Home > Proteomics Services > 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
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
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Cy3
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Cy5
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Gel 1
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Standard
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Sample 1 | Sample 2 |
Gel 2
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Standard
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Sample 3 | Sample 4 |
Standard = Sample 1-4 |
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Data Report Protein expression ratio between any 2 samples |
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
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Cy3
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Cy5
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Gel 1
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Standard
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C_1
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T_1
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Gel 2
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Standard
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T_2
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C_2
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Gel 3
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Standard
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C_3
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T_3
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Gel 4
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Standard
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T_4
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C_4
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Standard
= C1-4, T1-4
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Data Report 1. Average protein expression
ratio between 2. Statistical analysis of Control vs. Test |
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
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Cy3
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Cy5
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Gel 1
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Standard
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CA_1
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CB_1
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Gel 2
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Standard
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TA_1
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TB_1
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Gel 3
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Standard
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CA_2
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TA_2
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Gel 4
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Standard
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TB_2
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CB_2
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Gel 5
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Standard
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TB_3
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CA_3
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Gel 6
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Standard
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CB_3
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TA_3
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Standard
= CA_1, 2, 3; CB_1, 2, 3; TA_1, 2, 3; TB_1, 2, 3
|
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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) |
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
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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 |