When parsing a Mascot identification result the manipulated data are :

• queries : a spectra submitted to Mascot for identification
• peptide : peptide sequence identified by a query and matching a protein (issued from the searched data bank). Mascot assigns up to ten peptide sequences of each submitted spectra.
• protein groups (or hits) : collection of proteins identified by a set of peptides or peptide-sequence matches (PSM). Proteins that span the same set of peptides, or a subset pf peptides, are collapsed into a single hit.

More definitions on terms used in IRMa

• unassigned queries : Queries that or not matching any peptide sequence.
• unassigned peptides queries : Queries matching one or more peptide sequences, but whose peptides are not collapsed into hit.
• ambiguous peptides queries : Queries matching one or more peptides that are not collapsed into hits (unassigned peptides queries) or that are classified as ambiguous.
• assigned peptides queries : Queries matching at least one peptide sequence classified as significant or duplicated into one or more hits.

• Protein Groups represented by protein P1 and identified by peptides pe1, pe2 and pe3, contains a same set peptides protein : P11
• Protein Groups represented by protein P3 and identified by peptides pe4, pe5 and pe6 and pe7, contains a subset peptides protein P31 identified by peptides pe6 and pe7