Proteins, groups and peptides
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