1. Right-click on the context node of your choice in the MSIExplorer view to display context sensitive menu and select “Algorithms→Group proteins…”
2. If needed, change settings for protein grouping (see explanations below), and Ok
3. When grouping process is finished, the color of the context name change to red in the MSIExplorer view.

Protein grouping settings:

• Peptides having same sequence and mass are gathered together, but to avoid rejecting peptides very “close” to each other, you can specify a mass tolerance (ppm)
• Optionnally, you can filter peptides according peptide length. For example, remove all peptides with a sequence lower than 6
• Optionnally, you can filter reverse proteins and/or proteins identified with a given number of low score peptides