The purpose is to search for similar protein groups, i.e. protein groups:

• having the same set of proteins
• identified by a same set of peptides

The Dice coefficient is used to measure similarity (result ranges from 0 to 1).

Main steps:

1. Retrieve selected contexts to compare
2. Compare selected contexts to their union (i.e. a parent context that 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 union parent must be created in case 1: it is called virtual as it is only created in-memory for the process
• the union parent already exists in case 2

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:

1. Checking the similarity of their peptide sets
2. Checking the similarity of their protein sets (sameset and subset)

Case 1: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred

Case 2: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred

Case 3: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred

Case 4: if a Protein Group (context1) is compared to the 2 following Protein Groups (Context2), PG2 will be preferred

When the comparison algorithm execution has finished, a window displays on the screen.
The most left column (“Union reference”) displays protein groups (master protein accession) from the (virtual) union parent context.
For each protein group of the Union Reference context, the table displays the most “similar” protein group in each compared contexts.
For each compared context a default set of properties are displayed. You can change them by selecting/deselecting items in the droplist (right side).

Protein group properties:

• “ProtSim”: similarity on the samesets of proteins of the two protein groups
  
• “AllProtSim”: similarity on the samesets and subsets of proteins of the two protein groups
  
• “PepSim”: similarity on peptides of the two protein groups
• “isSameTypical”: indicates if the typical protein is the same between the two protein groups
• “Typical”: the accession of the master protein group
• “Score”: score for the protein group
• “#Pep”: number of peptides for the protein group
• “#AllProt”: number of proteins in the protein group. 'X(Y,Z)' means a total of X proteins for the whole protein group (X=Y+Z) with Y sameset proteins and Z subset proteins
• If Spectral Count algorithm is run previously, Spectral Count values will be available as well

When comparing two protein groups using “Protein” and “Peptide” similarity criteria, you can get four main situations: