All peptides identifying a protein are grouped in a Peptides Set. A same Peptides Set can identify many proteins, represented by one Proteins Set. In this case, one protein of this Protein Set is chosen to represent the set, it is the Typical Protein. If only a sub set of peptides identify a (or some) protein(s), a new Peptide Set is created. This PeptideSet is a subset of the first one, and identified Proteins are Subset Proteins.

• In first example, P2 and P5 are identified by the same peptide set {pe1, pe4, pe5, pe8}. P2 was chosen as typical protein. One SubSet composed of {pe4, pe5, pe8} identify subset protein P4.
• In second example, Another Protein Set represented by P3, shares some peptides with ProteinSet represented by P2. Both ProteinSets have specific peptides.
• Sharing could involve many ProteinSet as shown in example 3.

All Peptides Sets and associated ProteinSets are represented, even if there are no specific peptides. In both cases of above example, no choice is done on which ProteinSet / PeptideSet to keep. These ProteinSets could be filtered after inference (see Protein sets filtering).