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.

1. Select the two contexts (for which protein grouping has been executed) you want to compare each other
2. Right-click and select “Algorithms→Compare with→Each Other”
3. The comparison window display the result
4. You can save results as a .xls, .pdf or .html file using the “Export” button

1. Select the context of your choice (first, protein grouping needs to be run for this context and its childs)
2. Right-click and select “Algorithms→Compare with→Children”
3. The comparison window display the result
4. Select the characteristic you want to compare