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).

It compares every protein groups of the first context with every protein groups of the second context.
Comparing two protein groups each other means:

• Checking the similarity of their protein sets ( sameset and subset)
• Checking the similarity of their peptide sets
• Checking if “master” proteins are identical

This comparison is similar to the previous one: similarity measure and “best alignment”
Each context is compared with a “unique reference”. First of all, this reference is built from the identification union, i.e. the parent context.