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The purpose is to search for similar protein groups, i.e. protein groups:
The Dice coefficient is used to measure similarity (result ranges from 0 to 1).
The purpose is to select contexts to compare, then to compare them to their union, i.e. a parent context, which contains selected children contexts, and for which peptide/protein grouping has been executed.
There are 2 possibilities, either the parent union already exists or the parent union needs to be created.
In the image below:
The algorithm will then compare every protein groups of the union parent context to every protein groups of each children context in order to find the best alignment.
Comparing two protein groups each other means:
Case 1: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred
PG1 | PG2 | |
---|---|---|
peptideSimilarity | 0.2 | 0.5 |
proteinSimilarity | 0.4 | 0.6 |
AllProtSimilarity | - | - |
Case 2: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred
PG1 | PG2 | |
---|---|---|
peptideSimilarity | 0.5 | 0.5 |
proteinSimilarity | 0.4 | 0.6 |
AllProtSimilarity | - | - |
Case 3: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred
PG1 | PG2 | |
---|---|---|
peptideSimilarity | 0.5 | 0.5 |
proteinSimilarity | 0.6 | 0.6 |
AllProtSimilarity | 0.5 | 0.6 |
Case 4: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred
PG1 | PG2 | |
---|---|---|
peptideSimilarity | 0.0 | 0.0 |
proteinSimilarity | 0.6 | 0.8 |
AllProtSimilarity | - | - |
When the comparison algorithm execution is finished, a window displays on the screen. For each compared context a default set of properties are displayed. You can change them by selecting/deselecting items in the droplist (right side).
In the short view, the “Typical reference” column lists the protein groups of the parent context. There are as much columns as there are direct child contexts for this parent context. These columns display the value of the parameter selected in the droplist (“#peptides”, “Typical”, “Score”, “Pep. similarity”, “Prot. similarity”, “All Prot. similarity”).
Different criteria to compare protein groups:
If Spectral Count algorithm has been run previously, Spectral Count properties will also be available.
When comparing two protein groups using “Protein” and “Peptide” similarity criteria, you can get four main situations:
Low Protein similarity | High Protein similarity | |
---|---|---|
Low Peptide similarity | Proteins groups are not alike | We have identified the same proteins but with different peptides (rare) |
High Peptide similarity | See image (on the left) to have an example of how to get this situation. It's usefull to check the “All Protein” similarity to have an information on proteins in subset | protein group are alike |
The most left column (“Protein (ref)”) displays protein groups from the first context. The most right column (“Protein (comp)”) displays protein groups from the second context.
For each protein group of the first context, the table proposes the most “similar” protein group in the second context (“Protein similarity”, “All protein similarity”, “Peptide similarity”,“Same typical”).