====== Proteins, groups and peptides ======

[[principle|Back Concepts]]


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.


{{:grouping.png| }}

  * 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