MIAPE document  
Gel Electrophoresis Informatics MIAPE document  
Based on the original guidelines: MIAPE GI v1.0  
 

1. General features
ID #: 
397
Name: 
DIGE analysis for 96hr samples
Last update: 
2/8/2011 4:55:38 PM
 
1.1 Responsible person or role
Name: 
Jenna
Last name: 
Kenyani
Email: 
j.kenyani@liverpool.ac.uk
Address: 
School of Veterinary science
Locality: 
Brownlow Hill, Liverpool
Country: 
Uk
Institution: 
University of Liverpool
Position:
researcher
 
1.2 Electrophoresis type: 
difference gel electrophoresis
 
1.3 Electrophoresis context: 
MIAPE GE reference: 663
Link to the report: http://estrellapolar.cnb.csic.es/proteored/MIAPE/MIAPE_GE.asp?pmCodigoAcceso=ae31268d&pmIDUsuario=2378&pmId=663
 
1.4 Image (1/13)
ID: 
1533
Name: 
Gel1-Cy2_internalstandard
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_STANDARD_CY2.gel
 
1.4 Image (2/13)
ID: 
1534
Name: 
Gel1-Cy3-Control
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY3.gel
 
1.4 Image (3/13)
ID: 
1535
Name: 
Gel1-Cy5-Treated
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY5.gel
 
1.4 Image (4/13)
ID: 
1536
Name: 
Gel2-Cy2_internalstandard
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_STANDARD_CY2.gel
 
1.4 Image (5/13)
ID: 
1537
Name: 
Gel2-Cy3-Control
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY3.gel
 
1.4 Image (6/13)
ID: 
1538
Name: 
Gel2-Cy5-Treated
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY5.gel
 
1.4 Image (7/13)
ID: 
1539
Name: 
Gel3-Cy2_internalstandard
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_STANDARD_CY2.gel
 
1.4 Image (8/13)
ID: 
1540
Name: 
Gel3-Cy5-Control
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY3.gel
 
1.4 Image (9/13)
ID: 
1541
Name: 
Gel3-Cy3-treated
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY3.gel
 
1.4 Image (10/13)
ID: 
1542
Name: 
Gel4-Cy2_internalstandard
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_STANDARD_CY2.gel
 
1.4 Image (11/13)
ID: 
1543
Name: 
Gel4-Cy3-treated
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY3.gel
 
1.4 Image (12/13)
ID: 
1544
Name: 
Gel4-Cy5-Control
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2357 pixels
Y: 1807 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_54942_crop_CY5.gel
 
1.4 Image (13/13)
ID: 
1545
Name: 
PickGel_Sypro
Type 
DIGE scans
Format: 
Tagged Image File Format
Dimensions:
X: 2354 pixels
Y: 1564 pixels
Resolution:
252 dots per inch
Bit-depth: 
16
Standard image orientation: 
Normal orientation
Stored in: 
http://estrellapolar.cnb.csic.es/proteored/MIAPE/Ficheros/462/96hr_rat_PICKGEL_sypro_crop_SYPRO_Ruby_2.jpg
 
1.5 Image analysis software
DeCyder - Version: 6.5
Vendor: 
GE Healthcare Life Sciences
Description: 
DIA module (Differencial in Gel Analysis)
BVA module (Biological Variation Analysis)
 
2. Gel analysis design
ID: 315
Name: 
Design card
2.1 Type: 
Directed, 2 groups
2.2 Replicates: 
4 Biological replicates
2.3 Groups: 
Control1 Cy3 - Treatment1 Cy5 - IntStand1 Cy2
Control2 Cy3 - Treatment2 Cy5 - IntStand2 Cy2
Control3 Cy5 - Treatment3 Cy3 - IntStand3 Cy2
Control4 Cy5 - Treatment4 Cy3 - IntStand4 Cy2

Grouped according to Control or Treatment
2.4 Standards: 
internal standards - an aditional sample run in the same physical gel to normalize results, from an equal pool of control and treated
 
3. Image preparation
 
3.2 Image preparation step
Name: 
Cropping step
Type: 
Cropping- To remove strip at top of image so not to interfer with spot detection
Step number: 
1st
 
4. Image processing
Name: 
Loading images in to DeCyder
4.1 Input image reference (from section 1): 
ID:1533- Name:Gel1-Cy2_internalstandard
ID:1534- Name:Gel1-Cy3-Control
ID:1535- Name:Gel1-Cy5-Treated
ID:1536- Name:Gel2-Cy2_internalstandard
ID:1537- Name:Gel2-Cy3-Control
ID:1538- Name:Gel2-Cy5-Treated
ID:1539- Name:Gel3-Cy2_internalstandard
ID:1540- Name:Gel3-Cy5-Control
ID:1541- Name:Gel3-Cy3-treated
ID:1542- Name:Gel4-Cy2_internalstandard
ID:1543- Name:Gel4-Cy3-treated
ID:1544- Name:Gel4-Cy5-Control
ID:1545- Name:PickGel_Sypro
 
4.2 Image processing software
DeCyder
Vendor: 
GE Healthcare
Description: 
Image loader module
 
4.3 Processing step
Name: 
Loading of images
Step number: 
2nd
 
5. Data extraction process
Name: 
Data extraction
 
5.1 Feature detection
Algorithm name/version: 
Spot detection
Step number: 
3rd
Feature editing: 
Automaticaly in DIA module
 
5.2 Matching
Algorithm name/version: 
Spot matching
Feature reference image used (from section 1): 
ID:1539- Name:Gel3-Cy2_internalstandard
Landmarks: 
Manually assigned
Match editing: 
Automaticaly in BVA molule and reviewed manualy
 
5.3 Feature quantitation
Algorithm name/version: 
Quantitation in DeCyder
Type: 
ratios of normalized volumes
 
5.3.1 Quantitation
DeCyder™ DIA algorithm
Parameters: 
co-detection, background subtraction, normalization, and quantitation of spots in images
 
5.3.3 Normalization
DeCyder™ DIA algorithm
Parameters: 
co-detection, background subtraction, normalization, and quantitation of spots in images
 
6. Data analysis
Name: 
Analysis
Analysis intent: 
Finding the spots with a statistical significant differential expression
Type: 
student’s T test was performed and averaged ratios
Parameters: 
Any protein spots which appeared in nine of the twelve gels and had a +/- fold change of 1.5 or above (p<0.05) was highlighted as a spot of interest.
 
6.2 Data analysis software
DeCyder
Vendor: 
GE Healthcare
Description: 
BVA protein statistics