Call
510.887.0889

Email: support@appliedbiomics.com
Serving Your Proteomics Needs


   


Cross-gel Analysis

Ideal for comparing more than 3 samples, or multiple replicates in each experimental group

An Internal Standard made up of equal amounts of each sample is run on all gels.

Importance Of Internal Standard
o Represents all protein spots
o Decreases gel-to-gel variation and enables gel-to-gel matching
o Enables fully automated, accurate spot statistics
o Allows detection of real biological variance

How Many Replicates Do I Need?
o Cell lines: 4
o Mice: 4+
o Humans: more are better within the constraints of reality

Study Designs (Click to see more details)
o Study Design 1: More than 3 individual samples
o Study Design 2: Two groups of samples, Multiple replicates per group
o Study Design 3: Two groups of samples, Two conditions per group, Multiple replicates
o Study Design 4: Multiple groups of samples, Multiple conditions per group, Multiple replicates

Study Design 1: Example

Type of samples
o Four individual samples: sample 1, 2, 3, 4
o No replicates

Number of gels: 2

Data analysis: Pair-wise comparison in any of the 2 samples

Cy2
Cy3
Cy5

Gel 1
Standard
Sample 1
Sample 2
Gel 2
Standard
Sample 3
Sample 4

Standard = Sample 1-4


Data Report

Protein expression ratio between any 2 samples

Study Design 2: Example

Type of samples
o Two Groups of samples: Control (C) and Test (T)
o Four replicates in each group: C_1, 2, 3, 4; T_1, 2, 3, 4

Number of gels: 4 (Dye swap labeling)

Data analysis: comparison between the two groups

Cy2
Cy3
Cy5

Gel 1
Standard
C_1
T_1
Gel 2
Standard
T_2
C_2
Gel 3
Standard
C_3
T_3
Gel 4
Standard
T_4
C_4

Standard = C1-4, T1-4


Data Report

1. Average protein expression ratio between control and test group

2. Statistical analysis of Control vs. Test









Study Design 3: Example

Type of samples
o Two Groups of samples: Control (C) and Test (T)
o Two Conditions in each group: A, B
o Three replicates each: CA_1, 2, 3; CB_1, 2, 3; TA_1, 2, 3; TB_1, 2, 3;

Number of gels: 6 (Dye swap labeling)

Data analysis: one way and two way ANOVA

Cy2
Cy3
Cy5

Gel 1
Standard
CA_1
CB_1
Gel 2
Standard
TA_1
TB_1
Gel 3
Standard
CA_2
TA_2
Gel 4
Standard
TB_2
CB_2
Gel 5
Standard
TB_3
CA_3
Gel 6
Standard
CB_3
TA_3
Standard = CA_1, 2, 3; CB_1, 2, 3; TA_1, 2, 3; TB_1, 2, 3




Data Report

1. Average protein expression ratio between any two groups

2. Statistical analysis on Control vs. Test

3. Statistical analysis on A vs. B

4. Statistical analysis on the interaction of 2 conditions (2-way ANOVA)

 

Study Design 4: Example

Type of samples

o Multiple Groups of samples: Group 1, 2, 3, 4
o Multiple Conditions in each group: Condition A, B, C, D
o Multiple replicates each

Number of gels
o Total number of samples divided by 2
o Dye swap labeling and random pairing

Data analysis: one way and two way ANOVA



Data Report

1. Average protein expression ratio between any two groups

2. Statistical analysis on each condition

3. Statistical analysis on the interactions between any 2 conditions


 



Call our tech support at 510-887-0889 or send email to support@appliedbiomics.com with any technical questions.


Copyright ©2009 Applied Biomics, Inc.. All rights reserved. Terms