labelled protein samples
to be separated on the same 2-D gel. This provides the opportunity to
include an internal standard for every protein in the experiment, on
each gel.
The internal standard is created by pooling an aliquot of all biological
samples in the experiment and labelling it with one of the CyDye DIGE
Fluor minimal dyes (usually Cy2 for a 3-dye experiment). The internal
standard is then run on every single gel along with each individual
sample. This means that every protein from all samples will be
represented in the internal standard, which is present on all gels.
Linking every sample in-gel to a common internal standard offers a
number of advantages:
• Accurate quantification and accurate spot statistics between gels;
• Increased confidence in matching between gels;
• Flexibility of statistical analysis depending on the relationship
between samples;
• Separation of induced biological change from system variation and
inherent biological variation.
The examples below illustrate the benefits of an internal standard.
Figures 2-2 and 2-3 both show the theoretical scan results of two gels.
Each gel contained two protein samples labelled with CyDye DIGE
Fluor Cy3 or Cy5 minimal dyes and the same pooled internal standard
sample labelled with CyDye DIGE Fluor Cy2 minimal dye.
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Experimental design
If the gels illustrated in Fig 2-2 were analyzed without an internal
standard (shown on the left in yellow), the conclusion would be that the
treatment of samples 3 and 4 resulted in the loss of the protein spot
circled in samples 1 and 2. However, reference to the internal standard,
which is an identical pooled sample run on both gels, shows that the
spot present in gel A is absent from gel B. This proves that the absence
of the protein in samples 3 and 4 is due to gel-to-gel variation, for
example gel distortions or differences in first dimension focusing, and
not due to an induced biological change in the sample.
Gel
Cy2 Standard
Cy3
Cy5
A
Standard: pool
samples 1–4
sample 1 - untreated
sample 2 - untreated
B
Standard: pool
samples 1–4
sample 3 - treated
sample 4 - treated
Fig 2-2. Example to illustrate the benefits of an internal standard in comparing
treated samples 3 and 4 with untreated samples 1 and 2.
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Experimental design
If the gels illustrated in Fig 2-3 were analyzed without an internal
standard, the conclusion would be that the volume of the highlighted
protein spot in samples 1 and 2 has remained the same but is increased
slightly in sample 3 and further in sample 4. However, reference to the
internal standard shows that gel-to-gel variation has resulted in an
increased spot volume in gel B compared to gel A. This means that
instead of an increasing trend in spot volume from samples 1 to 4, the
relative volume of the protein spot in sample 3 is reduced in comparison
to samples 1, 2 and 4 where the spot volume ratios are identical.
Gel
Cy2 Standard
Cy3
Cy5
A
Standard: pool
samples 1–4
sample 1 - untreated
sample 2 - untreated
B
Standard: pool
samples 1–4
sample 3 - treated
sample 4 - treated
Fig 2-3. Example to illustrate the benefits of an internal standard in correctly
identifying differences between samples 1, 2, 3 and 4.
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Experimental design
2.2.2
DeCyder Differential Analysis Software co-detection and
matching using the internal standard
To compare protein spot volumes across a range of experimental
samples and gels, two distinct steps are required:
• Intra-gel co-detection of sample and internal standard protein
spots.
• Inter-gel matching of internal standard samples across all gels
within the experiment.
Both of these analysis steps can be performed with minimal user
intervention by the DeCyder Differential Analysis Software.
Intra-gel co-detection
CyDye DIGE Fluor minimal dyes enable up to two differently treated
samples and an internal standard to be separated on the same 2-D gel.
Up to three scans will be made of each gel; a Cy2, Cy3 and Cy5 scan.
Scanned images of each sample and the internal standard are overlaid
in DeCyder Differential Analysis Software. The algorithms within the
software co-detect the spots present in each scan, effectively identifying
the position of each spot within the gel (Fig 2-4). The spot boundaries
that result are identical for each image in the gel. This minimizes
variation from detection and background subtraction, with the added
benefit that every protein in the sample is intrinsically linked to the
corresponding protein spot in the internal standard sample. Spot
volume (i.e. the sum of the pixel values within a spot, minus
background) for each experimental sample is compared directly to the
internal standard by DeCyder Differential Analysis Software. The
protein abundance for each spot in each sample is expressed as a
(normalized) ratio relative to the internal standard e.g.,
[Cy3 sample 1:Cy2 standard] and [Cy5 sample 2:Cy2 standard]. From
this analysis, cross-sample comparisons can be made.
Fig 2-4. Intra-gel co-detection - All samples are co-detected with the internal
standard.
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Experimental design
Inter-gel matching
Experimental design ensures that each gel contains the same internal
standard. This enables inter-gel comparisons of spot abundance. Before
this can be done, it is important to ensure that the same protein spots
are compared between gels. DeCyder Differential Analysis Software
achieves this using the internal standard to match the position of each
protein across all gels within the experiment. An internal standard
image is assigned as the 'Master'. Following co-detection, each image
has a spot boundary map. The spot boundary map for the internal
standard assigned as the master, is used as a template to which all
remaining spot boundary maps for the other internal standards
(intrinsically linked to their co-detected sample images) are matched
(Fig 2-5).
Fig 2-5. Inter-gel matching - only the internal standards need to be matched.
These are derived from the same sample and therefore this aids matching.
Once the spots from the internal standard have been matched across
the gels, the ratio of protein abundance between samples can be
determined. The inclusion of the same internal standard within all the
experimental gels overcomes differences that may arise during the
process of 2–D electrophoresis. For example, variation in spot intensity
due to experimental factors such as protein loss during sample transfer,
will be the same for each sample within a single gel, including the
internal standard. This means that the relative ratio of sample:standard
will not be affected by this variation.
Ratios for sample:standard are used to generate a plot of standardized
relative abundance for each protein across a set of samples. This
provides a more accurate comparison between samples than the
conventional approach using raw spot volumes. DeCyder Differential
Analysis Software applies statistical tests to the data such as Student’s
T-test and Analysis of Variance (ANOVA).
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Statistical tests are important and give the user a level of confidence by
taking into account the inherent biological variation within a group
compared to the induced difference between groups and assigning a
confidence rating as to whether this change is above the biological
variation. The data generated in DeCyder Differential Analysis
Software can be exported for use in other software packages or added
to a database.
For more information about DeCyder Differential Analysis Software
please refer to Chapter 9 or the DeCyder Differential Analysis Software
User Manual (code 18-1173-16).
2.3 Examples of experimental design
In order to maximize the value of CyDye DIGE Fluor minimal dyes and
DeCyder Differential Analysis Software, it is important to carefully
consider the experimental testing regime. Two case studies are
presented below to illustrate some examples of experimental design:
Example 1
Two color analysis - comparison of protein abundance between three
differently treated samples (A-C) each with four biological replicates
using CyDye DIGE Fluor Cy2 and Cy3 minimal dyes.
Features:
• Internal standard labelled with CyDye DIGE Fluor Cy2 minimal
dye;
• All experimental samples labelled with the same dye (CyDye DIGE
Fluor Cy3 minimal dye);
• 12 gel experiment.
Mix 50 µg of each of the 12 samples A - C together to create 600 µg of
the internal standard. Label the internal standard with CyDye DIGE
Fluor Cy2 minimal dye and individually label 50µg of samples A1 to
A4, B1 to B4 and C1 to C4 with CyDye DIGE Fluor Cy3 minimal dye.
A minimum of 12 gels are required, loaded as follows:
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Experimental design
Gel
Cy2 Standard
Cy3
1
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample A1
2
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample A2
3
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample A3
4
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample A4
5
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample B1
6
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample B2
7
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample B3
8
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample B4
9
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample C1
10
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample C2
11
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample C3
12
50µg (4.17µg each of A1-4, B1-4, C1-4)
50µg sample C4
Total gels = 12
It is possible to halve the number of gels required by increasing the
number of dyes used from two to three as shown below.
Example 2
Three color analysis - comparison of protein abundance between three
differently treated samples (A-C) each with four biological replicates
using CyDye DIGE Fluor Cy2, Cy3 and Cy5 minimal dyes.
Features:
• Internal standard labelled with CyDye DIGE Fluor Cy2 minimal
dye;
• To conform to best experimental practice, randomized design is
strongly recommended. Sample replicates from group A, B and C
labelled with either CyDye DIGE Fluor Cy3 or Cy5 minimal dyes.
Samples evenly distributed between the CyDye DIGE Fluors, Cy3
and Cy5, in addition to even distribution between gels;
• 6 gel experiment.
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Gel
Cy2 Standard
Cy3
Cy5
1
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample A1
50 µg sample C3
2
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample B1
50 µg sample A3
3
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample C1
50 µg sample B3
4
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample A2
50 µg sample C4
5
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample B2
50 µg sample A4
6
50 µg (4.17µg each of
A1-4, B1-4, C1-4)
50 µg sample C2
50 µg sample B4
Total gels = 6
In this example, by using three instead of two dyes (as described in
example 1), it has been possible to halve the number of gels required.
The amount of material required is also reduced as half the amount of
internal standard is used (six gels instead of twelve gels).
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Experimental design
Three scans will be made of each gel, a Cy2, Cy3 and Cy5 scan. The codetection algorithms within DeCyder Differential Analysis Software
enable comparison of the protein abundance for each experimental
sample to the internal standard (Fig 2-6). For gel 1, this gives a ratio of
[Cy3 sample A1:Cy2 standard] and [Cy5 sample C3:Cy2 standard].
For gel 2, this gives a ratio of [Cy3 sample B1:Cy2 standard] and
[Cy5 sample A3:Cy2 standard]. For Gel 3, this gives a ratio of
[Cy3 sample C1:Cy2 standard] etc. From this analysis, cross-sample
comparisons can be made.
Fig 2-6. Quantitation of protein abundance using co-detection algorithms. From
each gel, three scan images are generated, CyDye DIGE Fluor Cy2 minimal dye
for the internal standard, CyDye DIGE Fluor Cy3 and Cy5 minimal dyes for
experimental samples. The protein abundance for each spot in each sample is
expressed as a ratio relative to the internal standard.
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The position of each protein spot across every gel is then automatically
matched to a master image by DeCyder Differential Analysis Software,
see Fig 2-7.
Fig 2-7. Matching the internal standard spot patterns. Internal standard spot
patterns are matched across all the gels so that the position of each protein spot
is mapped to the identical spot on the master gel.
Once the protein spots have been matched, the ratio of protein
abundance between samples can be determined. Use of an identical
internal standard within all the experimental gels enables a comparison
of protein abundance between samples on different gels. This is
performed by comparison of the ratios of sample:standard, rather than
direct comparison of raw spot volumes.
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Table 2-1. Ratio of (sample A):(internal standard) and ratio of (sample B):(internal
standard)
Ratio of (sample A1 to
A4): (internal
standard) for a single
protein of interest.
Ratio of (sample B1 to
B4): (internal
standard) for a single
protein of interest.
A1
-2.1
B1
2.6
A2
-2.4
B2
2.5
A3
-1.9
B3
2.2
A4
-2.5
B4
2.4
Note: Down regulation of protein abundance relative to the internal
standard is denoted by a negative prefix, for example, a two-fold
decrease, or a conventional ratio of 0.5 is displayed as -2.0.
DeCyder Differential Analysis Software can graphically display the
relative abundance of each protein against the normalized internal
standard, see Fig 2-8.
Fig 2-8. Plot of sample ratios relative to normalized internal standards.
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Ratio of (sample A):(sample B)
A1:B1
-5.4
A2:B2
-6
A3:B3
-4.18
A4:B4
-6
Table 2-2. Ratio of (sample A):(sample B) calculated from sample:standard ratios
shown in Fig 2-8. This protein is down-regulated approximately 5-fold in sample
A compared to sample B.
DeCyder Differential Analysis Software will accurately quantify
protein abundance changes between samples. Statistical tests can then
be applied to the data, for example, Student’s T-test and ANOVA. The
statistical tests compare the average ratio and variation within each
group to the average ratio and variation in the other groups to see if any
change between the groups is significant. Experimental data can be
exported either as an XML file or text file for further analysis or
databasing.
2.4 Summary
The combination of CyDye DIGE Fluor minimal dyes and DeCyder
Differential Analysis Software exploits the multiplexing capability of
the 2-D DIGE methodology. Inclusion of a pooled internal standard
eliminates system variation, allowing highly accurate measurement of
protein abundance changes.
The use of biological replicates in the experimental design ensures a
true measurement of induced biological differences above the
background of inherent biological variation. Ettan DIGE system is
capable of routinely detecting and quantifying differences as small as
10% between samples (above system variation) with greater than 95%
statistical confidence.
Ettan DIGE system offers unsurpassed quantitative data for
comparative proteomics, providing the user with confidence that the
changes detected in protein abundance are real induced biological
changes.
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3 Sample preparation and labelling
3.1 Overview
• Ensure the sample is prepared in a buffer that is compatible with
the labelling method.
• Ensure the sample protein concentration is 5-10 mg/ml.
• Ensure the sample pH lies in the range pH 8.0–9.0.
• Create a pooled internal standard from all samples for inclusion on
every gel.
• The CyDye DIGE Fluor minimal dyes should be reconstituted to
form a stock solution.
• For labelling, an aliquot of the CyDye DIGE Fluor minimal dye
stock solution should be diluted to a concentration of 400 ρmol/µl.
• The ratio of protein to CyDye DIGE Fluor minimal dye should be
maintained at 50 µg: 400 ρmol.
• New protein samples should be checked for successful labelling.
3.2 Sample preparation
The preparation of a protein lysate that can be successfully labelled
with CyDye DIGE Fluor minimal dyes is detailed in this chapter. Some
of the methods described to prepare protein samples for conventional
2–D electrophoresis may not be compatible with Ettan DIGE system.
The reagents and conditions stated here are those which have been
found to be the most consistently useful across many sample types, for
full details see appendix E2. However, there will be cases where some
individual optimization of lysis conditions is required.
For details of recommended buffers see section 8.1. It is recommended
that the success of the CyDye DIGE Fluor minimal dye labelling is
checked by referring to Appendix C.1, Testing a new protein lysate for
successful labelling.
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3.2.1 Requirements for a cell wash buffer
This section assumes that the biological material under analysis is a cell
culture.
The requirements for a cell wash buffer are that it should not lyse the
cells, but it should dilute and remove any growth media, or reagents
that might affect the CyDye DIGE Fluor minimal dye labelling process.
Note: A cell wash buffer should not contain any primary amines.
Primary amines, such as ampholytes, will compete with the
proteins for CyDye DIGE Fluor minimal dyes. The result will be
fewer dye labelled proteins, which might affect the data after
scanning and spot detection. For further information on
compatible reagents for labelling, please refer to Appendix E.3.
As an alternative to the standard cell wash buffer, 75 mM phosphate
buffered saline (PBS) can be used with Ettan DIGE system. Any other
wash buffers should be tested for compatibility with the labelling step
in controlled experiments (see Appendix C.1, Testing a new protein
lysate for successful labelling).
3.2.2 Requirements for a cell lysis buffer
Note: It is essential that the pH of the protein solution used with a
CyDye DIGE Fluor minimal dye is between pH 8.0–9.0.
Ensure that the pH remains between pH 8.0–9.0, by including a buffer
such as Tris, HEPES or Bicarbonate in the protein solution. The buffer
should be at a concentration of approximately 30 mM. Higher buffer
concentrations may affect isoelectric focusing. Failure to include a
suitable buffer will mean that the pH of the solution may fall below
pH 8.0 resulting in little or no protein labelling. The standard cell lysis
buffer is required to work at +4 °C so the pH should be checked when
the solution is chilled.
Note: The protein solution should not contain any added primary
amine compounds BEFORE labelling as these will compete with
the protein for dye.
3.2.3
Preparing a cell lysate compatible with CyDye DIGE Fluor minimal
dye labelling
The example given here was used with an Escherichia coli model
system. Other wash buffers might be more appropriate for different cell
10
types. Approximately 4×10 E. coli cells will result in 5-10 mg of
protein in a total volume of 1 ml of standard cell lysis buffer.
1
32
Pellet the cells in a suitable centrifuge at +4 °C.
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2
Pour off all growth media, taking care not to disturb the cell pellet.
3
Re-suspend the cell pellet in 1 ml of standard cell wash buffer in a
microfuge tube.
4
Pellet the cells in a bench-top microfuge at 12 000 × g for 4 min at
+4 ºC.
5
Remove and discard the supernatant.
6
Re-suspend the cell pellet in 1 ml of standard cell wash buffer in a
microfuge tube.
7
Repeat steps 4 to 6 at least three times.
8
Ensure all the standard cell wash buffer has been removed.
9
Re-suspend the washed cell pellet in 1ml of standard cell lysis buffer
and leave on ice for 10 min.
Note: If the protein concentration is less than 5 mg/ml after protein
quantitation, re-suspend cells in a smaller volume of lysis buffer
in subsequent experiments. Alternatively, precipitate proteins
using Ettan 2–D Clean-Up Kit (code no. 80-6484-51), and resuspend in a smaller volume of standard cell lysis buffer.
10 Keep the cells on ice and sonicate intermittently until the cells are
lysed. See Appendix A, How to sonicate cells.
11 Centrifuge the cell lysate at +4 °C for 10 min at 12 000 × g in a
microcentrifuge.
12 Transfer supernatant to a labelled tube. This is the cell lysate.
Discard the pellet.
13 Check the pH of the cell lysate is still at pH 8.0 - 9.0 by spotting
3 µl on a pH indicator strip. If the pH of the cell lysate has fallen
below pH 8.0 then the pH of the lysate will need to be adjusted
before labelling. See Section 3.2.5, How to adjust the pH of the
protein sample.
14 The cell lysate can now be stored in aliquots, at –70 oC until protein
yield is to be determined.
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3.2.4 How to determine the concentration of a protein sample
The concentration of protein within all lysates should be determined
using a suitable protein assay, compatible with detergents and thiourea,
if these are present. Protein Determination Reagent (USB, code no.
30098) or Ettan 2-D Quant Kit (code no. 80-6483-56) are both suitable
for this activity.
3.2.5 How to adjust the pH of the protein sample
If the pH of the protein sample is outside the range pH 8.0–9.0, do not
proceed with labelling using CyDye DIGE Fluor minimal dye. Adjust
the pH.
In the following example, the lysate pH is at pH 7.5 which is too low
for effective labelling.
1
Make an identical standard cell lysis buffer, without the protein, at
pH 9.5.
2
Mix increasing volumes of the new lysis buffer with the protein
sample. This will increase the pH of the protein sample as more
lysis buffer is added. Stop when the pH of the protein sample is at
pH 8.5.
Alternatively, the pH of the lysate can be increased to pH 8.5 by the
careful addition of dilute sodium hydroxide (50 mM).
3
Test the sample pH by spotting a small volume (3 µl) on a pH
indicator strip.
3.2.6 Checklist
1 The protein concentration is 5-10 mg/ml.
34
2
The pH of the samples is in the range pH 8.0–9.0.
3
If the samples are suitable for labelling, proceed to Section 3.3,
Preparation of CyDye DIGE Fluor minimal dyes for protein
labelling.
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3.3 Preparation of CyDye DIGE Fluor minimal dyes for protein
labelling
3.3.1 Introduction
The reconstitution and storage of CyDye DIGE Fluor minimal dyes is
important to the success of sample labelling. If reagents, such as
dimethylformamide (DMF) are of a low quality, or the CyDye DIGE
Fluor minimal dyes are incorrectly stored, protein labelling will not be
efficient. If the protein labelling is poor this will cause problems later in
the experiment during gel scanning and image analysis.
3.3.2
Reconstituting the stock CyDye DIGE Fluor minimal dye in
dimethylformamide (DMF)
CyDye DIGE Fluor minimal dye is supplied as a solid and is
reconstituted in DMF giving a concentration of 1 nmol/µl. After
reconstitution in DMF the dye will give a deep color; Cy2-yellow,
Cy3-red, Cy5-blue.
It is recommended that a new bottle of DMF is opened every 3 months.
Note: The DMF must be high quality anhydrous (specification:
≤ 0.005% H2O, ≥ 99.8% pure) and every effort should be taken
to ensure it is not contaminated with water. DMF, once opened,
will start to degrade generating amine compounds. Amines will
react with the CyDye DIGE Fluor minimal dyes reducing the
concentration of dye available for protein labelling.
1
Take the CyDye DIGE Fluor minimal dye from the –20 ºC freezer
and leave to warm for 5 min at room temperature without opening.
This will prevent exposure of the dye to condensation which may
cause hydrolysis.
2
Take a small volume of DMF from its original container and
dispense into a microfuge tube.
3
From this tube remove the specified volume of the aliquoted DMF
(see specification sheet supplied with the CyDye DIGE Fluor
minimal dye) and add to each new vial of dye. For example, add
25 µl DMF to 25 nmol of dye.
4
Replace the cap on the microfuge tube containing the dye and
vortex vigorously for 30 seconds to dissolve the dye.
5
Centrifuge the microfuge tube for 30 seconds at 12 000 × g in a
benchtop microfuge.
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The dye stock solution (1 nmol/µl) is now prepared. The dyes will need
to be further diluted to the working dye solution before use in the labelling
reaction.
Note: Check that the dye solution is an intense color. During transport,
the dye powder may spread around the inside surface of the tube
(including the lid). If the dye is not an intense color, then pipette
the solution around the tube (and lid) to ensure resuspension of
dye. Vortex and spin down.
Note: After use, the CyDye DIGE Fluor minimal dyes should be stored
in a light excluding container, and be returned to the –20ºC
freezer as soon as possible. Once reconstituted, the dye stock
solution is stable for two months or until the expiry date on the
container, whichever is sooner.
3.4 Calculating the amount of CyDye DIGE Fluor minimal dye
required to label a protein lysate
Each tube of stock CyDye DIGE Fluor minimal dye has now been resuspended in DMF to create a 1 nmol/µl dye stock solution.
It is recommended that 400 ρmol of dye is used to label 50 µg of
protein. If labelling more than 50 µg of protein then the dye:protein
ratio must be maintained for all samples in the same experiment. Other
dye:protein ratios can be used but must be optimized for the sample by
testing the labelling on a 1-D gel (see Appendix C.1, Testing a new
protein lysate for successful labelling)
Prior to labelling, further dilution of the dye stock solution should be
carried out following the protocol below (remember to use the same
quality DMF as before):
1
Briefly spin down the dye stock solution in a microcentrifuge.
2
To make 400 ρmol/µl of working dye solution in 5 µl; take a fresh
microfuge tube and add 3 µl of DMF.
3
To the DMF add 2 µl of reconstituted dye stock solution. Ensure all
dye is removed from the pipette tip by pipetting up and down
several times into the working dye solution.
Note: In this example there are 2000 ρmol dye in 5 µl; therefore 1 µl
contains 400 ρmol.
The working dye solution is only stable for 2 weeks at –20ºC.
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Table 3-1 illustrates some examples of CyDye DIGE Fluor minimal dye
dilutions that are routinely used. The recommended dilution is
highlighted.
Table 3-1. Examples of some widely used CyDye DIGE Fluor minimal dye dilutions
for the working dye solution.
Volume of dye Volume of added
Total volume (µl)
stock solution (µl)
DMF (µl)
1
2
2
1
4
3
2
-
5
5
4
1
Concentration of
working dye
solution (ρmol/µl)
200
400
500
1000
3.4.1 Checklist
1 Use 99.8% anhydrous DMF, less than 3 months old for all
applications.
2
Make sure the dye stock solutions are stored at –20 °C.
3
Working dye solutions are only stable for 2 weeks at –20 °C.
After reconstitution, dyes can be used for protein labelling. Proceed
to Section 3.5, Protein sample labelling.
3.5 Protein sample labelling
It is recommended that all new protein lysates or samples containing
new chemical components are checked for successful labelling. Please
refer to Appendix C.
The dye labelling reaction is designed to be simple and should take
about 45 min to perform. It is recommended that the ratio of dye to
protein is maintained at 400 ρmol dye:50 µg protein.
If the ratio of dye:protein is too low, sensitivity may be decreased.
If the ratio of dye:protein is too high, there is a possibility of multiple
dye molecules per protein and this could lead to multiple spots per
protein on the gel.
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3.5.1 Preparation of an internal standard
To use the recommended experimental design, a pooled internal
standard should be created from all of the samples, see section 2.3,
Examples of experimental design. Sufficient internal standard must be
prepared to allow enough to be included on every gel in the experiment.
3.5.2 Protein labelling with the CyDye DIGE Fluor minimal dyes
The recommended concentration of the protein sample is
5-10 mg/ml. Although samples containing 1 mg/ml have been
successfully labelled using the protocol below.
The example below illustrates labelling of an E. coli lysate using
400 pmol of dye to label 50 µg of protein.
1
Add a volume of protein sample equivalent to 50 µg to a microfuge
tube. Bulk labelling reactions can be performed by scaling up as
required.
2
Add 1 µl of working dye solution to the microfuge tube containing the
protein sample (i.e. 50 µg of protein is labelled with 400 ρmol of
dye for the labelling reaction).
3
Mix dye and protein sample thoroughly by vortexing.
4
Centrifuge briefly in a microcentrifuge to collect the solution at the
bottom of the tube. Leave on ice for 30 min in the dark.
5
Add 1 µl of 10 mM lysine to stop the reaction. Mix and spin briefly
in a microcentrifuge. Leave for 10 min on ice, in the dark.
Labelling is now finished. The labelled samples can be processed
immediately or stored for at least 3 months at -70 °C in the dark.
3.6 Preparing labelled protein samples for the
first dimension
The main difference between conventional 2-D electrophoresis and
Ettan DIGE system is that the latter will enable up to three different
protein samples to be run on a single 2-D gel. To achieve this you need
to mix the differently labelled protein samples BEFORE the first
dimension run.
At this stage the protein sample will have undergone labelling and the
reaction will have been quenched by the addition of 10 mM lysine, as
described in Section 3.5, Protein sample labelling.
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It is recommended that 50 µg of each labelled protein sample is
combined for each gel.
1
Combine the two or three differentially labelled samples into a
single microfuge tube and mix. One of these samples should be the
pooled internal standard.
2
Add an equal volume of 2× sample buffer to the labelled protein
samples and leave on ice for at least 10 minutes.
The samples are now ready for the first dimension isoelectric focusing
step.
Once 2× sample buffer has been added, it is recommended that the
sample is run immediately on an Immobiline DryStrip. Proceed to
Chapter 4, Focusing using the Ettan IPGphor isoelectric focusing
system, or Chapter 5, Focusing using the Multiphor II isoelectric
focusing system.
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Focusing using the Ettan IPGphor isoelectric focusing system
4 Focusing using the Ettan IPGphor isoelectric
focusing system
4.1 Overview
• Decide whether to rehydrate in the absence (protocol 1) or
presence (protocol 2) of protein sample.
• Wear gloves when handling the Ettan IPGphor IEF unit and related
components to minimize protein contamination.
• Clean all components with IPGphor Strip Holder cleaning solution
(code no. 80-6452-78) and Milli-Q water to remove traces of
protein before and after use.
• Use damp electrode pads.
• Ensure the Immobiline™ DryStrip does not dry out.
• Ensure correct orientation of the Immobiline DryStrip and the
Immobiline DryStrip holder on the Ettan IPGphor™ IEF unit.
• Cover the apparatus to exclude light, taking care not to cover air
vents, ideally use the Ettan IPGphor cover (code no. 80-6465-13)
Metallic covers must not be used under any circumstances.
• Use running conditions appropriate to the protein sample type/load
and Immobiline DryStrip.
• Do not programme the Ettan IPGphor IEF unit to deliver more
than 50 µA per Immobiline DryStrip.
The aim of this chapter is to describe how to use the Ettan IPGphor
Isoelectric Focusing (IEF) System for the first dimension run. Use of
Immobiline DryStrips is also described.
Protein samples, labelled with the different CyDye DIGE Fluor minimal
dyes, are mixed together so that they are focused on the same
Immobiline DryStrip. This ensures that the protein samples, labelled
with different dyes, are subject to exactly the same electrophoretic
running conditions.
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Focusing using the Ettan IPGphor isoelectric focusing system
Please read the 2-D Electrophoresis, Principles and Methods Handbook
(code no. 80-6484-89) and the Ettan IPGphor Isoelectric Focusing
System User Manual (code no. 80-6415-35) prior to operation of the
Ettan IPGphor (IEF) System for detailed instructions and safety
information.
4.2 Immobiline DryStrip rehydration
For all recommended buffer components, please refer to section 8.3.
Immobiline DryStrips must be rehydrated prior to isoelectric focusing.
This can be done with or without the protein sample being present in
the rehydration buffer. Up to 12 Immobiline DryStrip holders, or 8
IPGphor Cup Loading Strip Holders, of the same length can be placed
on the Ettan IPGphor IEF unit for any one protocol. There are two
protocols that can be followed using the Ettan IPGphor IEF unit. For
samples under 100 µl the cup loading method is recommended. For
dilute protein samples and preparative gels (> 350 µg), the in-gel
rehydration method may be more appropriate. However other factors
may also influence the choice of protocol.
Protocol 1: rehydration in the absence of protein sample
The Immobiline DryStrips are rehydrated in the Immobiline DryStrip
Reswelling Tray. The protein samples are loaded onto the Immobiline
DryStrip using a cup loading technique. The protein samples are then
focused on the Ettan IPGphor IEF unit.
Protocol 2: rehydration in the presence of protein sample
The Immobiline DryStrips are rehydrated in the Immobiline DryStrip
Reswelling Tray in the presence of the protein samples. The protein
samples are then focused on the Ettan IPGphor IEF unit. Both the
Immobiline DryStrip holders and the IPGphor Cup Loading Strip
Holders can be used for this protocol. However, only the use of
IPGphor Cup Loading Strip Holders will be described here.
Information on using Immobiline DryStrip holders can be found in the
Ettan IPGphor Isoelectric Focusing System User Manual (code no.
80-6415-35).
4.2.1
Calculating the volume of buffer required to rehydrate an
Immobiline DryStrip
Rehydration buffer is used to rehydrate Immobiline DryStrips and can be
used on its own (protocol 1) or combined with labelled protein
(protocol 2).
Up to three CyDye DIGE Fluor minimal dye labelled protein samples
can be mixed together and separated on a single Immobiline DryStrip.
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When using protocol 1 (rehydrating in the absence of protein sample),
rehydrate with rehydration buffer only. The volume of rehydration buffer
must not exceed the determined volumes for the Immobiline DryStrip
size shown in Table 4-1. For example, rehydrate a 24 cm Immobiline
DryStrip in 450 µl rehydration buffer.
When using protocol 2 (rehydrating in the presence of protein sample),
rehydrate with rehydration buffer mixed with the protein samples. The
volume of rehydration buffer used will depend on the volume of protein
(and 2× sample buffer) required.
Table 4-1. Rehydration volumes of Immobiline DryStrips
Immobiline DryStrip length (cm)
7
11
13
18
24
Total volume per strip (µl)
125
200
250
350
450
4.3 Protocol 1 – Rehydration of Immobiline DryStrips in the
absence of protein samples
The Immobiline DryStrip Reswelling Tray has 12 independent reservoir
slots that each hold a single Immobiline DryStrip. Separate slots allow
the rehydration of individual Immobiline DryStrips in the correct
volume of solution.
1
Slide the protective lid completely off the tray. Ensure that the tray
is clean and dry.
2
Level the tray by turning the levelling feet until the bubble in the
spirit level is centred.
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3
Pipette the appropriate volume of rehydration buffer into each slot
(Table 4-1). Deliver the buffer slowly along the slot. Remove any
large bubbles.
Note: To ensure complete sample uptake, do not apply excess
rehydration buffer.
4
Remove the protective cover from the Immobiline DryStrip.
5
Position the Immobiline DryStrip with the gel side down and the
pointed (acidic) end of the strip against the end of the slot closest to
the spirit level. Lower the Immobiline DryStrip onto the solution.
To help coat the entire Immobiline DryStrip, gently lift and lower
the strip along the surface of the solution. Be careful not to trap
bubbles under the Immobiline DryStrip.
6
Overlay each Immobiline DryStrip with PlusOne™ DryStrip Cover
Fluid to prevent evaporation and urea crystallization.
7
Slide the lid onto the Immobiline DryStrip Reswelling Tray and
allow the Immobiline DryStrips to rehydrate at room temperature.
A minimum of 10 h is required for rehydration; overnight is
recommended.
4.3.1
Cup loading the labelled protein sample onto the Immobiline
DryStrip
When performing first dimension IEF better separations can be
obtained by applying samples via cup loading onto separately
rehydrated Immobiline DryStrips. The IPGphor Cup Loading Strip
Holder features a movable, disposable sample cup that can be easily
and securely sealed against the gel surface for applying up to 100 µl of
sample solution. The movable electrodes of the IPGphor Cup Loading
Strip Holder can be positioned to accommodate Immobiline DryStrip
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lengths up to 24 cm. Paper electrode pads should be used with the
electrodes to minimize protein streaking.
Fig 4-1. IPGphor Cup Loading Strip Holder (bottom) and 24 cm Immobiline
DryStrip Reswelling Tray (top) for use with Immobiline DryStrip gels.
Fig 4-2. IPGphor Cup Loading Strip Holder. With movable electrodes and sample
cup, the IPGphor Cup Loading Strip Holder accommodates Immobiline DryStrips
up to 24 cm long.
After the Immobiline DryStrip has been rehydrated for at least 10 h in
the Immobiline DryStrip Reswelling Tray, the Immobiline DryStrip can
be transferred to the IPGphor Cup Loading Strip Holder.
1
Pre-prepare electrode pads by cutting 5 mm × 15 mm pieces from
the IEF Electrode Strips (code no. 18–1004–40). Place on a clean
dry surface such as a glass plate and soak with distilled water.
Remove excess water by blotting with filter paper.
Note: It is important that the pads are damp and not wet. Excess water
may cause streaking.
2
To remove an Immobiline DryStrip from its slot in the Immobiline
DryStrip Reswelling Tray, slide the tip of a pair of forceps along the
sloped end of the slot and into the slight depression under the
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Focusing using the Ettan IPGphor isoelectric focusing system
Immobiline DryStrip. Hold the end of the strip with the forceps and
lift the strip out of the tray.
3
Allow excess PlusOne DryStrip Cover Fluid to run off the
Immobiline DryStrip onto a piece of tissue. Do not allow the gel
side to touch the tissue as it may stick to it.
4
Place the Immobiline DryStrip gel side up with the basic end (flat
end of Immobiline DryStrip) flush with the flat end of the IPGphor
Cup Loading Strip Holder.
5
Place a pre-prepared damp electrode pad onto the acidic and basic
ends of the gel.
6
Clip down the electrodes firmly onto the electrode pads. Ensure
that there is good contact with the Immobiline DryStrip and the
metal on the outside of the strip holder.
Note: Determine the point of sample application. The optimal
application point depends on the characteristics of the sample.
When the proteins of interest have acidic pIs or when SDS has
been used in sample preparation, sample application near the
cathode is recommended. Anodic sample application is
necessary with pH 6-11 gradients and preferred when pH 3-10
gradients are used. The optimal application point can vary with
the nature of the sample. Empirical determination of the optimal
application point is best. See Appendix E for recommended
running conditions.
7
Clip a loading cup onto either the acidic or basic end of the strip so
it is positioned between the two electrodes. The cup should form a
good seal with the Immobiline DryStrip.
8
To check for a good seal fill the cup to the top with PlusOne
DryStrip Cover Fluid. Observe the level of the fluid to check if it is
decreasing. If a leak is detected remove the PlusOne DryStrip Cover
Fluid and reposition the sample cup.
9
Apply at least 4 ml of PlusOne DryStrip Cover Fluid to the IPGphor
Cup Loading Strip Holder allowing the oil to spread so it
completely covers the Immobiline DryStrip.
10 Mix together the labelled protein samples and add an equal volume
of the 2× sample buffer (See Section 3.6). Up to 100 µl of a protein
sample can now be loaded into the bottom of the sample cup.
11 Put the clear plastic strip cover onto the strip holder. The strip
holder is now ready to load on the Ettan IPGphor IEF unit.
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12 Go to section 4.4.1, Loading IPGphor Cup Loading Strip Holders
onto the Ettan IPGphor IEF unit.
4.4 Protocol 2 – Rehydration of Immobiline DryStrips in the
presence of protein sample
Note: This is an alternative to Protocol 1 described in Section 4.3, to
load protein samples onto the Immobiline DryStrip.
1
Mix together the labelled protein samples and add an equal volume
of the 2× sample buffer (See Section 3.6).
2
The total volume of labelled protein needs to be made up to the
volume required for each Immobiline DryStrip using the rehydration
buffer (See Section 4.2.1). The following example is given for a
24 cm Immobiline DryStrip:
• One protein sample labelled with one of the dyes: 20 µl
• Three protein samples combined: 20 µl × 3 = 60 µl
• Add an equal volume 2× sample buffer: 60 µl
• Total volume: 120 µl
• A 24 cm Immobiline DryStrip needs a total of 450 µl so add
(450 µl – 120 µl) 330 µl rehydration buffer.
3
Deliver the labelled protein solution slowly to the centre of the slot
in the Immobiline DryStrip Reswelling Tray. Remove any large
bubbles.
4
Now continue with the rehydration instructions given in
Section 4.3 from point 4, page 44.
5
Transfer the rehydrated Immobiline DryStrip, following the
instructions in Section 4.3.1 but omitting points 7, 8 and 10.
4.4.1
Loading IPGphor Cup Loading Strip Holders onto the Ettan
IPGphor IEF unit
Place the IPGphor Cup Loading Strip Holders in the correct position on
the Ettan IPGphor IEF unit platform. The anodic (acidic) and cathodic
(basic) plate areas have designated marks on them for the correct
positioning of the strip holders with respect to the strip length.
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4.4.2 Recommended isoelectric focusing parameters
A series of recommended programmes for the first dimension are given
in Appendix E. Instructions are also given in the Ettan IPGphor
Isoelectric Focusing System User Manual (code no. 80-6415-35) for
programming the instrument and in the pack leaflet supplied with the
Immobiline DryStrips.
Focusing parameters for different pH gradients of Immobiline
DryStrips and different protein loadings need to be optimized but there
are some general rules that can be followed:
1
The more protein that is loaded onto an Immobiline DryStrip the
greater the total power, measured in voltage hours (Vh) needed to
completely focus the protein sample.
2
Wide range Immobiline DryStrips such as the pH 3–10 range will
require fewer Vh to focus an equal amount of protein loaded on a
narrow range Immobiline DryStrip such as a pH 5.5–6.5.
3
Longer Immobiline DryStrips such as a pH 3-10, 24 cm will require
more Vh to completely focus a protein sample than its 18 cm,
13 cm or 7 cm counterparts.
Cover apparatus to exclude light taking care not to cover the air vents,
ideally use the IPGphor cover. Do not use a metallic cover.
4.5 How to store Immobiline DryStrips after the proteins
have been focused
If the Immobiline DryStrip is not run immediately on the second
dimension gel, it can be stored at –70 °C in a sealed container. The
container has to be rigid because a frozen Immobiline DryStrip is very
brittle and can easily be damaged, equilibration tubes are therefore
recommended, (code no. 80-6467-79).
Do not equilibrate Immobiline DryStrips prior to storage, this must be
carried out immediately before the second dimension separation.
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Focusing using the Multiphor II
isoelectric focusing system
5.1 Overview
• Decide whether to rehydrate in the absence (protocol 1) or
presence (protocol 2) of protein sample.
• Use damp electrode pads.
• Ensure the Immobiline DryStrip does not dry out.
• Ensure correct orientation of the Immobiline DryStrip and the gel
aligner.
• Cover the apparatus to exclude light.
• Use running conditions appropriate to the protein sample type/load
and Immobiline DryStrip.
The Multiphor™ II IEF unit can be used instead of the Ettan IPGphor
IEF unit to focus proteins in the first dimension on an Immobiline
DryStrip.
Please read the 2-D Electrophoresis, Principles and Methods Handbook
(code no. 80-6484-89) and the Multiphor II Isoelectric Focusing System
User Manual (code no. 18-1103-43) prior to operation of the Multiphor
II system for detailed instructions and safety information.
There are two commonly used methods to rehydrate the Immobiline
DryStrips for use on the Multiphor II IEF unit. Both methods will be
described here.
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For samples under 100 µl the cup loading method is recommended. For
dilute protein samples and preparative gels (> 350 µg), the in-gel
rehydration method may be more appropriate. However other factors
may also influence the choice of protocol.
Protocol 1: rehydration in the absence of protein sample
The Immobiline DryStrips are rehydrated in the Immobiline DryStrip
Reswelling Tray then the protein samples are loaded onto the
Immobiline DryStrips using a cup loading technique. The protein
samples are then focused on the Multiphor II IEF unit.
Protocol 2: rehydration in the presence of protein sample
The Immobiline DryStrips are rehydrated in the Immobiline DryStrip
Reswelling Tray in the presence of the protein sample. The protein
samples are then focused on the Multiphor II IEF unit.
5.2 Protocol 1 - Rehydration of Immobiline DryStrips in the
absence of protein sample
The Immobiline DryStrip Reswelling Tray has 12 independent reservoir
slots that can each hold a single Immobiline DryStrip. Separate slots
allow the rehydration of individual Immobiline DryStrips in the correct
volume of solution.
1
Slide the protective lid completely off the tray. Ensure that the tray
is clean and dry.
2
Level the tray by turning the leveling feet until the bubble in the
spirit level is centered.
3
Pipette the appropriate volume of rehydration buffer into each slot
(Table 5-1). Deliver the buffer slowly to the centre of the slot.
Remove any large bubbles.
Note:
50
To ensure complete sample uptake, do not apply excess
rehydration buffer.
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Table 5-1. Total volume required per Immobiline DryStrip length in the absence of protein
Immobiline DryStrip length
(cm)
7
11
13
18
24
Total volume per strip
(µl)
125
200
250
350
450
4
Remove the protective cover from the Immobiline DryStrip.
5
Position the Immobiline DryStrip with the gel side down and the
pointed (acidic) end of the strip against the end of the slot closest to
the spirit level. Lower the Immobiline DryStrip onto the solution.
To help coat the entire Immobiline DryStrip, gently lift and lower
the strip along the surface of the solution. Be careful not to trap
bubbles under the Immobiline DryStrip.
6
Overlay each Immobiline DryStrip with PlusOne DryStrip Cover
Fluid to prevent evaporation and urea crystallization.
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7
Slide the lid onto the Immobiline DryStrip Reswelling Tray and
allow the Immobiline DryStrips to rehydrate at room temperature.
A minimum of 10 h is required for rehydration; overnight is
recommended.
After the Immobiline DryStrip has been rehydrated in the Immobiline
DryStrip Reswelling Tray, the strips can be transferred to the Multiphor
II IEF unit.
5.3 Preparing the Immobiline DryStrip Kit
This section deals with the set-up and running of the rehydrated
Immobiline DryStrips on the Multiphor II IEF unit.
Before removing the Immobiline DryStrips from the Immobiline
DryStrip Reswelling Tray, prepare the Multiphor II Immobiline
DryStrip Kit and the electrode strips.
The components of the 2–D Immobiline DryStrip Kit include a tray and
electrode holder, anode and cathode electrodes, a DryStrip aligner, a
sample cup bar and sample cups.
5.3.1 Preparing the Immobiline DryStrip Kit
1 Clean all components of the Immobiline DryStrip Kit with a
suitable detergent. Rinse thoroughly with Milli-Q water, and allow
to dry.
52
2
Confirm electrical connections on the Multiphor II IEF unit. Check
that the red bridging cable in the Multiphor II IEF unit is connected.
3
Set the temperature on MultiTemp™ III Thermostatic Circulator to
20 °C. Position the cooling plate on the Multiphor II IEF unit and
ensure that the surface is level. Turn on MultiTemp III Thermostatic
Circulator.
4
Pipette approximately 10ml of PlusOne DryStrip Cover Fluid onto
the cooling plate.
5
Position the Immobiline DryStrip tray on the cooling plate so the
red (anodic) electrode connection of the tray is positioned at the top
of the plate near the cooling tubes. Remove any large bubbles
between the tray and the cooling plate; small bubbles can be
ignored. The PlusOne DryStrip Cover Fluid at this point serves to
ensure good thermal contact between the cooling plate and the tray.
6
Connect the red and black electrode leads on the tray to the
Multiphor II IEF unit.
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7
Pour about 15 ml of PlusOne DryStrip Cover Fluid into the
Immobiline DryStrip tray.
8
Place the Immobiline DryStrip aligner groove-side up, into the tray
on top of the PlusOne DryStrip Cover Fluid. The presence of air
bubbles between the strip positions under the DryStrip aligner will
not affect the experiment. Avoid getting PlusOne DryStrip Cover
Fluid on top of the aligner at this point, as it interferes with
visualization of the grooves.
9
Cut two IEF electrode strips to a length of 110 mm.
10 Place the electrode strips on a clean flat surface such as a glass plate.
Soak each electrode strip with distilled water. Blot with filter paper
to remove excess water.
Note: Electrode strips must be damp, not wet. Excess water may cause
streaking.
11 To remove an Immobiline DryStrip from its slot in the Immobiline
DryStrip Reswelling Tray, slide the tip of a pair of forceps along the
sloped end of the slot and into the slight depression under the
Immobiline DryStrip. Hold the end of the strip with the forceps and
lift the strip out of the tray. Allow excess of PlusOne DryStrip
Cover Fluid to run off the Immobiline DryStrip onto a piece of
tissue. Do not allow the gel side to touch the tissue as it may stick
to it.
12 Immediately transfer the rehydrated Immobiline DryStrips to
adjacent grooves of the aligner in the Immobiline DryStrip tray,
ensuring that the gel side is uppermost.
13 Place the strips with the pointed (acidic) end at the top of the tray
near the red electrode (anode). The blunt end should be at the
bottom of the tray near the black electrode (cathode). Align the
Immobiline DryStrips so that the gel edges are lined up.
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14 Place the moistened electrode strips across the cathodic and anodic
ends of the aligned Immobiline DryStrips. The electrode strips must
be in contact with the gel surface of each Immobiline DryStrip.
15 Each electrode has a side marked red (anode) or black (cathode).
Align each electrode over an electrode strip, ensuring that the
marked side corresponds to the side of the tray giving electrical
contact.
16 When the electrodes are properly aligned, press them down to
contact the electrode strips.
17 Check that the Immobiline DryStrips are still aligned in their
grooves.
If following Protocol 1, go to Section 5.4, Application of sample after
gel rehydration.
If following Protocol 2, the strips are now ready for isoelectric focusing.
For recommended IEF running conditions, please refer to the pack
leaflet supplied with the Immobiline DryStrips.
After the samples have been focused on the Immobiline DryStrip, the
strips can be run immediately on the second dimension gel apparatus
such as the Ettan DALT system or they can be stored for up to 3 months
at -70 °C.
5.4 Application of sample after gel rehydration
If the sample was not applied by means of the rehydration solution, it
must be applied using the sample cups, immediately prior to isoelectric
focusing. When using the Multiphor II IEF unit for Ettan DIGE system
experiments, further optimization of sample loads must be performed.
Note: Determine the point of sample application. The optimal
application point depends on the characteristics of the sample.
When the proteins of interest have acidic pIs or when SDS has
been used in sample preparation, sample application near the
cathode is recommended. Anodic sample application is
necessary with pH 6-11 gradients and preferred when pH 3-10
gradients are used. The optimal application point can vary with
the nature of the sample. Empirical determination of the optimal
application point is best.
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1
Position the sample cup bar: place sample cups on the sample cup
bar, high enough on the bar to avoid touching the gel surface.
2
Check that the strips are correctly positioned in the DryStrip
aligner.
3
Position the sample cup bar so that the sample cups are a few
millimeters away from the cathodic or anodic electrode, depending
on your sample. The sample cups must face the electrode. The
sample cup bar has a spacer on one side.
4
Slide the sample cup bar toward the anode/cathode until the spacer
just touches the anodic/cathodic electrode.
5
Press the sample cups halfway down without touching the
Immobiline DryStrips: move the sample cups into position, one
sample cup above each Immobiline DryStrip, making sure the cup
sits in the middle of the gel. Then press the sample cups down to
ensure good contact with each Immobiline DryStrip.
6
Once the sample cups are properly positioned, pour 70-80 ml of
Immobiline DryStrip Cover Fluid into the tray to completely cover
the Immobiline DryStrips. If the PlusOne DryStrip Cover Fluid
leaks into the sample cups, correct the position of the sample cups,
remove the fluid from the cups with a pipette, and check for leakage
again.
7
Add approximately 150 µl of additional PlusOne DryStrip Cover
Fluid to the sample cups. The Immobiline DryStrips are submerged
under a layer of PlusOne DryStrip Cover Fluid to prevent drying of
the Immobiline DryStrip, precipitation of the components of the
rehydration buffer, and diffusion of gasses into the Immobiline
DryStrip.
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8
Apply the sample as prepared in Section 3.6 (up to 100 µl per strip)
into the sample cups by pipetting under the surface of the PlusOne
DryStrip Cover Fluid. The sample should sink to the bottom of the
cup.
Note:
When sample is applied via sample cups, precipitates can
form at the application point.
For recommended IEF running conditions, please refer to the pack
leaflet supplied with the Immobiline DryStrips.
After the samples have been focused on the Immobiline DryStrip, the
strips can be run immediately on the second dimension gel apparatus
such as the Ettan DALT system or they can be stored for up to 3 months
at –70 °C.
5.5 Protocol 2 - Rehydration of Immobiline DryStrips in the
presence of protein sample
This method is similar to Protocol 1 except that the strips are
rehydrated in the presence of the labelled protein samples.
Mix the protein samples together and add an equal volume of the
2× sample buffer (See Section 3.6, Preparing labelled protein samples for
the first dimension).
The total volume of your labelled protein needs to be made up to the
volume required for each Immobiline DryStrip using the rehydration
buffer (See Table 5-1).
The following example is given for a 24 cm Immobiline DryStrip:
56
1
One protein sample labelled with one of the dyes: 20 µl
2
Three protein samples combined: 20 µl × 3 = 60 µl
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3
Add an equal volume 2× sample buffer: 60 µl
4
Total volume: 120 µl
5
Mix sample and buffer thoroughly.
6
A 24 cm Immobiline DryStrip needs an total of 450 µl so add
(450 µl – 120 µl) 330 µl rehydration buffer
7
Deliver the labelled protein solution slowly to the centre of the slot
in the Immobiline DryStrip Reswelling Tray. Remove any large
bubbles.
8
Now follow the instructions as given in Section 5.2, points 4–7.
9
For preparation of the Immobiline DryStrip Kit see Section 5.3,
Preparing the Immobiline DryStrip Kit.
For recommended IEF running conditions, please refer to the pack
leaflet supplied with the Immobiline DryStrips.
After the samples have been focussed on the Immobiline DryStrip, the
strips can be run immediately on the second dimension gel apparatus
such as the Ettan DALT system or they can be stored for up to 3 months
at –70 °C.
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2–D electrophoresis using Ettan DALT electrophoresis system
6 2–D electrophoresis using Ettan DALT
electrophoresis system
6.1 Overview
• Low fluorescence glass plates must be used for gel electrophoresis
within Ettan DIGE system. Low fluorescence glass plates ensure the
lowest background pixel values of scanned images. See Appendix
H for recommended Amersham Biosciences glass plates. For buffer
details, see section 8.4.
• Low fluorescence glass plates must not be scratched as the
scratches will appear on the image.
• Ensure that the entire casting system is clean, dry and free of any
polymerized acrylamide.
• For best results filter dust and insoluble matter from the acrylamide
solution, prior to APS and TEMED addition.
• Equilibrate focused strips immediately before positioning at the top
of the SDS-PAGE gel.
• Ensure that you use the recommended gel running buffer which
contains 0.2% (w/v) SDS.
• To prepare a gel for spot picking, remember to attach reference
markers to the glass plate treated with Bind-Silane.
• To spot pick from a CyDye DIGE Fluor minimal dye labelled gel,
the gel must be post-stained with SYPRO Ruby to enable
visualization of the unlabelled protein.
6.2 Casting homogeneous Ettan DALT gels
Ettan DALT electrophoresis system is recommended for second
dimension separation. Ettan DALT gels are large enough to
accommodate the longest Immobiline DryStrips (24 cm) and can be run
in batches of up to 12 gels at a time.
For Ettan DIGE system applications it is strongly recommended that low
fluorescence glass plates are used (see Appendix H for ordering details).
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2–D electrophoresis using Ettan DALT electrophoresis system
Ettan DALT gels are poured using the gel caster. Up to 14 Ettan DALT
gels can be prepared in a single batch. For detailed information on
loading gels into the caster and casting Ettan DALT gels consult the
Ettan DALTtwelve system user manual (code no. 80-6476-53) and the
Ettan DALTsix system user manual (code no. 80-6492-49).
Fig 6-1. Ettan DALTsix (left) and Ettan DALTtwelve (right) electrophoresis systems.
Note: If a gel is required for spot picking go to Section 6.6, Preparing
Ettan DALT gels for use with the Ettan Spot Picker.
WARNING! Acrylamide is a neurotoxin. Never pipette by mouth and
always wear protective gloves when working with acrylamide solutions,
Immobiline DryStrips, or surfaces that come into contact with
acrylamide solutions.
6.2.1 Casting homogeneous 2–D gels
1 Ensure the entire gel casting system is clean, dry, and free of any
polymerized acrylamide.
2
Prepare a sufficient volume of water-saturated butanol. Allow 1-2 ml
for each cassette.
3
Make up 100 ml of displacing solution.
4
For a full 14-gel set, make up 900 ml of acrylamide gel stock
solution without adding the 10% (w/v) ammonium persulphate
(APS) or 10% (v/v) N,N,N',N'-tetramethylethylenediamine
(TEMED). This amount of gel solution will provide sufficient
volume to cast gels using either a funnel or a peristaltic pump.
Note: To get the best results from Ettan DALT gels, it is important to
remove dust and insoluble matter from the acrylamide solution.
Any dust in the gel will fluoresce during scanning and will affect
the quantitative results from DeCyder Differential Analysis
Software. To remove dust make up the acrylamide solution
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omitting the APS and TEMED. Filter this solution with a
standard bottle top filter apparatus. After filtering add the APS
and TEMED.
5
Assemble the gel caster, as described in the Ettan DALT
electrophoresis unit user manuals (code nos. 80-6476-53 or 806492-49). The caster should be placed on a level bench or on a
levelling table so that the gel tops are level.
6
Connect the feed tube to either a funnel held in a ring-stand above
the top of the gel caster (about 30 cm) or a peristaltic pump. Insert
the other end of the feed tube into the grommet in the bottom of the
balance chamber.
7
Fill the balance chamber with 100 ml of the displacing solution.
8
Add the appropriate volumes of APS and TEMED only when ready
to pour the gels, and mix thoroughly. Once these two components
are added, polymerization begins and the gel solution should be
completely poured within 10 min.
9
Pour the gel solution into the funnel, taking care to avoid
introducing any air bubbles into the feed tube. If a peristaltic pump
is being used, the flow rate should be increased slowly to the desired
speed to avoid introducing any air bubbles into the feed tube.
10 Introduce the gel solution into the caster until it is about 1-2 cm
below the final desired gel height. Stop the flow of acrylamide and
remove the feed tube from the balance chamber grommet. Once the
feed tube is removed, the dense displacing solution flows down the
connecting tube, filling the V-well and sloped trough at the bottom
of the caster. The remaining acrylamide solution is forced into the
cassettes to the final gel height. The amount of gel solution required
will be 800 to 850 ml for 14 gels.
11 Immediately pipette 1-2 ml of water-saturated butanol onto each gel.
If a peristaltic pump was used to pour the gels, rinse the gel solution
from the pump before it begins to polymerize.
12 Allow the homogeneous gels to polymerize for at least 3 h before
disassembling the caster.
13 Once gels are completely polymerized, remove water-saturated
butanol to a suitable container, and cover the top of the gel with
SDS electrophoresis running buffer for Ettan DALT.
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6.2.2 Checklist
• It is recommended that the gels are prepared at least one day in
advance to ensure reproducible results.
• The gels can be stored in an airtight container at +4 ºC, submersed
in SDS electrophoresis running buffer for Ettan DALT to keep the gels
from drying out. Gels can be stored in this way for up to 2 weeks.
Note: The SDS electrophoresis running buffer for Ettan DALT
electrophoresis system contains 0.2% SDS.
6.3 2–D electrophoresis using Ettan DALT electrophoresis
system
After the Immobiline DryStrips have been focused, the strips can be run
immediately on the 2-D gel apparatus, such as the Ettan DALTtwelve
or the Ettan DALTsix electrophoresis systems.
The second dimension electrophoresis separates the proteins on the
basis of their molecular mass using sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE). The Ettan DALT
electrophoresis system is designed to handle multiple large format 2-D
gels in a simple, efficient, and reproducible manner.
For a more detailed description of the components for preparation of
Ettan DALT gels, consult the Ettan DALTtwelve electrophoresis system
User Manual (code no. 80-6476-53) or the Ettan DALTsix
electrophoresis system User Manual (code no. 80-6492-49).
6.3.1 Equilibration of focused Immobiline DryStrips
1 Prepare SDS equilibration buffer. Prior to use, prepare equilibration
solutions 1 and 2. Allow 10 ml per strip for each equilibration
solution.
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2
With forceps carefully remove the Immobiline DryStrip from the
IPGphor Cup Loading Strip Holder or the Multiphor II. If the
Immobiline DryStrips have been focused and stored frozen, allow
the strips to defrost completely beforehand.
3
Place the Immobiline DryStrips in individual equilibration tubes
(code no. 80-6467-79) with the support film toward the wall.
4
Add 10 ml of the DTT-containing equilibration solution 1 to each
tube.
5
Incubate the strips for 10 min with gentle agitation. Do not overequilibrate, as proteins can diffuse out of the strip during this step.
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6
During equilibration, the gel cassettes are prepared for loading by
rinsing the top of the gels with deionized water, then with SDS
electrophoresis running buffer for Ettan DALT, and draining all buffer
from the top of the gel. Before loading the Immobiline DryStrips,
make sure that the gel surface and plates are dry.
7
Pour off the equilibration solution 1 and add 10 ml of equilibration
solution 2. Incubate the strips for 10 min with gentle agitation. Pour
off the solution and drain thoroughly.
8
During the equilibration step prepare the agarose overlay solution.
6.3.2 Loading of focused Immobiline DryStrips
1 Place the gels in the Ettan DALT cassette rack.
2
After draining the equilibration solution 2, briefly rinse the
Immobiline DryStrips by submerging them in a measuring cylinder
containing SDS electrophoresis running buffer for Ettan DALT.
Note: The SDS electrophoresis running buffer for Ettan DALT
contains 0.2% SDS.
3
For each Immobiline DryStrip, if not prepared earlier: melt an
aliquot of agarose overlay solution in a heating block or boiling water
bath. Allow the agarose to cool slightly and slowly pipette the
molten agarose solution, along the upper surface of the gel, up to
the top of the glass plate. Take care not to introduce bubbles. Do
not allow the agarose to cool or solidify.
4
Holding one end of the Immobiline DryStrip with forceps, carefully
place the Immobiline DryStrip in-between the two glass plates of
the gel. Using a thin plastic spacer, push against the plastic backing
of the Immobiline DryStrip (not the gel itself) and slide the strip
between the two glass plates until it comes into contact with the
surface of the gel.
The strip should just rest on the surface of the gel. Avoid trapping
air bubbles between strip and the gel and avoid piercing the seconddimension gel with the strip.
By convention, the acidic, or pointed, end of the Immobiline
DryStrip is on the left when the shorter of the two plates is facing
the user. The gel face of the strip should not touch the opposite glass
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plate.
5
Once the agarose solution has completely set the gel should be run
in the second dimension as soon as practically possible.
6.3.3 Inserting gels into the Ettan DALT electrophoresis buffer tank
1 Fill the lower buffer tank with SDS electrophoresis running buffer for
Ettan DALT. Turn on the control unit, switch on the pump and set the
temperature to 15 ºC.
2
When the running buffer has reached the desired temperature,
insert the loaded gel cassettes with the Immobiline DryStrips in
place. Push blank cassette inserts into any unoccupied slots. Load
the unit from back to front. Gel cassettes and blank cassette inserts
slide much more easily into the unit if they are wet. Use SDS
electrophoresis running buffer for Ettan DALT from a wash bottle to wet
the cassettes and inserts as they are being loaded into the unit.
When all 12 slots are filled, the buffer level should be slightly below
the level of the buffer seal gaskets.
3
Pour SDS electrophoresis running buffer for Ettan DALT into the top of
the buffer tank to the fill line.
4
Program the desired run parameters into the control unit, close the
lid of the buffer tank, and press start/stop to begin electrophoresis.
Recommendation: For electrophoresis runs of six or fewer gels, it is
helpful to alternate gel cassettes with blank cassette inserts. Alternating
cassettes will make it easier to remove the cassettes from the unit
following the run. The blank cassette inserts are removed first, leaving
a larger gap that makes it easier to grasp and remove the gel cassettes.
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6.4 Recommended running conditions
16 h Overnight run, 15 °C
2 W per gel*
8 h duration, 15 °C
4 W per gel*
4 h duration, 15 °C
8 W per gel*
* Run until the bromophenol blue dye front reaches the bottom of the
gel.
Note: These run times are recommended for 12 gels. The run times
provided should only be used as guidelines. Decreasing the
number of gels per run allows increased Watts per gel (up to a
maximum of 10 W per gel) which reduces run times. Blank gel
cassettes must be substituted for gels when running reduced
numbers of gels.
6.5 Checklist
1
After the gels have run they can now be scanned immediately. Keep
the gels between the glass plates. Go to Chapter 7.
2
Protein spots in gels will diffuse so you should scan the gels as soon
as possible. If you cannot scan the gels immediately store in SDS
electrophoresis running buffer for Ettan DALT, at ambient temperature,
in the dark. This should only be a short term measure if the gels can
be scanned that day. Any longer than this, the gels should be stored
at +4 ºC and kept moist, but care should be taken to allow the gels
to reach room temperature before scanning. Gels scanned more
than a day after running are likely to show significant diffusion of
the protein spots.
3
Do not fix the gels in gel-fix before the gels are scanned as this may
affect DeCyder Differential Analysis Software quantitation of
CyDye DIGE Fluor minimal dye labelled proteins.
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6.6 Preparing Ettan DALT gels for use with the Ettan Spot
Picker
To identify proteins in a 2–D experiment the protein spots are picked
from the gel using the Ettan Spot Picker. Ettan Spot Picker and DeCyder
Differential Analysis Software have been designed specifically to
interact and pick spots from gels as large as the Ettan DALT gels. To
ensure that the correct protein spots detected in DeCyder Differential
Analysis Software are picked, the gels need to be cast with two
reference markers under the gel. The gel also has to be bound to the
glass plate to ensure that the gel does not deform during the staining,
imaging and picking processes.
6.6.1 Gel preparation
Spot picking with Ettan Spot Picker requires gels that are immobilized
on a backing. It is recommended that the glass plate is treated with a
Bind-Silane solution to immobilize the gel onto the glass plate.
Note: To scan a gel with fluorescently labelled proteins (either prelabelled or post-stained), it is important that commonly available
plastics are not used as the gel backing. Most plastic materials
will fluoresce intensely at the wavelengths used for scanning.
Ettan Spot Picker is designed to perform spot picking from
1-1.5 mm thick, 8-18% polyacrylamide gels.
6.6.2 Cleaning and Bind-Silane treating glass plates
The following protocol for treatment of glass plates was optimized for
PlusOne Bind-Silane from Amersham Biosciences (code no.
17-1330-01).
66
1
Thoroughly scrape off any residual bound gel with a plastic scraper
and wash the plate in 1% Decon™(v/v) (branded Contrad™ in the
USA) with a soft sponge to further remove the gel.
2
Leave the plate to soak in 1% Decon(v/v) overnight. On the
following day, wash the plate with a soft sponge.
3
Rinse the plate with water and leave the plate to soak in
1% HCl(v/v) for 1 h.
4
Wash the plate in 1% Decon(v/v) with a soft sponge, then rinse with
double distilled water.
5
Dry the plate using a lint-free tissue or leave to air dry in a dust free
environment. If not to be used immediately, please store in a dust
free environment.
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6
Prepare the Bind-Silane working solution:
Table 6-1. Bind-Silane working solution.
Reagent
Ethanol
Glacial acetic acid
Bind-Silane
Double distilled H2O
7
Quantity
8 ml
200 µl
10 µl
1.8 ml
Pipette 2-4 ml (depending on plate size) of the above solution over
the whole surface of the plate and wipe it over with a lint-free tissue
until it is dry. Cover the plate with a lint-free tissue to prevent dust
contamination and leave on the bench for 1.5 h (minimum one
hour) for excess Bind-Silane to evaporate.
Note: If the Bind-Silane is not left to dry sufficiently before the glass
plates are assembled for casting, the solution will evaporate off
the treated plate and coat the facing glass surface. This will cause
the gel to stick to both plates when it sets.
The gels will stay attached to Bind-Silane treated glass during
electrophoresis, staining procedures, scanning and storage.
6.6.3 Reference markers
If a gel is used for spot picking after electrophoresis, then the reference
markers (code no. 18-1143-34) must be attached to the treated glass
plate before gel pouring.
6.6.4 Positioning the reference markers
It is important that the markers are appropriately placed on the treated
surface of the Bind-Silanized plate. The markers should be placed
according to the following protocol. Take care not to place the markers
where they will interfere with the pattern of protein spots in the gel.
1
Measure the length of the treated plate edge.
2
Place the marker approximately half-way along this edge, away
from the spacer, but not so far as to interfere with the protein spot
pattern. The marker should not touch the spacer. Make sure that
the markers are firmly stuck to the plate by pressing down with a
lint free tissue or powder free glove.
3
Repeat steps 1 and 2 for the other edge of the treated backing plate.
4
When finished, the markers should be in positions similar to those
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shown below.
Fig 6-2. Diagram showing the preferred position of reference markers on the
gel backing, with the gel backing lowermost.
5
Pour gel following the instructions in Section 6.2.1, Casting
homogeneous 2–D gels.
6.6.5 Loading Immobiline DryStrips onto a picking gel
The orientation of the Immobiline DryStrip and the reference markers
are critical to ensure that the picking gel is easily matched to the
analytical gels in DeCyder Differential Analysis Software, and that the
correct spots are picked from the gel when the picklist is exported to
the Ettan Spot Picker.
1
After a picking gel has been poured containing suitable reference
markers, position the gel so the front of the reference markers are
facing you (i.e. adhered to the back glass plate).
2
Load the Immobiline DryStrip after equilibration described in
Section 6.3.1, Equilibration of focused Immobiline DryStrips,
ensuring that the acidic (pointed end) of the Immobiline DryStrip is
on the left hand side of the gel as shown in Fig 6-2.
3
The gel can now be run.
Refer to Appendix D for details of staining and scanning protocols for
spot-picking.
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7 Using Typhoon Variable Mode Imager with
Ettan DIGE system
7.1 Overview
• After switching on the Typhoon Variable Mode Imager, leave to
warm up for 30 min before scanning.
• Place the gel on the platen: Use the Gel Alignment Guides if scanning
assembled gels.
• Select Fluorescence Acquisition Mode and select the appropriate
Setup scan parameters.
• Select Tray setting.
• Select scan Orientation referring to the Gel Orientation Guide to ensure
the correct option is chosen.
• Select Press Sample if scanning assembled gels.
• Choose Pixel size. Use 500 or 1000 µm for pre-scans and 100 µm
for quantitative analytical scans.
• Select Focal Plane.
• Select DIGE File Naming Format to ensure that unique filenames can
be generated for each scan channel.
• Press SCAN to start.
The instructions in this chapter explain how to best to use Typhoon
Variable Mode Imager for imaging and contain details based on the
Ettan DIGE enhanced Typhoon Scanner Control Software, version 3.0
and ImageQuant Tools software, version 3.0. Users of earlier versions
of software will need to be aware of the following:
Typhoon Scanner Control
DIGE File Naming Format or Tray options are
Softwareonly available in version 3.0 onwards.
ImageQuant Tools Software- Image Cropping, Flicker Function or Export
Data to Excel functionalities are only available
in version 3.0 onwards.
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The changes in the version 3.0 software or later versions are designed
to give improved ease of use with Ettan DIGE system. Users not having
these versions will still be able to use Typhoon Variable Mode Imager
but will need to refer to specific instructions in Appendix F.8,
Instructions for users of Scanner Control Software and ImageQuant
Tools Software (pre-version 3.0). All Typhoon Imagers can be upgraded
to use the enhanced software, please contact your local sales office for
further details.
7.2 Scanning gels using Typhoon Variable Mode Imager
Fluorescence imaging is used for the identification of proteins that are
contained within a matrix. Proteins are separated by electrophoresis
either in one dimension, based on molecular size, or in two dimensions,
using ionic charge and molecular size. To allow the protein positions to
be visualized, the proteins have to be labelled with a fluorescent dye,
this can be done either before or after electrophoresis.
It is important that you read the safety instructions in the Typhoon User
Guide (code no. 63-0028-31) before you start work.
The summary capabilities of the 4 variants of the Typhoon 9000 series
imagers are listed:
Typhoon
Imager
model
8600
8610
9200
9210
9400
9410
Storage
Direct
Direct
Direct
Microarray
phosphor red excited green excited blue excited imaging
autofluorescence fluorescence fluorescence capability
radiography
yes
yes
yes
no
no
yes
yes
yes
no
yes
yes
yes
yes
no
no
yes
yes
yes
no
yes
yes
yes
yes
yes
no
yes
yes
yes
yes
yes
Cy3 dyes, Cy5 dyes and SYPRO Ruby can be detected using any of the
above instruments (SYPRO Ruby can use green 532 nm excitation).
Cy2 dyes require the blue laser. The blue laser also provides optimal
excitation for SYPRO Ruby at 457nm. The 9200 series can be
upgraded to give blue laser capability, please contact your local sales
office for further details. For Ettan DIGE system use, the Typhoon 9400
Variable Mode Imager is the recommended model as all three CyDye
DIGE Fluor minimal dyes can be detected.
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7.3 Turning on and warming up Typhoon Variable Mode
Imager
1
Turn on the Typhoon Variable Mode Imager by switching on the
power supply switch and the instrument on/off switch (situated at
the lower front right side of the instrument). If required, turn on the
power supply to the blue laser module.
2
Leave the instrument to warm up for at least 30 min prior to
scanning. The power indicator light at the front of the instrument
turns on and remains red during a short self-test sequence then
flashes green during initialization and finally remains green.
Typhoon Instrument State displays the status of the instrument, e.g.,
whether the instrument is ready to scan or is initializing. Once the
instrument is warmed up it will display READY status. For more
information refer to Appendix F.1, Typhoon Instrument States.
3
Turn on the computer and monitor following the manufacturer's
recommended procedure.
4
Start the Scanner Control software using the Start menu: Start:
Programs: MD Apps: Typhoon Scanner Control. The Scanner Control
window then appears (see Fig 7-1).
Fig 7-1. Scanner Control Software window.
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7.4 Fluorescence scanning software workflow
The fluorescence scanning software workflow is summarized in the
descriptions in Fig 7-2.
Fig 7-2. Software Workflow and Scanner Control Interface
There is no strict order required for performing the items in Fig 7-2
apart from selecting the Fluorescence mode prior to setting up the
fluorescence scan parameters. Scan modes other than Fluorescence are
available, these are covered in the Typhoon User Guide (code no. 630028-31).
7.5 Placing an assembled Ettan DALT gel or SE 600 Ruby gel
on the platen
For applications using Ettan DIGE system, the recommended glass
plates have low fluorescence characteristics. The gel can be scanned still
assembled within the plates. This has a number of advantages:
• Manipulation is easier and there is less risk of damage to the gel.
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• Scans may be taken prior to running the bromophenol blue dye
front off the gel so images of low molecular weight proteins, that
may otherwise be lost, can be obtained. Gels may then be replaced
in the electrophoresis unit to complete the run. Similarly runs can
be extended and multiple images captured to obtain greater
separation of higher molecular weight proteins.
Note: Wear powder free gloves. The powder used in laboratory gloves
can fluoresce and may also scatter light affecting image quality.
1
Ensure that the glass platen and sample lid are clean. Refer to
Appendix F.2, Cleaning the glass platen and sample lid.
2
Ensure that the gel glass plates are clean, dry and free from lint.
3
Position the main bar of the Gel Alignment Guide onto the platen
as shown in Fig 7-3 to 7-6. The gel alignment guides allow
assembled gels to be scanned. The Gel Alignment Guides position
Ettan DALT and SE 600 Ruby gels in a defined region of the platen,
so that the gel area selected is predefined in the software. When
using alternative gel formats, refer to Appendix F.3, Assembling
gels other than Ettan DALT and SE 600 Ruby onto the Typhoon
Platen.
4
Using the grippers, position the dried glass plate assembly with one
edge on the spacer and against the front location bar.
5
Gently lower the assembled gel onto the platen using the gripper. If
using an Ettan DALT plate, load the gel with the top of the gel
orientated to the left of the platen. If using an SE 600 Ruby plate,
load the gel with the top of the gel towards the top of the platen.
6
Close the sample lid.
grippers
front location bar
Fig 7-3. Ettan DALT Gel Alignment Guides in position
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The front location bar is an alignment guide that rests inside the platen
well at the edge closest to the user. Additionally it has spacers to lift the
gel above the platen surface. The bars at the back are grippers that have
a dual function. They enable the user to raise and lower the edge of the
gel easily and they also provide the spacer required to keep the gel clear
of the platen surface.
Fig 7-4. Ettan DALT Gel Alignment Guides in position on the Typhoon Variable
Mode Imager platen
Fig 7-5. Ettan DALT Gel Alignment Guides in Use
grippers
positioning bar
Fig 7-6. SE 600 Gel Alignment Guides
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The SE 600 Gel Alignment Guides are used in a similar manner to the
Ettan DALT Gel Alignment Guides except the gels are oriented with the
top of the gel towards the top of the platen. In addition up to four
SE 600 Ruby gels may be loaded at a time.
For details of how to position other gel sizes, naked gels or postelectrophoresis stained gels, please refer to Appendix F.3, Assembling
gels other than Ettan DALT and SE 600 Ruby onto the Typhoon Platen.
7.6 Selection of fluorescence acquisition mode
The options within the Acquisition Mode settings enable the scan
parameters to be defined.
1
Use the drop down window under the Acquisition Mode heading to
select Fluorescence. Scan modes other than Fluorescence are
available, these are covered in the Typhoon User Guide (code no.
63-0028-31).
2
Select the Setup button to activate the Fluorescence Setup Window as
shown below.
3
Select the number of scan channels to be programmed for the
sample on the platen. Between one and four channels can be
programmed. To select or deselect additional scan channels, click
the Use check box. Selection of the Use check boxes has to be
performed in sequential numerical order to select or deselect scan
channels.
4
Select appropriate emission filters from the Emission Filter list. This
list displays the filters that are installed on the Typhoon Variable
Mode Imager along with a description of the typical filter use. The
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Scanner Control software automatically suggests the laser to use
with the emission filter selected. If desired a different laser may be
selected by the user.
Note: Selecting an alternative laser to that suggested by the software
will cause a warning check message to be displayed. If you do
not want to see the message the Channel Data Warning check box
should be ticked. Switching off the Channel Data Warning message
will prevent the user being alerted in the event of alternative laser
settings being selected. Until the Channel Data Warning check
box is reselected, subsequent users will not be warned of
incorrect laser selection.
The following emission filters and laser combinations are
recommended:
Table 7-1. Emission filters and laser combinations
1
Dye
Emission Filter (nm)
Laser
Cy2
520 BP 40
Blue2 (488)
Cy3
580 BP 30
Green (532)
Cy5
670 BP 30
Red (633)
SYPRO Ruby
610 BP 30
1
Blue1 (457)
For SYPRO Ruby the Blue2 (488) laser also gives acceptable results
although PMT voltages would have to be adjusted. The Blue1 (457)
laser is recommended for Typhoon Variable Mode Imager (9400 and
9410) models, and the Green (532) laser can be used with all other
models.
The CyDye DIGE Fluor minimal dye filter and laser combinations
are selected to give the optimum results with minimal cross-talk.
76
5
Set the PMT voltage for each scan wavelength. This can be adjusted
by using either the up/down arrows or by clicking on the voltage set
and over-typing the new voltage. A quick pre-scan at 500 or
1 000 µm pixel resolution should be performed initially to identify
a suitable voltage. For further details, please refer to Appendix F.4,
Pre-scanning to identify a suitable PMT voltage.
6
Select the required sensitivity for each scan wavelength. There are
three options available: Normal; Medium and High. The Normal
scan setting is usually sufficiently sensitive for 2–D DIGE
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applications. For more information refer to the Typhoon User
Guide (code no. 63-0028-31).
7
Select the Sensitivity check box. It is essential that this is selected for
analytical gels to ensure that all scans are carried out as individual
scans. For further information about the Auto Link Mode and
Speed check box, please refer to Appendix F.5, Setting the required
sensitivity.
8
Click OK on completion of setting up the Fluorescence scan settings.
This will accept the changes prior to returning to the Scanner
Control window.
7.7 Selection of tray options
The Tray options can be used to define the scan area. There are two
options for setting the scan area:
• Option 1 - Predefined Tray area, e.g. DIGE Ettan DALT or
DIGE SE 600.
In this mode, the scan area is pre-defined and the software is able
to recognize where individual gels will be located. This will enable
it to pre-crop the individual gel areas, resulting in separate file
outputs for each gel. Further cropping is normally required to
remove supplementary data. DIGE Ettan DALT and DIGE SE 600
pre-defined trays should only be used with gels that have been
positioned using Gel Alignment Guides.
The Tray Editor can be used to create tray areas for gel types other
than Ettan DALT or SE 600 Ruby (see appendix F.9).
• Option 2 - User Select.
In this mode, only the scan area is pre-defined. The software is
unable to recognize where individual gels will be located, therefore
a single file output will be generated. Cropping will need to be
performed manually following the scan.
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7.7.1
1
Option 1 - Predefined Tray area, e.g. DIGE Ettan DALT or
DIGE SE 600.
Within the Tray set-up area, use the drop down window to select
the appropriate predefined tray, e.g., the DIGE Ettan DALT or DIGE SE
600 option.
2
Click on the numerical drop down window in the Tray set-up area.
3
Define the number of gels to be scanned. In the DIGE Ettan DALT
mode up to 2 gels can be selected whilst in the DIGE SE 600 mode
up to 4 gels can be selected. Fig 7-7 shows the effect of selecting the
DIGE Ettan DALT tray with 2 gels to be scanned, the area marked
with 1s shows the position of the first gel and the area marked with
2s shows the position of the second gel.
Fig 7-7. Selection of DIGE Ettan DALT tray.
Using these trays it is recommended that Ettan DALT gels are scanned
with the top of the gel or IEF strip oriented to the left edge of the platen
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and SE 600 Ruby gels are scanned with the top of the gel towards the
top (back edge) of the platen.
7.7.2 Option 2 - User Select
1 To select a scan area to use in the Scanner Control Software screen
platen view, ensure that User Select has been chosen in the Tray setup area.
2
Start from the bottom left corner of the area being defined and hold
the left mouse button down whilst moving to the upper right
extreme of the area required then release the button.
7.8 Setting gel orientation and scan resolution
The gel can be orientated in one of eight different ways, the selected
orientation is left to the discretion of the user, but the following
guidelines should help:
• The Typhoon Variable Mode Imager illuminates and collects data
from underneath the sample.
• To minimize the scan time:
place the gel near the A1 corner of the platen grid
position the gel so the shortest edge is along the numbered side
of the glass platen.
The physical gel orientation should be noted by the user, the gel
orientation option in the software determines the file output
orientation.
Fig 7-8. Scan Orientation screen
To aid selection of the correct character the Gel Orientation Guide can
be overlaid above the gel once it is in position on the Typhoon platen.
The appearance of the overlaid letter “R” on the Gel Orientation Guide
indicates which character to select on the Typhoon Scanner Control
Software screen.
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It is normal practice to view a scanned 2–D gel image in the orientation
shown in Fig 7-9.
Fig 7-9. Standard Gel Image Orientation
The orientation button in the Scanner Control Software window can be
used to obtain all combinations of the corresponding gel positions
viewed from above the platen. These are shown in Appendix F.7, Gel
orientations.
It is especially important to ensure the correct orientation has been
selected if the gel image is to be used either in combination with other
images, such as in DeCyder Differential Analysis Software multiple gel
analysis, or for generating pick lists, e.g. for use with Ettan Spot Picker.
If the user selects the wrong orientation and does not notice until the
scan has been completed there is a facility to re-orientate the data in
ImageQuant Tools Software using Image:Rotate Image.
80
1
Set the gel orientation by holding the left mouse button down with
the pointer over the letter “R” in the orientation window, within
the options menu.
2
Select the appropriate orientation. For more information, refer to
Appendix F.7.
3
Choose the most appropriate Pixel size. For the purpose of
performing a prescan, a 1000 µm or 500 µm pixel size is
recommended. For performing an analytical scan, a 100 µm pixel
size is selected for quantitative scans. Higher resolution using 50
µm pixel size does not generally add to the 2–D data but increases
the scan time and file size. Refer to Appendix F.4, Pre-scanning to
identify a suitable PMT voltage.
4
Select the Press Sample option if scanning gels between glass plates.
This will ensure that during the duration of the scan, the inner lid
of Typhoon Variable Mode Imager will exert pressure on the
sample to hold it steady.
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Note: The Press Sample feature should not be used with naked gels or
with wet gels as it can damage the instrument.
See section 9.2.5 of the Typhoon User Guide (code no. 63-0028-31) for
additional information.
5
Select the appropriate Focal Plane. Platen is used for samples in
direct contact with the platen. +3 mm is used for assembled gels or
samples held on a glass plate. This is the setting generally used for
most applications of the Ettan DIGE system.
6
Enter user comments if required (optional). Up to 4 000 characters,
including spaces may be entered. This information is associated
with the scanned image and can be viewed in ImageQuant or
ImageQuant Tools under File:Image Properties:Scan Info.
7.9 Starting a scan
CAUTION! Using a networked drive to save scanned data can slow, or
delay the scan and, at worst, can interrupt the scan. It is recommended
that scans are initially saved onto a local hard disc. Upon scan
completion the files should then be copied onto the networked drives
and successful transfer should be confirmed. To avoid filling up the local
hard disc the file on the local hard disc should then be deleted.
1
Check that the gel is in place and that the Typhoon Variable Mode
Imager instrument lid is shut.
2
Confirm that all the parameters are correct in the Scanner Control
and Fluorescence Setup windows.
3
Check the DIGE File Naming Format box.
Note: Two scan acquisition modes are available. The mode that is used
depends on whether the DIGE File Naming Format check box
has been selected or not. For 2–D DIGE applications, it is
generally recommended that the check box is ticked. Not using
this mode may require file re-naming and re-location of files to
alternative directories at a later stage depending on the analysis
to be performed.
For DIGE file naming format see section 7.9.1.
For Standard file naming format, see section 7.9.3.
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7.9.1 DIGE file naming format
Using the DIGE File Naming Format option results in all files having user
defined (and ideally unique) filenames. All scan images from a given
experiment can be saved into a single user defined folder. This method
of file naming and folder selection results in structures that can be
directly used by DeCyder Differential Analysis Software.
If a single scan setting has been chosen, e.g. for a SYPRO Ruby stained
gel, then the resulting output on scan completion will be a filename.gel
file in the selected folder.
If two or more scan parameter settings were chosen, e.g. for a
Cy2/Cy3/Cy5 gel, then the resulting output upon scan completion will
be a filename.ds file in the selected folder and a new folder called
filename.dir. In this new folder will be the user named.gel files. The
filename.ds file allows the scanned images to be overlaid in
ImageQuant whilst the user named.gel files are the individual scan
channel outputs and can be viewed as separate files.
1
In the Scanner Control window, click the Scan button.
If the tray option is set to User Select, the DIGE File Naming
Format window in Fig 7-10 appears.
If the DIGE Ettan DALT or DIGE SE 600 tray options are selected,
an additional window appears as discussed in Section 7.9.2, Tray
setting with "DIGE Ettan DALT" or "DIGE SE 600" options.
Fig 7-10. DIGE File Naming Format window
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The terms STANDARD, Cy2, Cy3 and Cy5 are automatically
appended to the file. The terms Cy2, Cy3 and Cy5 are picked up from
the emission filter selected for the scan. These terms are also
automatically picked up during DeCyder Differential Analysis
Software image analysis so reducing the requirement for user input.
The term STANDARD can be assigned to any one of the scan channels
by clicking the relevant check box, if not required the STANDARD
name can be removed by clicking the NONE check box. The filenames
can also be manually edited.
2
Once filenames have been set then start the scan by clicking the
Scan button.
7.9.2 Tray setting with "DIGE Ettan DALT" or "DIGE SE 600" options
With either of these tray modes active an additional window appears
on selecting the Scan button within the Scanner Control Software
window, as shown in Fig 7-11.
Fig 7-11. Multiple Sample Naming window.
In the above example two gels have been set-up for scanning, by
selecting Edit Sample File Name… the user can choose the folder and
filename for each gel individually. Entering details using Folder or Base
File Name, allows the user to Set common details for all gels in a single
operation. The Browse option in both cases allows the user to select
existing folders or file name structures. Whichever method is used the
options allow the user to set-up a number of gels for a single scan run
and obtain unique filenames for each gel image.
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7.9.3 Standard file naming format
The DIGE File Naming Format check box is left unselected in this mode.
1
Click the Scan button in the Scanner Control Software window.
If the Tray option is set as User Select, the Save As window appears
(Fig 7-12).
If the DIGE Ettan DALT or DIGE SE 600 tray options are selected an
additional window appears as discussed in Section 7.9.2.
Fig 7-12. The Save As window
2
Type a name in the File name box within the Save As window,
Fig 7-12.
3
Create or select a folder to store the data in.
4
Start the scan by clicking on Save.
If a single scan channel setting has been chosen, e.g. for a SYPRO Ruby
stained gel, then the resulting output on scan completion will be a
filename.gel file in the selected folder. If two or more scan parameter
settings were chosen, e.g. for a Cy2/Cy3/Cy5 gel, then the resulting
output on scan completion will be a filename.ds file in the selected
folder and a new folder called filename.dir. In this new folder will be a
filename.ds file and files called UNSEP1.gel, UNSEP2.gel and
UNSEP3.gel. The filename.ds file allows the scanned images to be
overlaid in ImageQuant whilst the UNSEPn.gel files are the individual
scan channel outputs and can be viewed as separate files.
The use of the standard filenaming format with multiplexed images,
results in the same UNSEPn.gel file format for every gel that is scanned.
This repeat use of the same filenames is not compatible with DeCyder
Differential Analysis Software. See section 7.9.1 for recommended
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filenaming format if DeCyder Differential Analysis Software analysis is
required.
7.10 Monitoring the scan progress
Once the scan has started, the preview window appears. For unlinked
scans a single image channel appears for each scan programmed, the
images appearing one at a time. For linked scans, two image channels
appear simultaneously. Where more than one gel is scanned using the
DIGE Ettan DALT or DIGE SE 600 tray settings, a drop down
numerical menu appears allowing the user to monitor each of the gels
as the images are generated.
Saturated data is displayed in red in the preview window. If saturated
data is seen the user can cancel the scan and re-set the PMT voltage
without having to complete the whole scan.
7.11 Image file output and cropping nonessential
information
7.11.1 File output
The image files created are labelled as filename.gel. This uses a modified
16 bit TIF format. An additional text file, filename.ds, also exists and
this links image file data together for image overlays in ImageQuant.
To exclude nonessential information from the image files, ImageQuant
Tools should be used to crop the images prior to analysis in DeCyder
Differential Analysis Software.
7.11.2 Image cropping
The Typhoon platen area is sufficiently large enough to enable multiple
gel scanning to be performed. A single scan image may be captured for
each scan channel and then the individual gel areas are saved using
ImageQuant Tools. For 2–D DIGE users it is recommended that the gel
alignment guides are used and the Tray option set to DIGE Ettan DALT
or DIGE SE 600 as appropriate, this pre-crops the individual gel areas
although further cropping is normally required to remove
supplementary data.
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1
Enlarge the overlaid dataset images to maximize the critical data
using the Create Frame button.
2
Define an area of interest within ImageQuant Tools using the
dashed square button (or Tools:Define Region of Interest or Ctrl+R).
Either use the “Tools” menu or select the
button.
Fig 7-13. Defining a Region of interest in ImageQuant
86
3
Define the region of interest by moving the mouse cursor to an
appropriate start point (e.g. upper left) then hold the left mouse
button down whilst dragging the pointer to an appropriate end
point (e.g. lower right). Crop using Edit:Crop Dataset or the crop
current dataset button on the toolbar.
4
For DeCyder Differential Analysis Software analysis, save the
cropped images by selecting:
File:Export Gel Files from Dataset to Folder, select an appropriate folder
and confirm or enter a suitable filename. This method only saves
the name.gel files and allows images from multiple gels to be saved
in a common folder.
5
To retain dataset functionality, save the cropped images by
selecting: File:Save As…, select an appropriate folder and confirm or
enter a suitable filename.
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7.12 Creating and using templates
Templates can be created containing frequently used scan parameters.
1
Follow the scan setup procedures in Section 7.6, Selection of
fluorescence acquisition mode
2
Press Templates at the top of the Scanner Control screen.
3
Select Save As Template and the window below appears.
4
Check box labelled Set as Default Template if the new template is to
be set as the default.
Note:
5
Comments in the User Comment box and the Press Sample
parameter are not saved with the template.
Select Templates:Load to load templates in the Scanner Control
window.
See the Typhoon User Guide for additional information (code no.
63-0028-31).
7.13 Shut-down procedure.
1
Turn the Typhoon Imager off using the switch at the front right
hand side of the instrument.
2
Close down all software on the computer
3
Shut down the computer using the start menu: Start:Shut down:
Shut down the computer.
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8 Recipes
8.1 Sample preparation and labelling
8.1.1
Standard cell wash buffer
Reagent
Quantity
Final concentration
Tris (100 mM, pH 8.0)
5.0 ml
10 mM
Magnesium acetate (1 M)
0.25 ml
5 mM
Make up to 50 ml with distilled water
Store at 4 ºC. Stable for 1 month.
8.1.2 How to make the standard cell lysis buffer
1 Decide whether to use cell lysis buffer 1 or 2. The cell lysis buffer
option 1 is very similar to option 2 except that thiourea is added,
which has been shown to solubilize many more proteins.
2
While the cell lysis buffer is still cold (due to the dissolving urea and
thiourea) adjust the whole solution to pH 8.5 using dilute HCl. It
is important to adjust the pH of the solution while it is still chilled,
as labelling will be carried out on ice.
3
Confirm the pH of your cell lysis buffer by spotting 5 µl on a pH
indicator strip.
4
Make the volume of the cell lysis buffer up to 100 ml.
5
The cell lysis buffer can now be aliquoted and stored at –20 ºC.
8.1.3
Standard cell lysis buffer (option 1) - contains thiourea.
Reagent
Quantity
Final concentration
Tris (1M not pH’d)
3.0 ml
30 mM
Thiourea (MW 76.12)
15.22 g
2M
Urea (MW 60.06)
42.0 g
7M
CHAPS (MW 614.89)
4g
4% (w/v)
Dilute HCl
–
–
Make up to 100 ml with distilled water
Adjust to pH 8.5 with the dilute HCl. Small aliquots can be stored
at –20 ºC, for up to 3 months.
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8.1.4
Standard cell lysis buffer (option 2)
Reagent
Quantity
Final concentration
Tris (1 M, not pH’d)
3.0 ml
30 mM
Urea (MW 60.06)
48.0 g
8M
CHAPS (MW 614.89)
4g
4% (w/v)
Dilute HCl
–
–
Make up to 100 ml with distilled water
Adjust to pH 8.5 with the dilute HCl. Small aliquots can be stored
at –20 ºC, for up to 3 months.
8.1.5
10 mM Lysine
Reagent
Quantity
Final concentration
L-Lysine (MW 182.6)
0.018 g
10 mM
Make up to 10 ml with distilled water
Store at -20 ºC. Stable for 6 months.
8.1.6
1 M Magnesium acetate
Reagent
Quantity
Final concentration
Magnesium acetate
21.45 g
1M
(MW 214.5)
Make up to 100 ml with distilled water
Store at 4 ºC. Stable for 3 months.
8.2 Gel preparation and running
8.2.1
2× Gel loading buffer
Reagent
Quantity
Final concentration
Tris (1 M, pH 6.8)
12 ml
120 mM
Glycerol (87% [v/v])
23 ml
20% (v/v)
SDS (MW 288.38)
4g
4% (w/v)
DTT (MW 154.2)
3g
200 mM
Bromophenol Blue
A few grains
trace
Make up to 100 ml with distilled water
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8.2.2
12.5% 1-D PAGE gel composition (for SE 600 Ruby)
Reagent
Quantity for 100 ml of a 12.5% gel
Acrylamide/Bis 40% (w/v)
32.0 ml
Tris (1.5M, pH 8.8)
25.0 ml
10% (w/v) SDS
1.0 ml
10% (w/v) APS
1.0 ml
(undiluted) TEMED
40 µl
*add immediately prior to use*
Make up to 100 ml with distilled water
8.2.3
1% (w/v) Agarose gel sealant
Reagent
Quantity
Final concentration
Low melting agarose prep
1g
1% (w/v)
Make up to 100 ml with distilled water
Store at room temperature. Stable for 1 month.
8.2.4
1.5 M Tris, pH 8.8
Reagent
Quantity
Final concentration
Tris (MW 121.14)
545 g
1.5 M
6M HCl to adjust to pH 8.8 About 150 ml
Make up to 3 000 ml with distilled water
Adjust to pH 8.8 and store at 4 ºC. Stable for 1 month.
8.2.5
10% (w/v) SDS
Reagent
Quantity
Final concentration
SDS
100 g
10%
Make up to 1 000 ml with distilled water
Store at room temperature. Stable for 6 months.
8.2.6
10% (w/v) APS
Reagent
Quantity
Final concentration
Ammonium Persulphate
1g
10%
Make up to 10 ml with distilled water
Prepare fresh on day of use then discard.
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8.2.7
1× SDS electrophoresis running buffer
Reagent
Quantity
Final concentration
Tris (MW 121.14)
60.5 g
25 mM
Glycine (MW 75.07)
288 g
192 mM
SDS (MW 288.38)
20 g
0.1% (w/v)
Make up to 20 l with distilled water
Store at room temperature for up to 3 months.
8.2.8
1.0 M Tris, pH 8.0
Reagent
Quantity
Final concentration
Tris (MW 121.14)
121.1 g
1.0 M
6M HCl to adjust to pH 8.0
–
–
Make up to 1 000 ml with distilled water
Adjust to pH 8.0 and store at 4 ºC. Stable for 1 month.
8.2.9
Water saturated butanol
Reagent
Butan-2-ol
Distilled water
Quantity
50 ml
50 ml or more
until two layers
are visible
Final concentration
–
–
Shake to mix and once completely separated, use the top layer to
overlay gels. Store at room temperature. Stable for 6 months.
8.2.10 2× sample buffer
The 2× sample buffer and rehydration buffer used both contain the same
concentration of urea, thiourea (if present) and CHAPS. A stock
solution is prepared containing these core components and is aliquoted
for storage at -20 °C. Immediately prior to use, DTT and Pharmalytes
are added to this stock solution to give either 2× sample buffer or
rehydration buffer. Once DTT and pharmalytes have been added, the
solutions are unstable and must be used the same day, discarding any
unused material.
If you used standard cell lysis buffer (option 1) use 2× sample buffer
(option 1) and rehydration buffer (option 1).
If you used standard cell lysis buffer (option 2) use 2× sample buffer
(option 2) and rehydration buffer (option 2).
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2× Sample/rehydration buffer stock (option 1)
Reagent
Quantity
Final concentration
Urea (MW 60.06)
10.5 g
7M
Thiourea (MW 76.12)
3.8 g
2M
CHAPS (MW 614.89)
1g
4% (w/v)
Make up to 25 ml with distilled water
Small aliquots (e.g. 2.5 ml) can be stored at -20 ºC. Stable for 6 months.
2× Sample/rehydration buffer stock (option 2)
Reagent
Quantity
Final concentration
Urea (MW 60.06)
12 g
8M
CHAPS (MW 614.89)
1g
4% (w/v)
Make up to 25 ml with distilled water
Small aliquots (e.g. 2.5 ml) can be stored at -20 ºC. Stable for 6 months.
2× Sample buffer
Reagent
2 × sample/rehydration
buffer stock*
Pharmalyte™, broad range
pH 3-10
DTT (MW 154.2)
Quantity
2.5 ml
Final concentration
50 µl
2% (v/v)
50 mg
2% (w/v) (20mg/ml,
130 mM)
Do not store, prepare fresh before use.
*Use buffer stock option 1 or 2, depending on the 2× sample buffer
required.
8.2.11 40% (w/v) CHAPS
Reagent
Quantity
Final concentration
(3-[(3-Cholamidopropyl)20 g
40%
dimethylammonio]-1propane sulfonate)
Make up to 50 ml with distilled water
Store at –20 ºC. Stable for 6 months.
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8.3 First dimension IEF
8.3.1 Rehydration buffer
The 2× sample buffer and rehydration buffer used both contain the same
concentration of urea, thiourea (if present) and CHAPS. A stock
solution is prepared containing these core components and is aliquoted
for storage at -20 °C. Immediately prior to use, DTT and Pharmalytes
are added to this stock solution to give either 2× sample buffer or
rehydration buffer. Once DTT and pharmalytes have been added, the
solutions are unstable and must be used the same day, discarding any
unused material.
If you used standard cell lysis buffer (option 1) use 2× sample buffer
(option 1) and rehydration buffer (option 1).
If you used standard cell lysis buffer (option 2) use 2× sample buffer
(option 2) and rehydration buffer (option 2).
2× Sample/rehydration buffer stock (option 1)
Reagent
Quantity
Final concentration
Urea (MW 60.06)
10.5 g
7M
Thiourea (MW 76.12)
3.8 g
2M
CHAPS (MW 614.89)
1g
4% (w/v)
Make up to 25 ml with distilled water
Small aliquots (e.g. 2.5 ml) can be stored at -20 ºC. Stable for 6 months.
2× Sample/rehydration buffer stock (option 2)
Reagent
Quantity
Final concentration
Urea (MW 60.06)
12 g
8M
CHAPS (MW 614.89)
1g
4% (w/v)
Make up to 25 ml with distilled water
Small aliquots (e.g. 2.5 ml) can be stored at -20 ºC. Stable for 6 months.
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Rehydration buffer
Reagent
2× sample/rehydration
buffer stock*
Pharmalyte, broad range
pH 3-10
DTT (MW 154.2)
Quantity
2.5 ml
Final concentration
25 µl
1% (v/v)
5 mg
0.2% (w/v)
(2 mg/ml, 13 mM)
Do not store, prepare fresh before use.
*Use buffer stock option 1 or 2, depending on the rehydration buffer
required.
8.3.2
SDS Equilibration buffer stock solution
Reagents
Quantity
Final concentration
Tris (1.0 M, pH 8.0)
20 ml
100 mM
Urea (MW 60.06)
72.07 g
6M
Glycerol (87% [v/v], MW
69 ml
30% (v/v)
92.09)
SDS (MW 288.33)
4g
2% (w/v)
Make up to 200 ml with double distilled water
This stock solution can be stored at room temperature. Stable for 6
months. Add DTT or Iodoacetamide for equilibration solution 1 or 2.
8.3.3
Equilibration solution 1
Reagent
SDS equilibration buffer
stock solution
DTT (MW 154.2)
Quantity
100 ml
Final concentration
–
0.5 g
0.5% (w/v)
Solution should be used immediately. Do not store.
8.3.4
Equilibration solution 2
Reagent
SDS equilibration buffer
stock solution
Iodoacetamide (MW 185.0)
Quantity
100 ml
Final concentration
–
4.5 g
4.5% (w/v)
Solution should be used immediately. Do not store.
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8.4 Loading and running 2–D gels
8.4.1
10% (v/v) TEMED
Reagent
Quantity
Final concentration
TEMED (MW 116.2)
0.5 ml
10%
Make up to 5 ml with distilled water
Prepare fresh on day of use then discard.
8.4.2
12.5% 2–D PAGE gel composition for Ettan DALT
Reagents
Quantity for 900 ml of a 12.5% gel
Acrylamide/Bis 40% (w/v)
281.25 ml
Tris (1.5 M, pH 8.8)
225 ml
10% (w/v) SDS
9.0 ml
10% (w/v) APS
9.0 ml
10% (v/v) TEMED
1.24 ml
* Add immediately prior to use*
Make up to 900 ml with distilled water
Prior to addition of APS and TEMED, filter complete solution through
a 0.2 micron filter into a clean bottle. Allow solution to warm to room
temperature prior to addition of APS and TEMED and before pouring
the gel.
8.4.3
Displacing solution
Reagents
Quantity
Final concentration
Tris (1.5 M, pH 8.8))
25 ml
375 mM
Glycerol (87% (v/v))
57.5 ml
50% (v/v)
Bromophenol blue
A few grains
Trace
Make up to 100 ml with distilled water
Prepare fresh and use immediately. Do not store.
8.4.4
SDS electrophoresis running buffer for Ettan DALT
Reagents
Quantity
Final concentration
Tris (MW 121.14)
60.5 g
25 mM
Glycine (MW 75.07)
288 g
192 mM
SDS (MW 288.38)
40 g
0.2% (w/v)
Make up to 20 l with distilled water
Store at room temperature. Stable for 3 months.
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8.4.5
0.5% (w/v) Agarose overlay solution
Reagent
SDS electrophoresis running
buffer for Ettan DALT
Low melting point agarose
prep
Bromophenol blue
Quantity
100 ml
Final concentration
-
0.5 g
0.5% (w/v)
Few grains
Trace
Mix components in a 250 ml conical flask and heat on a low setting in
the microwave for 1 minute. Ensure all the agarose has melted. Allow
the solution to cool slightly before use. Store at room temperature. Do
not keep for more than 1 month.
8.5 Post staining gels
8.5.1
SYPRO Ruby gel fix
Reagent
Methanol
Acetic acid
Make up to 1 000
Quantity
Final concentration
300 ml
30% (v/v)
75 ml
7.5% (v/v)
ml with distilled water
Store at room temperature. Stable for 3 months.
8.5.2
SYPRO Ruby gel destain
Reagent
Methanol
Acetic acid
Make up to 1 000
Quantity
Final concentration
100 ml
10% (v/v)
60 ml
6% (v/v)
ml with distilled water
Store at room temperature. Stable for 3 months.
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Recipes
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Introduction to DeCyder Differential Analysis Software
9 Introduction to DeCyder Differential Analysis
Software
9.1 Introduction
DeCyder Differential Analysis Software is a fully automated image
analysis software suite for detection, quantitation, positional matching
and differential protein abundance analysis. The algorithms and
workflow of the software have been specifically designed for the
analysis of multiplexed images generated using CyDye DIGE Fluor
dyes. This maximizes the advantages of running more than one sample
per gel thus enabling the inclusion of a spot-specific pooled internal
standard.
This chapter briefly outlines the features and capabilities of the
software. For a detailed guide, please refer to the DeCyder Differential
Analysis Software User Manual (code no. 18-1173-16) which includes
a series of tutorials designed to provide new users with the means to
gain a rapid understanding of the software’s capabilities. The tutorials
comprise step-by-step guides that take the user through the main
applications of the software by employing real data. The DeCyder
Differential Analysis Software User Manual also provides a detailed
technical account encompassing all aspects of the built-in functionality
of the software, which can be used as a source of further information.
9.2 Integration of DeCyder Differential Analysis Software
within Ettan DIGE system
9.2.1 Overview of Ettan DIGE system and experimental design
Ettan DIGE system is based on the technique of two-dimensional
difference gel electrophoresis (2–D DIGE). In this approach, protein
samples are labelled with up to three spectrally distinct, mass and
charge matched, fluorescent dyes. Labelled proteins are then mixed and
resolved simultaneously on the same 2–D gel. Sample multiplexing
greatly refines the detection of changes between samples at the protein
level. Spot maps can be overlaid and compared directly for samples
resolved on the same 2–D gel. In addition, variation in spot intensities
due to experimental factors (for example protein loss during sample
entry into the strip) will be the same for each sample on the same 2–D
gel. Thus the relative concentrations of the samples in a gel will be
effectively unchanged. This increases the confidence with which protein
differences can be both detected and quantified using Ettan DIGE
system. The sample multiplexing capability enables accurate protein
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abundance quantitation by the inclusion of a pooled internal standard
on each gel. The pooled internal standard represents the average of all
the samples being analyzed. Consequently, every protein present across
all samples within the experiment, will be represented within each gel.
Each gel will therefore contain one image, generated from an identical
sample, facilitating inter-gel spot matching and quantitation (for more
details on the features and use of a pooled internal standard, see
Chapter 2). A further advantage of this approach is that the number of
gels run in an experiment is halved (when three dyes and the
recommended experimental design are used).
9.2.2
Advantages of using DeCyder Differential Analysis Software with
Ettan DIGE system
DeCyder Differential Analysis Software was developed as part of the
Ettan DIGE system and therefore all the advantages of the 2–D DIGE
technique are utilized in the software.
• The novel co-detection algorithm in the software takes advantage
of the identical spot patterns generated when multiple samples are
separated on the same gel. The algorithm performs identical spot
detection on images originating from the same gel.
• The software utilizes an experimental design incorporating a
pooled internal standard by performing gel-to-gel matching on
pooled internal standard images only. The spot patterns of each
internal standard are mapped to a master image (usually the
internal standard image with the most spots). This process enables
the comparison of protein abundance between samples on different
gels.
• DeCyder Differential Analysis Software allows the analysis of
experimental designs with various degrees of complexity. A simple
control/treated experiment through to a multi-condition
experiment addressing factors such as dose and time can be
performed in a single analysis.
• The presence of the same pooled internal standard on every gel
enables accurate normalization of the individual experimental
samples, decreasing gel-to-gel and software analysis variation. Use
of a pooled internal standard also allows the relationship between
any number of samples to be accurately quantified and statistically
analyzed. This approach results in unparalleled accuracy allowing
experimental conclusions to be drawn with high confidence. No
other 2–D electrophoresis technique currently available is capable
of resolving multiple samples in this manner and hence Ettan DIGE
system is exceptional in exploiting the use of a pooled internal
standard on every gel.
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9.3 Structure of DeCyder Differential Analysis Software
9.3.1 Introduction
Image analysis is performed in DeCyder Differential Analysis Software
using a number of algorithms, some of which are patent pending. The
complex algorithms associated with each step in the analysis form part
of the in-built functionality of DeCyder Differential Analysis Software,
and are performed automatically with minimum user intervention.
DeCyder Differential Analysis Software comprises four modules that
are schematically represented in Fig 9-1. below.
Fig 9-1. Scheme showing the image analysis workflow in DeCyder Differential
Analysis Software
The functionality of the four modules is briefly outlined below, with a
more detailed description of each given in Sections 9.3.2-9.3.5.
DIA (Differential In-gel Analysis)
Protein spot detection and quantitation on a set of images, from the
same gel. Features include background subtraction, in-gel
normalization and gel artefact removal.
BVA (Biological Variation Analysis)
Matching of multiple images from different gels to provide statistical
data on differential protein abundance levels between multiple groups.
Batch Processor
Fully automated image detection and matching of multiple gels without
user intervention.
XML Toolbox
Extraction of user specific data facilitating automatic report
generation.
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DeCyder Differential Analysis Software is compatible with Windows™
XP Professional operating system. It employs operator-friendly
graphical user interface (GUI), with pull-down menus and toolbars.
Powerful spot detection, background removal, quantitation and
matching algorithms are utilized in the software to analyze the digital
data from the gel images. These algorithms provide accurate
quantitative data for each protein spot thereby allowing differential
protein abundance analysis to be performed.
The combination of text and XML output files means that all the data
generated within the DeCyder Differential Analysis Software can be
easily stored and accessed for further investigation.
9.3.2
DIA (Differential In-gel Analysis)
Fig 9-2. Scheme showing spot co-detection on images from a single gel in the
DeCyder DIA module.
The DeCyder DIA module processes the images from a single gel
(usually the pooled internal standard image and experimental sample
images), performing spot detection and quantitation. The DIA
algorithms detect spots on a cumulative image derived from merging
multiple images from the same gel. This method of co-detection ensures
that all spots are represented in all images. The DIA module quantifies
the spot volumes for each image and expresses these values as a ratio,
thereby indicating changes in abundance by direct comparison of
corresponding spots. This ratio parameter can be used, in small scale
experiments, to directly evaluate changes between two labelled protein
samples (e.g. control and drug treated samples). Alternatively, the ratio
can be used for protein spot quantitation of a sample against a pooled
internal standard (Fig 9-2.) to allow accurate inter-gel protein
abundance comparisons (see Chapter 2).
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Once spot maps incorporating an internal standard have been analyzed
in the DIA module, the spot data can be used in DeCyder BVA for
accurate quantitative inter-gel studies. Generally when multiple gel
analyses are performed, only the spot detection and quantitation
algorithms are utilized in the DIA module. Data is then transferred to
the BVA module for inter-gel analysis. Data can be exported in XML or
text file format file format for multi-gel analysis in DeCyder BVA,
querying in DeCyder XML toolbox or copying and pasting into
applications such as Microsoft™ Word™ and Excel™.
9.3.3
BVA (Biological Variation Analysis)
Fig 9-3. Scheme showing matching between images from three gels and
statistical analysis in the DeCyder BVA module.
DeCyder BVA processes multiple gel images, performing gel-to-gel
matching of spots and enabling quantitative comparisons of protein
abundance across multiple gels. The BVA module processes gel image
sets that have undergone spot detection in the DIA module. DeCyder
BVA utilizes the .XML files (co-detected spotmap) generated in the DIA
module together with the original scanned image files. The images are
matched to a single master image, identifying common protein spots
across the gels. Using the recommended experimental design, this step
usually involves matching between the pooled internal standard images
from each gel. Various experimental designs can be assigned within the
BVA module, facilitating the statistical analysis tools to highlight
proteins that demonstrate significant changes in abundance under
different experimental conditions.
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Additional in-built functionality allows post-matching activities to be
performed:
• Molecular weight calculation
• Isoelectric point calculation
• Database linkage
• Spot picking list generation
Data can be saved in a .BVA file format from which spot picking lists
can be exported as text files. Data can also be exported in an .XML
format for querying in DeCyder XML toolbox or copying and pasting
into applications such as Microsoft Word and Excel.
9.3.4 Batch Processor
The Batch Processor executes both the DeCyder DIA and BVA
processes, performing fully automated spot co-detection and inter-gel
matching of multiple gel images. Once the Batch Processor has been set
up with the necessary image files and parameters, the gels are processed
sequentially without user intervention. The Batch Processor module
significantly reduces the hands-on analysis time required.
9.3.5 XML Toolbox
Large amounts of data are generated when a workspace is created and
analyzed using DeCyder Differential Analysis Software. It is useful to
be able to save this data in a format that can be efficiently stored and
queried. Data is exported from the different software modules using a
common .XML file format called DeCyder XML. XML is a structured
file format, making it easy to access data from DeCyder Differential
Analysis Software workspaces for other applications. The .XML file
format is partly used to transfer data between the different modules of
the software but it is also used to make data available for processing by
other software tools such as database building packages. The XML
Toolbox also provides an interface for linking Ettan DIGE system data
with Ettan Laboratory Workflow System. DeCyder XML Toolbox is a
toolbox shell housing a range of tools for extraction of data from the
different .XML files produced within DeCyder Differential Analysis
Software. Two basic tools are supplied to create Tabbed text files and
Web tables. This enables users to create tools to convert their data into
text files or html files (potentially other data formats can be supported
for conversion).
Note: For further details on all aspects of the DeCyder Differential
Analysis Software, please refer to the DeCyder Differential
Analysis Software User Manual (code. no. 18-1173-16). This is
available as a hard copy or from the Amersham Biosciences
website (http//www.AmershamBiosciences.com/dige)
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A.1
Appendix A How to sonicate cells
A.1 How to sonicate cells
Sonication with a small (micro) probe sonicator provides the best and
most consistent method for disrupting cells for use in analyses using
Ettan DIGE system. Sonication will completely disrupt the cells and
will also shear the DNA and RNA in the cell, resulting in better 2–D
gels. The presence of large amounts of unsheared nucleic acids can
cause vertical streaking in a 2–D gel. DNase and RNase can be added
but these might appear as protein spots on the 2–D gel.
This protocol has been used to disrupt a range of cell and tissue types.
1
Clean the probe of the sonicator with 70% (v/v) Ethanol and dry
thoroughly with a clean tissue.
2
Place the sample tube in a beaker of ice water to keep it cold during
sonication.
Note: If the sample is allowed to heat up in the presence of urea, some
proteins will be carbamylated which will alter the charge (pI) of
the protein, producing charge trains of protein across the gel.
3
Ensure that the sonicator microtip is suspended with its tip well
below the surface of the liquid in the sample tube, but not touching
the sides.
4
Start with the sonicator set initially at a low setting, such as 25%
power or 5 µm amplitude. Increase the sonication gradually so that
small white bubbles appear around the tip of the probe. This is the
ideal sonication level. When the bubbles appear, do not increase the
power further as this will cause the protein sample to froth. If the
samples do froth, briefly microfuge them and then continue
sonicating.
5
When the sonication level has been optimized, sonicate for
20 second bursts followed by a 1 minute cooling period. Repeat this
process five times. Alternatively some sonicators have a pulse
facility which can be used to achieve the equivalent sonication time.
This process is completed when the sonicated solution is less cloudy
than the starting solution.
6
After sonication, centrifuge the samples at 12 000 g for 5 min at
+4 °C. Transfer the supernatant to a new tube and discard any
pellet.
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A.1
106
7
Now return to Section 3.2.3, step 13. to check the lysate pH prior
to protein quantification.
8
Protein quantification may now be performed using the Protein
Determination Reagent (USB, code no. 30098) or Ettan 2-D Quant
Kit (code no. 80-6483-56).
9
Samples may now be aliquoted and stored at -70 °C.
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Appendix B How to prepare and run a 1-D PAGE
gel on the Hoefer SE 600 Ruby
Standard Vertical Electrophoresis gel
system
The Hoefer™ SE 600 Ruby gel system is a vertical gel system that
allows wells to be formed in the top of the acrylamide gel so that up to
15 different protein samples can be run simultaneously on the same
1-D gel.
The Hoefer SE 600 Ruby gel casting system is used in conjunction with
low fluorescence glass plates (measuring 18 × 16 cm) and 1 mm thick
× 2 cm wide grey spacers. For detailed information on how to use the
SE 600 Ruby consult the Hoefer SE 600 Ruby User Manual. (code no.
80–6353–79).
Fig B-1. The SE 600 Ruby electrophoresis system
Acrylamide is a neurotoxin. Gloves must be worn throughout this
procedure.
B.1 Gel plate preparation
For Ettan DIGE system applications it is strongly recommended that low
fluorescence glass plates are used (see appendix H for ordering details).
Note: Do not use plates that are scratched. Scratches may appear on
the images, and may affect the accuracy of the data analysis.
1
Wash glass plates with detergent using a soft sponge. This prevents
the plates from acquiring scratches. Rinse with double distilled
water.
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B.1
2
Preferably allow the plates to air dry. If necessary, dry the plates
with lint-free tissue.
3
Clean the spacers.
4
Place the sealing gasket in the base of the casting stand.
5
Loosen all of the screws on both of the grey gel clamps and slot
them into either side of the gel casting stand.
6
Lay one of the glass plates down horizontally on a sheet of lint-free
tissue. Place the spacers at either edge of the plate. Carefully lay the
other glass plate on top.
7
Lift the plates up into a vertical position and slot into the gel casting
stand, so that the edges of the plates with the spacers fit against the
clamps. Make sure that the gel plate edges are flush with the edge
of the spacers and that the spacers are aligned with the edges of the
gel clamps all the way down the side of the plates. Tighten the
screws onto the plates.
8
Place the black cams into the holes at the bottom of the gel casting
stand and twist 180° together to lock the gel plates onto the stand.
Fig B-2. Components of the SE 600 Ruby system.
9
108
Pipette molten 1% (w/v) agarose gel sealant around the bottom edge
of the gel plates to prevent any leakage when the gel is poured.
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B.2 Preparing an acrylamide gel
1
Make a 12.5% 1-D PAGE gel (for SE 600 Ruby) as described in
Section 8.2.2, 12.5% 1-D PAGE gel composition (for SE 600
Ruby).
2
Pour the acrylamide mix between the glass plates until it reaches the
top.
3
Immediately after pouring insert a 1 mm plastic comb with
15 wells.
4
Leave the gel to set for at least 2 h.
B.3 Loading the protein samples on the gel
1
Remove the plastic comb and wash the wells thoroughly with
distilled water followed by a final rinse with electrophoresis
running buffer.
2
Replace the gel assembly in the casting stand and hold in place with
the black cams. Use a blank cassette on the other side of the casting
stand if only one gel has been cast.
3
Prepare and load samples following the instructions given in
Appendix C.1, Testing a new protein lysate for successful labelling.
4
Attach the upper chamber to the buffer tank.
5
Transfer the black cam into the holes at the top of the upper
chamber and rotate 90° to lock the gel. Do the same again for the
second gel or blank cassette. Complete the locking by twisting the
cam a further 90°.
6
Carefully lift the whole assembly and remove any excess agarose
stuck to the bottom of the plates.
7
Transfer the whole assembly to the electrophoresis buffer tank.
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B.4
B.4 Running the 1-D SDS-PAGE gel
110
1
Half-fill the Hoefer electrophoresis lower buffer tank with SDS
electrophoresis running buffer for Ettan DALT and pre-cool to 20 °C.
2
Gently fill the upper reservoir with electrophoresis running buffer,
making sure not to disturb the protein samples that have been
loaded into the wells.
3
Check for leaks prior to starting electrophoresis. This can be done
by filling the reservoir to the noted level and checking after 15 min
to see if the buffer level has changed. If the level has dropped, the
upper reservoir must be removed and replaced, checking that a
tight seal has been formed between the reservoir and the top of the
gel cassettes.
4
Attach the electrophoresis lid assembly to the top of the
electrophoresis apparatus. Check that the electrodes are in the
correct orientation.
5
Set the power pack to deliver 25 mA constant current per gel for 20
min then increase to 40 mA constant current per gel until the
bromophenol blue dye front has reached the bottom of the gel. The
gels must not be allowed to run after this point, to ensure that low
molecular weight proteins of interest are not lost.
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Appendix C Testing a new protein lysate for
successful labelling
C.1 Testing a new protein lysate for successful labelling
It is important to check that labelling of the proteins has worked before
the samples are taken through the 2-D electrophoresis process.
The method involves running a small sample of the freshly labelled
lysate on a 1-D SDS-PAGE gel along with a control lysate already
known to label successfully. The gel is then scanned at the appropriate
wavelength for the relevant CyDye DIGE Fluor minimal dye. The total
fluorescence of each labelled sample is then compared. The method
should also be used to test protein lysates that contain previously
untested chemical components.
1
Label 50 µg of the new protein sample with 400 ρmol of CyDye
DIGE Fluor Cy5 minimal dye. CyDye DIGE Fluor Cy5 minimal dye
has negligible cross talk with the SYPRO Ruby post-stain that
might be used later in the experiment.
2
Add a volume of each CyDye DIGE Fluor minimal dye-labelled
protein lysate equivalent to 50 µg, to a microfuge tube.
3
Add an equal volume of the 2× gel loading buffer to the labelled
protein lysate.
4
Heat the samples at 95 ºC for 5 min to ensure full reduction of the
proteins.
5
Make a serial dilution of each of the lysates in the 2× gel loading
buffer, e.g. 25 µg, 12.5 µg and 6.25 µg.
6
Make a 12.5% SDS-PAGE gel using low fluorescence glass plates.
The gel should be made with wells where the samples will be
loaded. See Appendix B.
7
Load each protein serial dilution in successive lanes on the gel.
8
Run the samples until the Bromophenol Blue dye front has nearly
reached the bottom of the gel.
9
Thoroughly clean the outside of the glass plates with double
distilled water.
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C.1
10 Scan the gel at the appropriate wavelength with Typhoon Variable
Mode Imager.
11 Insert the gel into the scanner in the correct orientation, see Chapter
7, Using Typhoon Variable Mode Imager with Ettan DIGE system.
Fig C-1. CyDye DIGE Fluor Cy5 minimal dye scanned image
12 Quantify the labelling of each protein sample using ImageQuant
software.
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13 Carry out the statistics by opening the image in ImageQuant
software. Draw a single box over the first lane using the
Object:Rectangle Tool. Copy and Paste the rectangle for all of the
samples that need to be tested in the remaining lanes.
Fig C-2. CyDye DIGE Fluor Cy5 minimal dye scanned image. Lanes are
overlaid with identical boxes to give a volume report in ImageQuant.
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C.1
14 In Analysis:Volume Report Setup highlight the boxes Object Name,
Volume, Area and select Results Only in the Print Format section.
15 Generate a volume report by clicking Analysis:Volume Report... in the
drop down menu.
16 Select all the relevant RECT in the Inspector window so that they
are highlighted blue.
17 Generate a volume data set by selecting the Report button in the
Inspector window.
18 Determine the labelling efficiency by comparing the volume of the
new protein samples and the control sample, which are on the same
gel. The labelling efficiency of these should be equivalent.
If labelling is comparable between the control and the new protein
lysates tested (see note below) then samples can now be run on 2-D
gels. See Section 3.6, Preparing labelled protein samples for the first
dimension.
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C.1
Note: If the labelling of the new lysate is poor compared to the control
sample then the reason must determined. The pH of the sample
should be satisfactory, as this has previously been checked with
pH test strips. The simplest explanation is that less of the new
lysate was loaded on the gel than the control lysate. Alternatively
it is possible that a component of the lysate is interfering with the
labelling. Testing by post-staining the gel for total protein using
SYPRO Ruby gel stain can be used to investigate the cause of the
problem, see Fig C-3.
Fig C-3. Decision tree for troubleshooting labelling using 1-D gels.
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C.2
C.2 SYPRO Ruby staining a 1-D gel
1
Dismantle the gel apparatus and prise apart the glass plates.
2
Put the gel into a polypropylene, polycarbonate or polyvinyl
chloride tray. Add the SYPRO Ruby gel fix solution and incubate for
at least 2 h on a shaking platform.
3
Pour off the fixing solution. Cover the gel with SYPRO Ruby stain.
4
Protect from the light, and incubate the gel for at least 2 h with
gentle shaking.
5
Pour off the SYPRO Ruby stain and wash by incubating in
deionized water for 2 h with gentle shaking. Four changes of
deionized water should be used during this step.
6
Wash the gel in SYPRO Ruby gel destain for 1–2 h. Continue to
protect the gel from the light.
7
On completion of the staining protocol, clean and dry two low
fluorescence glass plates with lint free wipes.
8
Place the gel onto one of the clean, dust-free glass plates, with the
wells to one side.
9
Wet the farthest edge of the gel with distilled water.
10 Take a clean piece of low-fluorescence glass and, holding it so it is
angled down and away, place one edge along the farthest edge of
the gel.
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11 Slowly lower the new glass plate onto the gel, taking care not to
form bubbles. A good way to avoid bubbles is to make sure there is
plenty of water on the gel and to gently tap the upper glass plate as
it is lowered onto the gel.
12 Once the gel is held between both glass plates, pick the gel cassette
up and let any excess water drain away. Clean the outside surface
of the glass plates with distilled water and dry with a lint-free wipe.
Care must be taken to ensure that the gel and glass plates do not
slip apart.
13 Place the gel onto the Typhoon Variable Mode Imager platen using
the appropriate Gel Alignment Guide. Scan at the wavelength for
SYPRO Ruby. See Chapter 7, Using Typhoon Variable Mode
Imager with Ettan DIGE system.
14 Compare the volume of fluorescence for each sample following the
instructions from point 12 onwards, section C.1, Testing a new
protein lysate for successful labelling to determine the relative
amounts of protein present in each lane.
An equivalent amount of the new sample and the control sample loaded
on the gel should produce similar fluorescent volumes. If the amount of
protein detected for the new lysate is lower than for the control lysate,
then the samples are probably incorrectly quantified. Protein
quantification should be repeated and samples re-analyzed on a 1-D
SDS-PAGE gel. If the amount of protein detected is similar for both new
and control lysates, this would suggest that there is a chemical
component in the new lysate that is affecting the labelling reaction.
Each non-standard cell lysis buffer should be tested for its effect on the
labelling efficiency using 1-D SDS-PAGE analysis, for standard cell lysis
buffers please refer to section 8.1, Sample preparation and labelling.
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C.2
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D.1
Appendix D Scanning and staining protocols for spot
picking
D.1 Staining protocols
To spot pick from a gel containing CyDye DIGE Fluor minimal dye
labelled samples, the gel must be post-stained, e.g. with SYPRO Ruby.
This ensures that the majority of the unlabelled protein is picked for
mass spectrometry (MS) identification. Other post-staining methods,
such as Coomassie and silver staining can be used, but using these stains
result in a more complex experiment. The migration differences
between the unlabelled and labelled proteins are due to the addition of
a single CyDye DIGE Fluor minimal dye molecule to the labelled
protein, an effect which is more marked for lower molecular weight
proteins. SYPRO Ruby staining allows visualization of the majority of
unlabelled protein which needs to be picked for MS identification.
Gel fixing
Ensure that the proteins on the gel are fixed to prevent the spots
diffusing and being washed away during the post staining process.
The gel fix that is recommended for this process is 30% methanol/7.5%
acetic acid. Use enough of this solution to ensure that the gel is
completely covered. Gels must be incubated in this solution for a
minimum of 2 h.
If a stronger fix (higher concentration of methanol and/or acetic acid)
is used, then the gel may peel away from the backing or crack. If a
weaker fix is used, then the gels must be incubated for a longer time to
ensure that they are fully fixed.
SYPRO Ruby
1
After fixing, place the gel directly into a polypropylene,
polycarbonate or polyvinyl chloride tray.
2
Cover the gel with the SYPRO Ruby stain.
3
Incubate the gel for 5 h or overnight with gentle shaking, protected
from the light.
4
Pour off the SYPRO Ruby stain and wash by incubating in
deionized water for 2 h with gentle shaking. Four changes of
deionized water should be used during this step.
5
Reassemble the gel for scanning as described in Section D.2.
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D.2
For detailed information on creating a spot picking list using the
DeCyder Differential Analysis Software, please refer to the DeCyder
Differential Analysis Software User Manual (code no. 18-1173-16).
D.2 Scanning post-stained gels
If a fluorescent post-electrophoresis stain has been used, follow the
steps outlined below. Work as quickly as possible as some fluorescent
post-stains have poor photo-stability.
120
1
When the staining protocol is finished, clean and briefly rinse with
double distilled water, then dry the back of the glass plate to which
the gel is affixed. Take care not to damage the gel at this point.
2
Place the gel (glass side down) onto a clean, dust-free surface, with
the wells to one side.
3
Wet the farthest edge of the gel with distilled water.
4
Take a clean piece of low-fluorescence glass and, holding it so it is
angled down away from you, place one edge along the farthest edge
of the gel.
5
Slowly lower the new glass plate onto the gel, taking care not to
form bubbles. A good way to avoid bubbles is to make sure there is
plenty of water on the gel and to gently tap the upper glass plate as
it is lowered onto the gel.
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6
When the new plate is flat on top of the gel, pick the gel up and let
any excess water drain away. Dry any water off the outside of the
plates.
7
Place the gel onto the Gel Alignment Guide appropriate for your gel
system and place into a Typhoon Variable Mode Imager. Please
refer to chapter Chapter 7 Using Typhoon Variable Mode Imager
with Ettan DIGE system.
8
Image the gel with the appropriate filter set and exposure times,
making sure that both reference markers are visible in the gel
image. It is recommended that the image resolution for the
analytical and preparative gels are set at the same level and are at
least 100 µm.
9
Ensure that both reference markers can be clearly seen and that
they appear as circles when the gel image is checked. If the markers
cannot be seen, then re-scan the gel, adjusting the area to be
scanned appropriately.
10 When scanning is finished, remove the top plate and place the gel
into gel fix solution for storage.
For instructions on spot picking from the stained gel, please refer to the
DeCyder Differential Analysis Software User Manual (code no.
18-1173-16).
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E.1
Appendix E Recommended experimental
conditions
E.1
Recommended running conditions for IPGphor IEF unit
E.1.1
Protocols for up to 150 µg total protein load
• 24cm pH 3–10NL strips. The following IEF focusing protocol is
recommended.
Anodic cup loading
1.
2.
3.
4.
5.
6.
step+hold
gradient
gradient
gradient
step+hold
step+hold
300 V
600 V
1 000 V
8 000 V
8 000 V
500 V
50 µA
50 µA
50 µA
50 µA
50 µA
50 µA
Total
900 Vh
1 350 Vh
2 400 Vh
13 500 Vh
32 000 Vh
3h
3h
3h
3h
4h
48 h
50 KVh
• Narrow range IPG strips, < pH 8. The following IEF focusing
protocol is recommended.
Cathodic cup loading
1.
2.
3.
4.
step+hold
step+hold
step+hold
step+hold
500 V
1 000 V
8 000 V
500 V
50 µA
50 µA
50 µA
50 µA
Total
500 Vh
1 000 Vh
96 000 Vh
1h
1h
12 h
48 h
97.5 KVh
• Basic IPG strips. The following IEF focusing protocol is
recommended.
Anodic cup loading
Use Destreak™ Rehydration Solution (code no. 17-6003-19) for
rehydration of strips. Destreak Rehydration Solution has been
specifically designed to maintain protein thiol groups in a single
oxidation state, irrespective of sample load, pH range or run length.
The use of Destreak Rehydration Solution for the rehydration of basic
IPG strips prevents streaking, simplifies the protein pattern and
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E.1
produces highly reproducible, well resolved, stable spot patterns, free
from distortion.
Note: Ensure that the concentration of DTT in the 2× sample buffer is
10 mM or less when using Destreak rehydration solution.
1.
2.
3.
4.
5.
6.
step+hold
gradient
gradient
gradient
step+hold
step+hold
300 V
600 V
1 000 V
8 000 V
8 000 V
500 V
50 µA
50 µA
50 µA
50 µA
50 µA
50 µA
Total
900 Vh
1 350 Vh
2 400 Vh
13 500 Vh
48 000 Vh
3h
3h
3h
3h
6h
48 h
66.2 KVh
E.1.2
Protocol for greater than 150 µg total protein loads
• 24cm pH 3–10 strip. The following IEF focusing protocol is
recommended.
In gel rehydration
Extra long and thick electrode pads soaked in rehydration buffer (see Fig E-1)
1.
2.
3.
4.
5.
6.
step+hold
gradient
gradient
gradient
step+hold
step+hold
300 V
600 V
1 000 V
8 000 V
8 000 V
500 V
50 µA
50 µA
50 µA
50 µA
50 µA
50 µA
Total
900 Vh
3h
1 350 Vh
3h
2 400 Vh
3h
13 500 Vh
3h
42 000 Vh 5.25 h
48 h
60.2 KVh
Fig E-1. Diagram illustrating size and positioning of electrode pads for separation
of high protein loads, e.g, preparative gels.
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E.2
The longer, thicker electrode pads, function to soak up unwanted salts.
This helps to maintain the correct pH gradient during the focusing
protocol.
Ideally, strips should be removed immediately on completion of the IEF
program. Programs may be concluded with a low voltage (500 V) step
for 48 hours. If strips cannot be removed immediately after focusing,
this step is intended to maintain the focusing of the proteins after the
IEF program is complete. Samples left at 500 V for more than 2 hours
should be refocused by ramping to 8 000 V over a period of 30 minutes,
before removing the strips.
An IPGphor lid cover should be placed over the IPGphor apparatus
while the strips are being focused.
E.2
Sample specific protocols
The following set of tables show protocols which have been used for a
wide range of sample types, alongside examples of the 2-D images
obtained.
All protein lysates were labelled at a concentration of 5-10 mg/ml
unless otherwise stated.
The protocols used here are not necessarily optimal methods for these
sample types but do present a useful methodology along with an
illustration of the image quality that can be obtained in each case.
All IEF programs used finished with a low voltage (500 V) step for
48 h. This step was intended to maintain the focusing of the proteins
after the IEF program had completed. The number of hours spent at
this voltage varied for each sample type but was generally significantly
lower than the full 48 h programmed into the IEF unit.
Strips were removed immediately upon completion of the IEF program.
Where this was not possible and samples were left at 500 V for more
than 2 h they were then refocused by ramping to 8 000 V over a period
of 30 min.
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E.2
Table E-1. Caenorhabditis elegans (C.elegans), pH 3-10 NL IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
3 mg/ml sample lysate in
water. Sample
precipitated using
acetone on ice for 1 h.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Supernatant discarded
and pellet resuspended in
lysis buffer. Lysate
concentration 2.5 mg/ml
prior to labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
25 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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Table E-2. Drosophila melanogaster (D. melanogaster), pH 3-10 NL IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
25 mM Tris,
4% CHAPS
(pH 8.0-8.5).
Method of cell or tissue
disruption
Whole flies
mechanically
homogenized, directly in
lysis buffer. Incubated
on ice for
1 h. Centrifuged at 4 °C
(12 000 × g, 20 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-3. Escherichia coli (E.coli) cell culture, pH 3-10 NL IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, cathodic
cup loading.
50 µA per strip.
1. 500 V, 1 h, step.
2. 1000 V, 1 h, step.
3. 8000 V, 8 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-4. Escherichia coli (E.coli) cell culture, pH 4-5 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 4-5 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-5. Escherichia coli (E.coli) cell culture, pH 4.5-5.5 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 4.5-5.5 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic cup
loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-6. Escherichia coli (E.coli) cell culture, pH 4-7 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 4-7 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-7. Escherichia coli (E.coli) cell culture, pH 5-6 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 5-6 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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Table E-8. Escherichia coli (E.coli) cell culture, pH 5.5-6.7 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 5.5-6.7 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-9. Escherichia coli (E.coli) cell culture, pH 6-9 IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Lysis buffer added to cell
pellet. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 6-9 Immobiline
DryStrip. Destreak reagent used.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-10. Human serum, pH 3-10 NL IPG strip.
Lysis buffer
8 M urea,
40 mM Tris,
4% CHAPS
(pH 8.0).
Method of cell or tissue
disruption
Not required. Sample
diluted directly in lysis
buffer to 10 mg/ml.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy3 minimal dye.
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E.2
Table E-11. Mouse cerebellum, lysed without thiourea, pH 3-10 NL IPG strip.
Lysis buffer
8 M urea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Washed 4× with saline
solution (0.9%, 10 ml).
Saline solution drained.
Cut into small pieces, lysis
buffer added and
mechanically homogenized
at room temperature.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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Table E-12. Mouse cerebellum lysed with thiourea, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
Washed 4× with saline
2 M thiourea, solution (0.9%, 10 ml).
30 mM Tris,
Saline solution drained.
4% CHAPS
Cut into small pieces, lysis
(pH 8.5).
buffer added and
mechanically homogenized
at room temperature.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-13. Mouse Striatum, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
Washed 4× with saline
2 M thiourea, solution (0.9%, 10 ml).
30 mM Tris, Saline solution drained.
4% CHAPS
Lysis buffer added and
(pH 8.5).
mechanically homogenized.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-14. Mouse skeletal muscle, lysed without thiourea, pH 3-10 NL IPG strip.
Lysis buffer
8 M urea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Washed 4× with saline
solution (0.9%, 10 ml).
Saline solution drained.
Cut into small pieces, lysis
buffer added and
mechanically homogenized
at room temperature.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-15. Mouse skeletal muscle lysed with thiourea, pH 3-10 NL IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Washed 4× with saline
solution (0.9%, 10 ml).
Saline solution drained.
Cut into small pieces. Lysis
buffer added and
mechanically homogenized
at room temperature.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-16. NIH 3T3 fibroblasts, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
Trypsinized cells washed
2 M thiourea,
twice with wash buffer
30 mM Tris,
and diluted 1 in 10 with
4% CHAPS,
lysis buffer. Sample
5 mM magnesium sonicated on wet ice
acetate (pH 8.5). with low-intensity 30 s
pulses until the lysate
turned clear. Centrifuged
at 4 °C (12 000 × g, 10
min). Pellet discarded
and supernatant used
for labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-17. Rat heart, pH 4-7 IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
1 g of tissue placed in
2 M thiourea,
10 ml of lysis buffer.
10 mM Tris,
Tissue mechanically
5 mM magnesium homogenized and then
acetate,
centrifuged at 10 °C
4% CHAPS
(12 000 × g, 1 h).
(pH 8.0).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 4-7 Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-18. Rat liver, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
1 g of tissue placed in
2 M thiourea,
10 ml of lysis buffer.
10 mM Tris,
Tissue mechanically
5 mM magnesium homogenized and then
acetate,
centrifuged at 10 °C
4% CHAPS
(12 000 × g, 1 h).
(pH 8.0).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-19. Rat Kidney, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
Washed 3× with saline
2 M thiourea,
solution and drained.
30 mM Tris,
Cut into small pieces,
5 mM magnesium lysis buffer added and
acetate,
mechanically
4% CHAPS
homogenized at room
(pH 8.5).
temperature.
Centrifuged at 4 °C
(13 000 rpm, 10 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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Table E-20. Rat plasma, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
8 ml of plasma mixed
2 M thiourea,
with 10 ml of lysis
30 mM Tris,
buffer.
5 mM magnesium Centrifuged at 10 °C
acetate,
(12 000 × g, 1 h).
4% CHAPS
Pellet discarded and
(pH 8.0).
supernatant used for
labelling.
Lysate concentration
10.9 mg/ml prior to
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
2 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.2
Table E-21. Saccharomyces cerevisiae (S. cerevisiae), pH 3-10 NL IPG strip.
Lysis buffer
7 M urea,
2 M thiourea,
30 mM Tris,
4% CHAPS
(pH 8.5).
Method of cell or tissue
disruption
Dried cell preparation
resuspended in lysis
buffer. Sonicated on wet
ice with low-intensity
30 s pulses until the
lysate turned clear.
Centrifuged at 4 °C
(12 000 × g, 5 min).
Pellet discarded and
supernatant used for
labelling.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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Table E-22. Bladder epithelial carcinoma T24 cell line, pH 3-10 NL IPG strip.
Lysis buffer
Method of cell or tissue
disruption
7 M urea,
Medium was removed,
2 M thiourea,
cells washed twice in
10 mM Tris,
PBS and scraped from
5 mM magnesium the flasks.
acetate,
Cells centrifuged and
4% CHAPS
pellets washed twice in
(pH 8.0).
wash buffer
(10 mM Tris, pH 8,
5 mM magnesium
acetate).
Pellets resuspended in
lysis buffer.
1st and 2nd dimension protocols
1st Dimension
24 cm, pH 3-10 NL Immobiline
DryStrip.
Ettan IPGphor IEF unit, anodic
cup loading.
50 µA per strip.
1. 300 V, 3 h, step.
2. 600 V, 3 h, gradient.
3. 1000 V, 3 h, gradient.
4. 8000 V, 3 h, gradient.
5. 8000 V, 4 h, step.
2nd Dimension
12.5% Ettan DALTtwelve
1.5 W per gel overnight.
Image
50 µg of protein labelled with CyDye DIGE Fluor, Cy5 minimal dye.
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E.3
E.3
Reagents tested for compatibility with Ettan DIGE system
This section contains examples of reagents commonly used in 2-D
electrophoresis experiments which have been tested for their
compatibility with labelling using CyDye DIGE Fluor minimal dyes.
This is not a complete list of reagents; if unlisted reagents or a
combination of these reagents are required in the cell lysis buffer it is
recommended that the labelling efficiency is checked following the
instructions in Appendix C, "Testing a new protein lysate for successful
labelling". These examples are only intended as a guide.
The recommended amount of dye is 400 ρmol:50 µg protein. Any
reduction in labelling efficiency can be offset by the addition of more
dye per 50 µg of protein. Up to 2 nmol of dye per 50 µg protein has been
shown to maintain a minimal labelling stoichiometry.
Reducing agents
DL-dithiothreitol (DTT) 2 mg/ml - slight reduction in labelling
5 mg/ml - 2× reduction in labelling
10 mg/ml - 10× reduction in labelling
CyDye DIGE Fluor minimal dyes
will react with thiols at high
concentration.
Tris-(2-carboxyethyl)
phosphine (TCEP)
0.5 to 1 mM - slight reduction in
labelling
2 mM - significant reduction in
labelling
ß-mercaptoethanol
Significantly reduces labelling
Detergents
Triton™ X-100
use at 1%
NP40
SDS
up to 1%
up to 1%
17% reduction in
labelling
No effect on labelling
No effect on labelling
Salts
Application of sample during rehydration
Application of sample via cup-loading
148
<10 mM
recommended
<50 mM
recommended
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E.3
Buffers
Tris
Recommend 10-40 mM
pH 8.0 - 9.0
pH is very important. pH 8.5 is optimal.
HEPES
Can cause focusing problems therefore not
recommended.
5 mM, pH 8.5 is acceptable
5 mM, pH 9–9.5 is acceptable
5 mM, pH 8. Expect a drop in labelling efficiency as
PPA is a primary amine.
Bicarbonate
CHES
PPA
Protease Inhibitors
4-(2-aminoethyl) benzenesulphonyl fluoride (AEBSF) (Pefabloc™) causes charge trains unless protector reagent is used.
Complete™ protease inhibitor cocktail - this product contains AEBSF,
so the same restrictions apply as above.
Aprotinin - compatible at recommended concentrations.
(4-amidino-phenyl) methane sulphonyl fluoride (APMSF) - compatible
at manufacturer's recommended concentrations.
EDTA - compatible between 0.5-10 mM.
Phenylmethylsulphonyl fluoride (PMSF) - compatible at
manufacturer's recommended concentrations.
Pepstatin A - compatible at manufacturer's recommended
concentrations.
Phosphatase inhibitors
Phosphatase inhibitor cocktail 1 (Sigma) - compatible at
manufacturer's recommended concentrations.
Phosphatase inhibitor cocktail 2 (Sigma) - compatible at
manufacturer's recommended concentrations.
Examples of compatible reagents in conjunction with Ettan DIGE gels
Following are some 2–D images of E. coli protein lysate, which has
been lysed and labelled in the presence of some of the reagents listed
previously.
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E.3
Table E-23. Experiment showing the effect of increasing dye concentration on the
scanning parameters and gel image quality.
1st and 2nd dimension protocols Images
Labelling
CyDye DIGE Fluor Cy5 minimal dye
E. coli samples labelled with
images
CyDye DIGE Fluor Cy5 minimal
dye
a) 50 µg protein labelled with 400
ρmol dye (control).
b) 50 µg protein labelled with 2
nmol dye (5× dye concentration)
First Dimension
24 cm, pH 3-10 NL Immobiline
DryStrips.
In-gel rehydration overnight. 50 µg
of labelled protein loaded per
strip.
Ettan IPGphor IEF unit, 50 µA per
a) Control (PMT = 520 V)
strip.
1. 200 V, 2 h step + hold
2. 500 V, 1 h Gradient
3. 1 000 V, 1 h Gradient
4. 8 000 V, 14 h Gradient
5. 8 000 V, 8 h step + hold
6. 500 V, 10 h step + hold
Strips frozen over the weekend
after focusing.
Second Dimension
12.5% Ettan DALTtwelve
electrophoresis unit
2 W per gel overnight
b) 5× dye concentration (PMT = 455V)
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Table E-24. Experiment showing the compatibility of DNase I treated protein lysate with CyDye DIGE Fluor minimal dye labelling.
1st and 2nd dimension protocols Images
Labelling
50 µg E. coli lysate labelled with
400 ρmol dye.
a) Standard cell lysis buffer
(control). Protein labelled with
CyDye DIGE Fluor Cy3 minimal dye
b) DNase I in cell lysis buffer.
Protein labelled with CyDye DIGE
Fluor Cy5 minimal dye
First Dimension
18 cm, pH 3-10 NL Immobiline
a) Control without DNase. CyDye DIGE
DryStrips.
Fluor Cy3 minimal dye image
In-gel rehydration overnight.
50 µg of labelled protein loaded
per strip.
Multiphor II IEF system.
Cathodic cup loading.
1. 500 V, 1 mA, 5 W, 1 Vh
2. 500 V, 1 mA, 5 W, 2 500 Vh
3. 3 500 V, 1 mA, 5 W, 10 000 Vh
4. 3 500 V, 1 mA, 5 W, 32 400 Vh
5. 500 V, 1 mA, 5 W, 10 000 Vh
(hold step).
Second Dimension
12.5% SE 600 Ruby
electrophoresis unit
10 A per gel overnight
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b) Lysate labelled in the presence of
DNase I. CyDye DIGE Fluor Cy5 minimal
dye image.
151
E.3
Table E-25. A comparison between the effect of CHAPS and NP40 detergents in
cell lysis buffer on CyDye DIGE Fluor minimal labelling.
1st and 2nd dimension protocols
Images
Labelling
50 µg E. coli lysate labelled with
400 ρmol CyDye DIGE Fluor Cy2
minimal dye.
a) Standard lysis buffer containing
4% CHAPS (control).
b) Lysis buffer containing 2% NP40.
First Dimension
24 cm, pH 3-10 NL Immobiline
DryStrips.
In-gel rehydration overnight. 50 µg of
each labelled protein loaded per
strip.
a) Control 4% CHAPS cell lysis buffer
Ettan IPGphor IEF unit, 50 µA per CyDye DIGE Fluor Cy2 minimal dye
strip.
image
1. 500 V, 500 Vh, step + hold
2. 1,000 V, 1 000 Vh, step + hold
3. 8 000 V, 64 000 Vh, step + hold
4. 500 V, 30 000 Vh, step + hold
Strips frozen over the weekend after
focusing.
Second Dimension
12.5% Ettan DALTtwelve
electrophoresis unit
2 W per gel overnight
b) 2% NP40 cell lysis buffer. CyDye
DIGE Fluor Cy2 minimal dye image
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Table E-26. A comparison between the effect of CHAPS and SDS detergents in
cell lysis buffer on CyDye DIGE Fluor minimal labelling.
1st and 2nd dimension protocols Images
Labelling
50 µg E. coli lysate labelled with
400 ρmol CyDye DIGE Fluor Cy2
minimal dye.
a) Standard lysis buffer containing
4% CHAPS (control).
b) Lysis buffer containing 2% SDS.
First Dimension
24 cm, pH 3-10 NL Immobiline
DryStrips.
In-gel rehydration overnight. 50 µg
of labelled protein loaded per strip.
Ettan IPGphor IEF unit, 50 µA per
a) Control 4% CHAPS cell lysis buffer
strip.
CyDye DIGE Fluor Cy2 minimal dye
1. 200 V, 2 h, step + hold
image
2. 500 V, 1 h, Gradient
3. 1 000 V, 1 h, Gradient
4. 8 000 V, 14 h, Gradient
5. 8 000 V, 14 h, step + hold
6. 500 V, 10 h, step + hold
Strips frozen over the weekend after
focusing.
Second Dimension
12.5% Ettan DALTtwelve
electrophoresis unit
2 W per gel overnight
b) 2% SDS cell lysis buffer. CyDye DIGE
Fluor Cy2 minimal dye image
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E.3
Table E-27. A comparison between the effect of CHAPS and Triton X-100 detergents in cell lysis buffer on CyDye DIGE Fluor minimal labelling.
1st and 2nd dimension protocols
Images
Labelling
50 µg E. coli lysate labelled with 400
ρmol CyDye DIGE Fluor Cy2 minimal
dye.
a) Standard lysis buffer containing 4%
CHAPS (control).
b) Lysis buffer containing 4% Triton X100.
First Dimension
24 cm, pH 3-10 NL Immobiline
DryStrips.
In-gel rehydration overnight. 50 µg of
a) Control 4% CHAPS cell lysis buffer
labelled protein loaded per strip.
CyDye DIGE Fluor Cy2 minimal dye
Ettan IPGphor IEF unit, 50 µA per
image
strip.
1. 500 V, 500 Vh, step + hold
2. 1 000 V, 1 000 Vh, step + hold
3. 8 000 V, 64 000 Vh, step + hold
4. 500 V, 30 000 Vh, step + hold
Strips frozen over the weekend after
focusing.
Second Dimension
12.5% Ettan DALTtwelve
electrophoresis unit2 W per gel
overnight
154
b) 4% Triton X-100 cell lysis buffer.
CyDye DIGE Fluor Cy2 minimal dye
image
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F.1
Appendix F Typhoon Variable Mode Imager
F.1
Typhoon Instrument States
The instrument status is shown in the upper left side of the Scanner
Control Software window, an example is shown below.
The instrument states that can appear in the Scanner Control Software
are:
Warming up
This message is displayed for 3 min after the instrument has been
turned on or the Initialize Scanner button has been clicked. During this
time, the Typhoon Variable Mode Imager stabilizes the lasers and
system components. Complete warm up takes 30 min once the
instrument has been turned on.
Ready
The instrument is ready to scan.
Sleep
The instrument has not been used for the amount of time (default 4 h)
set in the Typhoon Direct Instrument Access software (see Typhoon
User Guide, section 13.2, code no. 63-0028-31). After the selected time
elapses the lasers shut off and the Sleep message appears.
Initialization
After the Scan button is pressed the initialization message appears, this
remains displayed until the instrument starts scanning. If the prior state
was Ready then initialization takes approximately 1 min. If the prior
state was Sleep or Warming Up then initialization takes about 4 min.
Scanning
This message appears whilst a scan is in progress.
Service
If this message appears, then the instrument requires servicing and the
Amersham Biosciences Scanner Technical Support group should be
called. See the Assistance section in the Preface of the Typhoon User
Guide.
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F.2
If the instrument is not in the Ready state then the Initialize Scanner
button can be clicked whilst preparing the sample for scanning.
F.2
Cleaning the glass platen and sample lid
1
Clean the platen and sample lid with distilled water using a lint free
cloth. This is usually sufficient if using assembled gels held between
glass plates. If required 75% Ethanol may also be used.
2
If fluorescent material has come into direct contact with the platen
then a lint free tissue moistened with 10% hydrogen peroxide can
be used to remove this material, followed by cleaning with distilled
water.
For more comprehensive details see the Typhoon User Guide.
F.3
Assembling gels other than Ettan DALT and SE 600 Ruby
onto the Typhoon Platen
If gel types other than Ettan DALT or SE 600 Ruby are used then pairs
of grippers may be used to hold the plates enabling scanning of
assembled gels to be performed. For a 1 mm thick gel, the glass
thickness for this type of scanning should ideally be between 1.8 and
3.4 mm thick.
• Post-Electrophoresis Stained Gels
Gels that are stained after electrophoresis can result in one of two types:
Naked gels
Gels may be placed directly on the platen. This is not the preferred
method as contamination of the platen may occur and subsequent
cleaning may be required. Ideally naked gels should be reassembled
prior to scanning. If gels are scanned in this manner then squirt a small
amount of distilled water onto the platen, taking care to exclude air
bubbles as the gel is positioned. Plastic wrap may be placed over the gel
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F.4
to isolate it from the inner lid, although this will cause a slight increase
in background noise. The platen should be cleaned after gel removal
following the guidelines in F.2.
Bound gels
Gels that are cast on Bind-Silane treated glass plates remain attached to
the treated plate when the top plate is removed. Gel fixing and staining
is performed on the bound gel, e.g. using SYPRO Ruby stain. Once the
staining procedure has been completed the gel can be placed on the
platen in one of two ways:
1
Gel side down – place on the platen in the same manner as
described above for a Naked Gel.
2
Re-assembled (recommended) – the previously removed, untreated
plate can be replaced to reform the glass-gel-glass sandwich. To do
this a small quantity of the gel storage buffer, e.g. SDS
electrophoresis running buffer for Ettan DALT, needs to be applied to the
bound gel and the upper plate carefully lowered onto the gel taking
care to exclude air bubbles. Alternatively the bound gel can be kept
submerged in the gel storage solution and the upper plate applied.
In either case the outer plates need rinsing with de-ionized water
and then wiping dry with lint free tissues before being placed on the
platen.
F.4
Pre-scanning to identify a suitable PMT voltage
The PMT voltage can be set from 300 to 1 000 V although it is
recommended that, where possible, work is performed between 400
and 900 V. The voltage chosen depends on the type and quantity of dye
or stain present. A quick prescan at 500 or 1 000 µm pixel resolution
should be performed to identify a suitable voltage. This allows a rapid
scan at a relatively low resolution that should not be used for
quantitative analysis. It does however give an approximation of
expected signal values which will aid determination of the PMT voltage
required. The prescan can be opened in ImageQuant Software. Spots
showing the most intense signal should be selected using one of the
Object tools such as the rectangle. This is shown in the ImageQuant
Software screen image below. Higher resolution 100 µm scans must be
used to collect quantitative data. This resolution is required for
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F.4
subsequent data analysis using DeCyder Differential Analysis Software.
Using the Volume Review tool button displays the information associated
with the selected area in the format.
CAUTION: The maximum pixel value should not exceed 100,000 as this
indicates signal saturation has been reached and this will prevent
quantitative analysis being achieved.
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F.5
For the E.coli model system used at Amersham Biosciences the
following PMT voltages routinely give acceptable maximum pixel
values with 50 µg protein labelled with 400 ρmol CyDye DIGE Fluor
minimal dye, using 24cm pH3-10 NL Immobiline DryStrips separated
on Ettan DALT gels.
Fluorophore
CyDye DIGE Fluor minimal dyes
SYPRO Ruby
PMT Voltage
500 - 550
450 - 500
A target maximum pixel value of 50 000 to 80 000 is usually suitable.
When adjusting the voltage, relatively small increments of 20 to 50
volts are recommended. If only one or two spots show saturation then
only slight downward adjustments to the PMT voltage setting are
normally required. Once the voltage has been optimized for one gel in
an experiment, these settings can be used for all similar gels within the
same experiment. The maximum pixel value should be within the
specified range for all gels, to enable accurate quantitation of spot
volumes. If necessary, different PMT settings can be used for different
gels in the same experiment. Using different PMT settings will not affect
the data analysis or quantitation in DeCyder Differential Analysis
Software. To avoid problems with saturated images it is recommended
that users confirm that suitable image signals have been obtained
before discarding gels. The procedure for checking the signal output
using the volume review tool within ImageQuant Software is described
above.
F.5
Setting the required sensitivity
• Sensitivity
Three options are available:
1
Normal collects data from each pixel once. This is the recommended
setting.
2
Medium collects the data from each pixel four times and averages
the results.
3
High collects the data from each pixel eight times and averages the
results.
Using the Medium and High settings can help to detect weak spots by
reducing background noise. Selecting either of these options will
increase the scan time. The Normal scan setting is usually sufficiently
sensitive. For further details on these functions see the Typhoon User
Guide.
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F.5
• Linking Scans
In the Fluorescence Setup window at the bottom right hand corner of
the screen is the heading "Auto Link Mode". Selecting the Sensitivity check
box ensures all scans are carried out as individual scans. Changing this
so the Speed check box is selected, allows linkage of scans. Scans for
Cy3 and Cy5 channels may be linked as a single scan event thus halving
the Cy3/Cy5 scan time. There may be some cross-talk from the Cy3
channel into the Cy5 channel using this method so this mode should
only be selected if it is suitable for the scan purpose. For example,
linked scans are useful for determining optimal PMT voltage settings
during a pre-scan or nonquantitative scans such as checking the
progress of a gel run. An example of a linked scan selected is shown
below.
CAUTION: It is recommended that linked scans are NOT used to
generate data to be used for quantitative analysis because of cross-talk
from the Cy3 channel into the Cy5 channel.
CAUTION: When scans are linked, the Typhoon Variable Mode Imager
always scans the setting using the highest emission wavelength first,
even if the scans have been programmed with the lowest emission
wavelength first. The output files are named in scan order. If unsure as
to which image was scanned with which settings the scan information
can be viewed for each file in ImageQuant Software or ImageQuant Tools
Software using File:Image Properties and then selecting the Scan Info tab.
Details of the emission filters can be found in the Comments box.
For further details on scan linkage see the Typhoon User Guide.
Once the Fluorescence scan settings have been entered click OK to
accept the changes. This returns you to the Scanner Control Software
window.
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F.6
F.6
Additional ImageQuant Tools Software features
Additional features are also available in ImageQuant Tools Software
and include:
• Color Overlay and Flicker Function.
• Export to Microsoft Excel.
Color overlay and flicker function
Both Color Overlay and Flicker Function permit visualization of differences
between overlaid scan channels. The color overlay is automatically
performed when the filename.ds file is opened in ImageQuant Tools
Software. The flicker function is selected by either selecting View:Flicker
Display Channels or selecting the flicker button. The Static Channel to
Display should be set to None.
The user can then select the number of channels to flicker and the
flicker rate.
Export to Microsoft Excel.
This feature should only be used with relatively small image areas.If
large areas are selected Microsoft Excel will not have the capacity to use
the information. This feature allows the numerical data to be exported
to spreadsheets for manipulation. For example 3-D graphing can be
performed rapidly for presentations or to confirm that spots appearing
to be visually merged are in fact distinct. To access this function, change
from the color overlay image to the grayscale view by clicking on the
Side-by-side button. Opening name.gel files allows this function to be
used directly.
The area of interest from a single channel image is highlighted using the
Copy Region button and then dragging the cursor whilst holding the left
mouse button. Once a suitable area has been highlighted the data can
be copied using Edit:Copy Image Data for Excel 3D Chart or the equivalent
button.
To use the data, Microsoft Excel or a suitable spreadsheet must be
opened and the Paste command used to enter the data into the
spreadsheet. The data has column and row numerical headers that are
not required for the 3-D graphical plot but do allow positional
information associated with the image to be viewed.
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F.7
F.7
Gel orientations
Gel orientations and the relevant Orientation button to select for
standard gel image orientation output are shown in table Table F-2.
The recommended orientation to use for Ettan DALT and SE 600 Ruby
gels are shown in Table F-1, all available options are shown in
Table F-2.
Table F-1. Recommended multiple gel scanning layout
Gel Type
Scanner control
orientation button
Gel orientation viewed from
above the platen
Ettan DALT system
SE 600 Ruby System
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F.7
Table F-2. Gel orientation guide
Scanner
Gel orientation viewed
control
from above the platen
orientation
button
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Scanner
Gel orientation viewed
control
from above the platen
orientation
button
163
F.8
F.8
Instructions for users of Scanner Control Software and
ImageQuant Tools Software (pre-version 3.0).
• Scanner Control Software
Scan area selection
The tray option is not available so the user needs to define the area of
the platen to scan by using the instructions under Tray setting with "User
Select" Option in Section 7.7.2.
File naming
The only file naming format available is that described in Section 7.9.3
This means that individual scan channel images will have the filenames
UNSEPn.gel, where n is the scan channel number. This occurs for every
scan where more than one scan channel has been selected. If the user
wants to use DeCyder Differential Analysis Software to analyze a
number of gels then these filenames will need to be modified to make
them unique. Renaming files can be done using Internet Explorer, or
similar software, by clicking on the individual UNSEPn.gel file then
typing a new, unique name.
CAUTION: Renaming the UNSEPn.gel files loses the dataset
functionality, the renaming is best done after the image has been
cropped, see below.
• ImageQuant Tools Software.
Image cropping
Open the name.ds file so all scan channels are overlaid. Use Tools:Define
Region of Interest to highlight the selected image area. Use File:Save
Region of Interest As… to rename the image group. The individual scan
channels will then need renaming in Windows Explorer or similar to
give them unique filenames. Once renamed, the image files should then
be moved to a single folder if DeCyder Differential Analysis Software
is to be used for data analysis.
CAUTION: DeCyder Differential Analysis Software requires all individual
images from a multiplexed gel to have the same X/Y co-ordinates and
image size so cropping must be performed using the overlaid channels
rather than attempting to crop individual UNSEPn.gel image files.
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F.9
F.9
User defined tray editor
1
On the tool bar, select Tray:Tray editor.
2
Select New Tray and enter a unique name for the new tray, e.g., Iso
DALT.
3
When prompted, add sample details. This is done using New Sample
and details are added as X/Y co-ordinates using the letter and
numbers identified from the platen grid markings. The number of
sample trays that can be entered is dependent on the area for each
sample, areas cannot overlap each other.
4
Preview the tray details to confirm that the areas have been set
correctly.
If all details are correct then select Save Current Tray. This will add the
new tray to the existing list.
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F.9
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G.1
Appendix G Trouble shooting guide
The aim of this Appendix is to provide a help guide for problems that
might be encountered when running experiments. For general 2–D
troubleshooting problems please refer to the Amersham Biosciences
manual “2–D Electrophoresis Using Immobilized pH Gradients” (code
no. 80-6429-60).
G.1 Minimizing experimental variation in 2-D
electrophoresis experiments
Conventional one-color 2-D electrophoresis approaches are plagued
with many sources of experimental and user variation (system
variation). This can lead to irreproducible results that generate
misleading or false conclusions. Many of these issues are tackled by
Ettan DIGE system by features of the methodology itself but also by the
implementation of careful experimental design. The common sources
of system variation in 2-D electrophoresis experiments are listed below,
followed by the features within Ettan DIGE system designed to
overcome/minimize each one.
1
Entry into the Immobiline DryStrip and first dimension focusing
are very dependent on the lysis buffer composition, sample
preparation procedure and the focusing protocol. SDS
concentration in the running buffer, alkylation and running
conditions affect protein separation in the second dimension.
• All samples in the same experiment should be prepared using the
same extraction protocol and separated using identical buffers and
running conditions.
• Variation between different first or second dimension runs within
one experiment can be negated by incorporating a pooled internal
standard on every gel. This feature is made possible by the
multiplexing capabilities provided by the 2-D DIGE methodology.
For example, protein loss occurring during sample entry into the
IPG strip will be the same for each sample within a single 2-D
DIGE gel. Therefore the relative amounts of a protein between
samples in a gel will be unchanged. Using conventional “one
sample per gel” 2-D electrophoresis techniques, samples to be
compared are separated independently in different gels.
Consequently spot migration and intensity may differ between each
gel, resulting in inaccurate quantitation.
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G.2
2
2-D image analysis packages allow extensive user intervention
during spot detection and editing. This can lead to subjective data
analysis and may result in biased conclusions.
• DeCyder Differential Analysis Software is designed to provide
automated spot detection, normalization, background subtraction,
matching and spot statistics. The spot detection algorithms have
been highly optimized to work with multiplexed fluorescently
labelled proteins and this allows a high degree of automation.
Minimal user intervention is required. Where necessary, user
editing during matching and data analysis should be exercised in an
objective manner ensuring different users obtain the same results
from the same data-sets.
Note: As with all 2-D electrophoresis techniques, the resolution of
proteins in both first and second dimensions is important. If
spots appear to be too close together to be confidently separated,
then it is advisable that a more appropriate first dimension pH
range or second dimension gel is run. For example, use narrow
pH range IPG strips in the first dimension or a gradient gel for
the second dimension.
G.2 Protein preparation and labelling using CyDye DIGE Fluor
minimal dyes.
Problem
Low protein
yields from
the cell
lysate.
Cause
Lysis procedure
Remedy
Ensure cell culture densities were
optimal for cell lysis using sonication.
Ensure cell pellet was not lost after
centrifugation.
Ensure sonication was carried out for
long enough.
Insufficient protein in Remake protein lysate or concentrate
sample (protein con- sample by precipitation with Ettan 2–D
centration <1 mg/ml) Clean-Up Kit (code no. 80-6484-51).
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G.2
Weak
Insufficient sample
fluorescent buffering.
signal on 2–D
gel image.
Thiol agents present
in the sample
competing for dye.
Check if concentration
of DTT is >2 mg/ml in
protein sample
preparation method.
Use 30mM Tris to give sufficient
buffering capacity.
Dilute protein lysate with DTT-free lysis
buffer. Clean sample by precipitation
with Ettan 2–D Clean-Up Kit, or
increase the amount of dye in the
labelling reaction.
Primary amines such
as Pharmalytes or
ampholytes are
present in sample
during labelling,
competing for CyDye
DIGE Fluor minimal
dye.
Dilute protein lysate with amine-free
lysis buffer. Clean sample by
precipitation with Ettan 2–D Clean-Up
Kit, or increase the amount of dye in
the labelling reaction.
Incorrect
concentration of
protein in lysate.
Use a detergent or thiourea compatible
protein assay kit, e.g. Protein
Determination Reagent or Ettan 2-D
Quant Kit.
Check quality of DMF. Should be >99.8% anhydrous DMF
from a bottle that has not been open
for longer than 3 months.
Degraded dye due to
hydrolysis of
NHS-ester or
photodegradation of
fluorophore.
Ensure that the appropriate storage
conditions have been used for the
CyDye DIGE Fluor minimal dye (in dark
at –20°C). Check specific batch expiry
date and reconstitution date.
Incorrect dye:protein
ratio used.
400 ρmol of dye per 50 µg of protein
is recommended. If there is a large
concentration of other components
which can react with the dye, then
more dye (up to 2 nmol per 50 µg of
protein) can be used.
Low pH prior to
labelling.
Check pH is 8.5 immediately prior to
labelling. If necessary, increase pH
using higher pH lysis buffer containing
30 mM Tris (pH 9.0-10.0) or use
50 mM NaOH.
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169
G.3
Unexpected
protein spots
present in the
gel.
Contaminant proteins
have been introduced
into the sample prior
to the labelling
reaction.
Protein spots Proteins not
detected
denatured or
more strongly solubilized
with one dye. sufficiently.
Check that gloves are used throughout
the procedure.
Use combination of chaotrope in lysis
buffer, such as 7 M urea/2 M thiourea.
G.3 First Dimension
Problem
Current is
zero or too
low.
Cause
External electrode
contacts are poor.
Remedy
Ensure that the electrodes at the
bottom of the strip holder (one at each
end) make metal-to-metal contact with
the appropriate electrode area.
Internal electrode
contacts are poor.
Ensure that the gel makes contact with
both electrodes in the strip holder.
Immobiline DryStrip
not fully rehydrated.
Check that the Immobiline DryStrip is
fully rehydrated along its entire length.
Electrical contact at the electrodes is
reduced by incomplete rehydration.
No conduction
through electrode
wicks.
Current limit setting is
incorrect.
Check that the electrode wicks (if
used) were moistened prior to use.
Voltage too
low or does
not reach the
maximum set Incorrect number of
value.
Immobiline DryStrips.
Check that the current limit is properly
set.
Check that the correct number of strips
in place is set on the IPGphor program.
No Pharmalytes added The recommended Pharmalyte
to sample.
concentration is 1.0% (v/v).
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G.4
Sparking or
burning in
strips.
High current.
Do not exceed the recommended
setting of 50 µA per Immobiline
DryStrip.
Strips not rehydrated. Check that Immobiline DryStrips are
fully rehydrated along their entire
length.
Presence of bubbles. Check that any large bubbles trapped
under the Immobiline DryStrip after
wetting with rehydration solution are
removed prior to focusing.
Strips drying out
during focusing.
Ensure that sufficient Immobiline
DryStrip Cover Fluid has been applied.
High salt
concentration.
Clean sample to remove excess salts.
Follow a first dimension protocol such
as that described in appendix E.1.2
Proteins have Poor electrical contact Check that the strips are in contact
not focused. in first dimension.
with the strip holder electrodes.
G.4 Second dimension
Problem
No protein
spots are
visible on the
gel.
Cause
Incorrect labelling
protocol.
Remedy
Check the sample preparation and
labelling protocol.
Inefficient sample
solubilization.
Increase concentration of solubilizing
components in the sample solution.
The upper concentration limits for
common reagents are: Urea 9.8 M,
Thiourea 2 M, zwitterionic detergent
CHAPS 4%, Pharmalyte 1%,
DTT 2-3%.
No or insufficient SDS Ensure electrophoresis running buffer
in electrophoresis
is correctly formulated.
running buffer.
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171
G.4
Individual
spots appear
as multiple
bands or are
missing,
unclear, or in
the wrong
position.
Immobiline DryStrip
placement.
Ensure that the plastic backing of the
Immobiline DryStrip is against the
glass plate on the second dimension
gel, directly onto the top of the
acrylamide gel.
Protein oxidation
during
electrophoresis.
Prevent oxidation of oxygen-sensitive
proteins in the gel. Check the correct
equilibration conditions are used prior
to the second dimension separation.
DTT reduction, then treatment with
iodoacetamide alkylates the sulphydryl
groups and thus prevents the reduced
proteins from re-oxidizing.
Formation of Protein carbamylation. Check that all solutions containing
charge trains.
urea were prepared freshly and ensure
that all solutions containing urea were
not heated above 37°C at any time.
Horizontal
High sample load.
Reduce sample load by adding less
streaking or
sample to the rehydration solution.
incompletely
focused
Insufficient focusing Increase total Vh for focusing.
spots.
time.
Vertical
SDS depletion during Use 0.2% SDS in the running buffer
streaking or second dimension
for both top and bottom buffer tanks.
incompletely electrophoresis.
focused
Ensure that the gel has been prepared
spots.
with the correct concentration of SDS.
Over-alkylated
proteins.
Use lower pH, higher DTT
concentration or lower iodoacetamide
concentration when equilibrating
Immobiline DryStrips.
Insufficient chaotrope Ensure the correct solubilization
or detergent.
solution has been used.
Sample
insolubility
and
particulates. Cloudy sample
Poor first
dimension
focusing.
172
Remove insoluble material from the
sample using ultracentrifugation.
Ionic detergent
If SDS is used in sample preparation,
concentration too high the final concentration must not
in lysis buffer.
exceed 0.25% after dilution into the
rehydration solution. Also ensure that
the nonionic detergent is present in a
concentration at least 8 times higher
than the concentration of any ionic
detergent to ensure complete removal
of SDS from the proteins.
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G.5
Streaking or
smearing.
Sample
aggregation
or
precipitation.
Sample rich in nucleic
acids.
Focusing conditions
not optimized.
Add DNase and RNase, or sonicate to
hydrolyze nucleic acids.
Program a low initial voltage that
increases gradually, and/or increase
time at maximum voltage.
Extended focusing may result in
electro-endosmosis where water and
protein movement can produce
horizontal streaking. Minimize water
transport by employing a maximum
pH range Immobiline DryStrip and
apply electrode pads.
G.5 Typhoon Variable Mode Imager results
For a complete guide to troubleshooting Typhoon Imager results,
please refer to Typhoon User Guide (code no. 63-0028-31).
Problem
Protein spots
do not show
up on the gel
image.
Cause
Remedy
The wrong laser and Select correct laser and filter for each
emission filters have CyDye DIGE Fluor minimal dye.
been selected for the
CyDye DIGE Fluor
minimal dye used.
The labelling reaction Reconstitute stock dye or make fresh
working dye solution in fresh DMF.
has not been
performed correctly. Repeat the labelling.
The PMT voltage is too Rescan with higher PMT voltage.
low.
The gel image The PMT voltage is too Rescan with lower PMT voltage.
appears
high.
black.
Appearance Platen contaminated Clean platen, see appendix F.2. Rescan
of
with dye from
gel on different part of platen to
nonspecific scanning other gels. confirm that background does not
background
move with the gel.
on gel image.
Bacterial/mycoplasma Wash out all buffer tanks and
contamination in gel electrophoresis equipment and make
running equipment. fresh running buffer.
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173
G.5
Appearance
of
nonspecific
background
mainly in Cy3
image.
Appearance
of small spots
(sharp peaks
in gel image).
SYPRO stain from
preparative gel
processes
contaminating
electrophoresis
equipment.
Dirt and dust on gel
plates or platen.
Wash out all buffer tanks,
electrophoresis equipment and gel
storage containers. Do not use
preparative gel containers to store
analytical gels. Clean platen, see
appendix F.2.
Clean platen or gel plates. Rescan gel
on different part of platen to confirm
that background does not move with
gel.
Dirt in gel.
Filter acrylamide.
Precipitation or
contamination in
SYPRO stain.
Incorrect scan
resolution.
Filter SYPRO Ruby stain or dilute stain
solution.
DeCyder
Differential
Analysis
Software
gives poor
spot
boundaries.
Faint, illIncorrect focal plane
defined gel selected.
images,
possibly with
high
background.
174
Rescan gels with resolution set to
100 µm.
Re-scan with correct focal plane
selected, see section 7.8 Setting gel
orientation and scan resolution.
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H.1
Appendix H Related products and consumables
H.1 Related products
Item
Product Code
Hoefer SE 600 Ruby Series Vertical Gel
80-6479-57
Electrophoresis System
Low fluorescent glass plates (18 x 16 cm) 80-6442-14
Spacers for SE 600 Ruby (1mm thick)
80-6179-94
Ettan DALTsix Large Vertical System
80-6485-27
Ettan DALTtwelve Large Vertical System
80-6466-27
Ettan DALT Filler Sheets 1.0 mm
80-6467-60
Ettan DALT Separator Sheets 0.5mm
80-6467-41
Ettan DALT Blank Cassette Insert
80-6467-03
Low fluorescence plates with integral
80-6475-58
spacers for Ettan DALT
Ettan DALT Cassette Rack
80-6467-98
Ettan DALT Gel Caster
80-6467-22
Ettan IPGphor IEF System
80-6414-02
Multiphor II IEF System
18-1018-06
Electrophoresis Power Supply
18-1130-05
(EPS 3501 XL)
MultiTemp III Thermostatic Circulator
18-1102-78
2× Power Supply Adapter set
18-1129-59
Immobiline DryStrip Reswelling Tray
80-6465-32
7–24cm
PlusOne DryStrip Cover Fluid
17-1335-01
Cup Loading Strip Holder complete set
80-6459-43
IPGphor Strip Holder Cleaning Solution
80-6452-78
Ettan IPGphor cover
80-6465-13
Equilibration Tube Set
80-6467-79
Hoefer Wonder Wedge plate separation tool 80-6127-88
Reference Markers
18-1143-34
Typhoon Variable Mode Imager
for product
information please
inquire with your local
Amersham
Biosciences sales
office
Ettan DIGE Gel Alignment Guides for
80-6496-29
Hoefer SE600
Ettan DIGE Gel Alignment Guides for Ettan 80-6496-10
DALT
Gel Orientation Guide
80-6496-67
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175
H.1
DeCyder Differential Analysis Software pre- 18-1163-05
installed on a PC and a single user licence
DeCyder Differential Analysis Software
18-1156-17
including single user licence
DeCyder Differential Analysis Software
18-1150-45
additional user licence
Ettan Spot Picker
18-1145-28
Ettan Spotter
For product
information please
inquire with your local
Amersham
Biosciences sales
office.
Ettan Digester 100-120V
18-1152-59
Ettan Digester 220-240V
18-1142-68
Ettan Spot Handling Workstation
18-1164-05
Ettan Spot Handling Workstation-LWS for 18-1164-06
integration with Ettan LWS
Ettan MALDI-ToF Pro 120 V
18-1156-54
Ettan MALDI-ToF Pro 240 V
18-1156-53
2–D Electrophoresis, Principles and
80-6484-89
Methods
Ettan DIGE Training CD
18-1164-39
Ettan DIGE system User Manual
18-1173-17
Ettan DIGE Quick Protocols
18-1164-41
DeCyder Differential Analysis Software
18-1173-16
User Manual
DeCyder Differential Analysis Software
18-1164-43
Tutorial CD
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H.2
H.2 Reagents/consumables
Item
CyDye DIGE Fluor Cy2 minimal dye
(25 nmol)
CyDye DIGE Fluor Cy3 minimal dye
(25 nmol)
CyDye DIGE Fluor Cy5 minimal dye
(25 nmol)
CyDye DIGE Fluor Cy2 minimal dye
(10 nmol)
CyDye DIGE Fluor Cy3 minimal dye
(10 nmol)
CyDye DIGE Fluor Cy5 minimal dye
(10 nmol)
CyDye DIGE Fluor Labelling Kit for Scarce
Samples
CyDye DIGE Fluor Labelling Kit for Scarce
Samples plus Preparative Gel Labelling
PlusOne Urea
PlusOne CHAPS
PlusOne DTT 5 g
Ettan 2–D Quant kit
Ettan 2–D Clean-Up kit
PlusOne Bromophenol Blue
PlusOne Tris
PlusOne SDS powder
PlusOne Glycerol (87%)
PlusOne ReadySol IEF (40% T, 3% C)
PlusOne TEMED
PlusOne Ammonium Persulphate
PlusOne Glycine
Ultrapure DMF
Destreak Rehydration Solution
Ettan DIGE System User Manual 18-1173-17 Edition AA
Product Code
RPK 0272
RPK 0273
RPK 0275
25-8008-60
25-8008-61
25-8008-62
25-8009-83
25-8009-84
17-1319-01
17-1314-01
17-1318-02
80-6483-56
80-6484-51
17-1329-01
17-1321-01
17-1313-01
17-1325-01
17-1310-01
17-1312-01
17-1311-01
17-1323-01
US14862
17-6003-19
177
H.2
178
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Appendix I Glossary
1-D. One-dimensional electrophoretic separation of proteins by a single
characteristic (e.g. pI or molecular weight).
2–D. Two-dimensional electrophoretic separation according to protein
pI and molecular weight.
Abundance. Quantity of protein present at a particular moment in
time.
Coomassie. Colored dye used to visualise proteins after electrophoretic
separation.
CyDye DIGE Fluor minimal dyes. Range of fluorescent dyes specifically
engineered for applications within the Ettan DIGE sytem.
DALT. A brand name for Amersham Biosciences electrophoretic
equipment. An abbreviation of Dalton.
DeCyder. Amersham Biosciences brand name for the software package
specific for Ettan DIGE system.
DIGE. Difference Gel Electrophoresis.
DIGE enabled. Having attributes to run applications within Ettan
DIGE system.
Dynamic range. Orders of magnitude where the response of e.g.,
fluorescent signal, is linear with concentration.
Electrophoresis. Separation of mixtures of proteins by charge or
molecular weight.
Emission. Light at specific wavelengths, released after excitation of a
fluorophore by incoming light of a shorter wavelength.
Ettan. Amersham Biosciences brand name for proteomics products/
platforms.
Excitation. Light of a specific wavelength used to excite a fluorophore,
causing emission of a fluorescent signal.
Experimental design. Method employed to define an experiment in
order to gain an answer to a scientific question.
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Flicker function. Ability to sequentially switch between multiplexed
images from a single gel enabling visualisation of differences in protein
abundance.
Fluorophore/Fluor. Molecule emitting fluorescence when excited by
light of a suitable wavelength.
Fluorescence. Emission of energy in the form of light, induced by
excitation with light at a shorter wavelength.
Gel Alignment Guides. Positioning tools for putting gels in the correct
place on to the Typhoon platen.
Gel Orientation Guide. Clear sheet marked with the letter 'R' to link
positioning the gel on the Typhoon Variable Mode Imager platen with
the selection of orientation choice in Typhoon Scanner Control
Software.
Gel-to-gel variation. Variation in position and intensity of protein
signal associated with differences in gel composition, protein migration
and running conditions.
Imaging. A process used to visualise, e.g., fluorescent signal from a gel
containing fluorescently labelled proteins.
Induced biological change. The differences that are caused by a disease
state/drug treatment/life-cycle stage etc., i.e. the effect we are trying to
measure in a 2–D DIGE experiment.
Inherent biological variation. The naturally occurring differences
between two individual animals/cultures/plants/flies etc., which have
been subjected to the same experimental conditions.
Intra-gel. Within the same gel.
Inter-gel. Between different gels.
Internal standard. A standard included on every analytical gel of a 2-D
DIGE experiment, used as a quantitative reference linking all the
experimental samples. Ideally this is formed from a pool of all
individual samples from a given experiment.
Isoelectric focusing. Separation of proteins migrating in an electric
field, until they reach a state of net neutral charge, i.e they have reached
their isoelectric point.
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Linearity. The range where signal intensity is directly proportional to
protein concentration.
Low fluorescence glass plates. Electrophoresis plates made from glass
that will not significantly fluoresce when light of specific wavelengths
are applied.
Matching. Association of the same protein within or between gels.
Minimal labelling. Technique describing the labelling of 1-2% of the
total lysine population in a protein lysate with CyDye DIGE Fluor
minimal dyes.
Multiplexing. Simultaneous separation and co-detection of two or
more differently labelled samples in the same gel.
NHS ester. N-hydroxy succinimide ester reactive group that reacts with
primary amines forming a covalent amide bond.
Normalization. The process of equalising signal intensities between
different images. A process also used to compare internal standards
from different gels.
Overlay. The matching together of images containing the same proteins
labelled with different dyes which run to exactly the same position
when separated on a single gel.
Overlabelling. Two spots representing the same protein each carrying a
different number of dye molecules generated when the ratio of CyDye
DIGE Fluor minimal dye to protein is too high.
PAGE. Polyacrylamide Gel Electrophoresis.
Peptide. Fragment of protein generated when enzymes such as trypsin
are used to breakdown a protein to smaller fragments.
Platen. Sample scanning platform where a gel is placed on the Typhoon
Variable Mode Imager.
Post-labelling. A labelling method employed after separation by
electrophoresis. The method is used to visualize proteins in a gel. This
technique is not capable of multiplexing.
Primary amine. Primary amines, e.g., R-NH2 which undergo
nucleophilic addition with aldehydes or ketones to give carbinolamines
which then dehydrate to give substituted imines.
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181
Pre-labelling. Labelling protein samples with CyDye DIGE Fluor
minimal dyes prior to performing any electrophoretic separation.
Scanning. A process used to visualise, e.g fluorescent signal from a gel
containing fluorescently labelled proteins.
Signal-to-noise. A term used to describe the ratio of specific signal
relative to background noise.
Silver staining. A method used to visualise proteins with silver after
electrophoretic separation.
Size and charge matched. Different CyDye DIGE Fluor minimal dyes
engineered to have similar charge and molecular weight so that proteins
labelled with these dyes will run to exactly the same position within the
same gel, after 2–D separation.
Spectrally resolved. The ability of two or more dyes to be specifically
detected in the presence of each other, without significant cross-talk,
using distinct excitation and emission wavelengths for each dye.
Spot picking. Extracting a gel plug containing protein for downstream
analysis and identification.
System variation. Variations that arise due to differences in gel running,
experimental conditions or the method of data analysis.
Typhoon Variable Mode Imager. Amersham Biosciences brand name
for a laser scanning instrument.
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List of Figures
Fig 1-1.
Fig 1-2.
Fig 2-1.
Fig 2-2.
Fig 2-3.
Fig 2-4.
Fig 2-5.
Fig 2-6.
Fig 2-7.
Fig 2-8.
Fig 4-1.
Fig 4-2.
Fig 6-1.
Fig 6-2.
Fig 7-1.
Fig 7-2.
Fig 7-3.
Fig 7-4.
Fig 7-5.
Fig 7-6.
Fig 7-7.
Fig 7-8.
Fig 7-9.
Fig 7-10.
Fig 7-11.
Fig 7-12.
Fig 7-13.
Fig 9-1.
Fig 9-2.
Fig 9-3.
Fig B-1.
Fig B-2.
Outline of Ettan DIGE system .................................................... 12
Schematic of the minimal labelling reaction. .............................. 13
Workflow for differential abundance analysis and protein
identification using Ettan DIGE system. ...................................... 15
Example to illustrate the benefits of an internal standard
in comparing treated samples 3 and 4 with untreated
samples 1 and 2........................................................................ 19
Example to illustrate the benefits of an internal standard
in correctly identifying differences between
samples 1, 2, 3 and 4................................................................ 20
Intra-gel co-detection................................................................. 21
Inter-gel matching .................................................................... 22
Quantitation of protein abundance using co-detection
algorithms. 26
Matching the internal standard spot patterns. ............................ 27
Plot of sample ratios relative to normalized internal standards..... 28
IPGphor Cup Loading Strip Holder and Immobiline DryStrip
Reswelling Tray ........................................................................ 45
IPGphor Cup Loading Strip Holder. ........................................... 45
Ettan DALTsix and Ettan DALTtwelve electrophoresis
systems. .................................................................................... 60
Diagram showing the preferred position of reference markers
on the gel backing, with the gel backing lowermost. ................... 68
Scanner Control Software window. ............................................. 71
Software Workflow and Scanner Control Interface....................... 72
Ettan DALT Gel Alignment Guides in position ............................. 73
Ettan DALT Gel Alignment Guides in position on the
Typhoon Variable Mode Imager platen ....................................... 74
Ettan DALT Gel Alignment Guides in Use ................................... 74
SE 600 Gel Alignment Guides .................................................... 74
Selection of DIGE Ettan DALT tray. ............................................. 78
Scan Orientation screen............................................................. 79
Standard Gel Image Orientation ................................................. 80
DIGE File Naming Format window.............................................. 82
Multiple Sample Naming window. .............................................. 83
The Save As window .................................................................. 84
Defining a Region of interest in ImageQuant............................... 86
Scheme showing the image analysis workflow in
DeCyder Differential Analysis Software ..................................... 101
Scheme showing spot co-detection on images from a
single gel in the DeCyder DIA module. ..................................... 102
Scheme showing matching between images from three
gels and statistical analysis in the DeCyder BVA module........... 103
The SE 600 Ruby electrophoresis system................................. 107
Components of the SE 600 Ruby system.................................. 108
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183
Fig C-1.
Fig C-2.
Fig C-3.
Fig E-1.
184
CyDye DIGE Fluor Cy5 minimal dye scanned image ................. 112
CyDye DIGE Fluor Cy5 minimal dye scanned image. ............... 113
Decision tree for troubleshooting labelling using 1-D gels. ........ 115
Diagram illustrating size and positioning of electrode pads for
separation of high protein loads, e.g, preparative gels. ............. 124
Ettan DIGE System User Manual 18-1173-17 Edition AA
Index
Numerics
0.5% (w/v) Agarose sealing solution (for Ettan DALT) ..........63, 97
1 M Magnesium acetate ........................................................... 90
1.5 M Tris, to pH 8.8 ................................................................ 91
10 mM Lysine ....................................................................38, 90
10% (w/v) APS ...................................................................60, 91
10% (w/v) SDS ......................................................................... 91
12.5% 1-D PAGE gel composition (for SE 600 Ruby) ................ 91
12.5% 2-D PAGE gel composition (for Ettan DALT) ................... 96
2× gel loading buffer ........................................................90, 111
2× sample buffer ...................................................................... 92
40% (w/v) CHAPS .................................................................... 93
A
Agarose gel sealant for SE 600 Ruby ......................................... 91
B
Batch Processor ..................................................................... 104
Bind-Silane treating glass plates ............................................... 66
BVA ....................................................................................... 103
C
Chemistry of minimally labelling proteins ................................... 12
Cleaning glass plates ........................................................66, 107
CyDye DIGE Fluor minimal dyes
description ........................................................................ 13
dye working solution .......................................................... 36
labelling reaction ............................................................... 13
labelling sample with CyDye DIGE Fluor minimal dye ......... 38
stability of stock dye solution ............................................. 36
stability of working solution ..........................................36, 37
stock solution .................................................................... 36
storage .............................................................................. 36
D
DeCyder Differential Analysis Software ...................................... 99
DeStreak Rehydration Solution ................................................ 123
DIA ........................................................................................ 102
DIGE File Naming Format ......................................................... 82
Displacing solution .............................................................60, 96
E
Equilibration of focused Immobiline DryStrips ........................... 62
Equilibration solution 1 .......................................................62, 95
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Equilibration solution 2 ....................................................... 63, 95
Ettan DALT
blank gel cassettes ............................................................ 65
casting gels ....................................................................... 59
inserting gels into buffer tank ............................................ 64
low fluorescence glass plates ............................................ 59
recommended running conditions ..................................... 65
removal of gel cassettes .................................................... 64
storage of gels prior to separation ...................................... 62
Ettan IPGphor
cup loading strip holder .................................................... 44
electrode pads .................................................................. 45
electrodes ......................................................................... 45
protocols ......................................................................... 123
Experimental design
co-detection ...................................................................... 21
creating a pooled internal standard ............................. 23, 24
inter-gel matching ............................................................. 21
internal standard ............................................................... 18
using three CyDye DIGE Fluor minimal dyes ...................... 24
using two CyDye DIGE Fluor minimal dyes ......................... 23
F
First dimension separation
Immobiline DryStrip .................................................... 42, 47
protocols ......................................................................... 123
storage after rehydration or focusing .................................. 48
I
Immobiline DryStrip
equilibration ...................................................................... 62
rehydration ....................................................................... 42
storage after rehydration or focusing .................................. 48
Immobiline DryStrip rehydration
absence of protein ...................................................... 42, 50
Immobiline DryStrip Reswelling Tray ........................... 43, 50
presence of protein ..................................................... 42, 50
Immobiline DryStrips
rehydration ................................................................. 50, 56
Induced biological change ...................................................... 180
Inherent biological variation .................................................... 180
Internal standard .............................................................. 18, 180
L
Labelling .................................................................................. 12
checking sample pH ......................................................... 34
chemistry .......................................................................... 12
labelling with CyDye DIGE Fluor minimal dyes ................... 37
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testing sample labelling .............................................37, 111
M
Multiphor II
DryStrip aligner ................................................................. 53
electrodes ......................................................................... 52
Immobiline Drystrip Kit ...................................................... 52
Immobiline DryStrip tray .................................................... 52
MultiTemp ........................................................................ 52
protocols ......................................................................... 123
sample cup bar ................................................................. 55
sample cups ..................................................................... 55
O
Office Addresses ........................................................................ 3
P
Patents and Licences ................................................................. 3
Pick list .................................................................................. 104
Pooled internal standard ............................................ 18–21, 180
R
Reference markers ................................................................... 67
Rehydration buffer .................................................42, 50, 55, 94
Related products .................................................................... 175
S
Sample preparation .................................................................. 31
cell wash buffer ................................................................. 32
checking sample pH ......................................................... 34
creating a pooled internal standard .................................... 23
internal standard ............................................................... 18
preparing the labelled protein samples for the first
dimension ......................................................................... 38
protein labelling with the CyDye DIGE Fluor minimal dyes .. 38
protein quantitation ........................................................... 33
requirements for lysis buffer .............................................. 32
sonication ....................................................................... 105
Scanning
creating and using templates ............................................. 87
emission filters .................................................................. 75
file output .......................................................................... 85
fluorescence acquisition mode .......................................... 75
fluorescence scan parameters ........................................... 75
fluorescence setup ............................................................ 81
focal plane ........................................................................ 81
gel alignment guide ........................................................... 73
gel orientation ................................................................... 79
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gel orientation guide .......................................................... 79
image cropping ................................................................. 85
monitoring scan progress .................................................. 85
pixel size ........................................................................... 80
PMT voltage ...................................................................... 76
press sample .................................................................... 80
sensitivity .......................................................................... 76
shut-down procedure ........................................................ 87
software workflow .............................................................. 72
tray options ....................................................................... 77
turning on and warming up the Typhoon scanner .............. 71
SDS electrophoresis running buffer .......................................... 96
SDS Equilibration buffer-stock solution ............................... 62, 95
SE 600 Ruby
assembly ........................................................................ 108
casting gels ..................................................................... 109
inserting gels into buffer tank .......................................... 109
running gels .................................................................... 110
washing glass plates ....................................................... 107
Second dimension separation
loading Immobiline DryStrips for spot picking .................... 68
loading of focused Immobiline DryStrips ............................ 63
low fluorescence glass plates ............................................ 59
protocols ......................................................................... 123
recommended running conditions ..................................... 65
running buffer ................................................................... 63
storage of gels post electrophoresis ................................... 65
washing glass plates ....................................................... 107
Standard cell lysis buffer .......................................................... 32
Standard cell lysis buffer (option 1) .......................................... 89
Standard cell lysis buffer (option 2) .......................................... 90
Standard Cell Wash buffer .................................................. 32, 89
SYPRO Ruby gel destain .......................................................... 97
SYPRO Ruby gel fix .......................................................... 97, 119
T
TEMED 10% ...................................................................... 61, 96
Trademarks ............................................................................... 3
Trouble shooting .................................................................... 167
W
Water saturated butanol ..................................................... 60, 92
X
XML Toolbox .......................................................................... 104
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Ettan DIGE System User Manual 18-1173-17 Edition AA
TC information, Uppsala. Printed in Sweden by TK in Uppsala AB.
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