Search Result

A Search Result (aka ResultSet in the database schema) is the raw interpretation of a given set of MS/MS spectra given by a search engine or a de novo interpretation process. It contains one or many peptides matching the submitted MS/MS spectra (PSM, i.e. Peptide Spectrum Match), and the protein sequences these peptides belong to. The Search Result also contains additional information such as search parameters, used protein sequence data-bank, etc.

A Search Result is created when a resultfile (Mascot .dat file, OMSSA .omx or an X! Tandem .xml) file is imported in Proline. In the case of a target-decoy search, two Search Results are created: one for the target PSMs, one for decoy PSMs.

Importing a resultfile creates a new Search Result in the database which contains the following information:

• Search Settings: software name and version, parameters values
• Peak-List and Spectrum information: file name, MS level, precursor m/z, …
• Search result data:
  • Protein sequences
  • Peptide sequences
  • Spectra
  • 2 kinds of Matches
    • Peptide Spectrum Matches, i.e. the matching between a peptide and a spectrum, with some related data such as the score, fragment matches…
    • Protein Matches, i.e. the proteins in the databank corresponding to the PSMs identified by the search engine

: todo : Mascot specificities

The peptide matches score correspond to Mascot ion score

: todo : OMSSA specificities

The peptide matches score correspond to the negative common logarithm of the E-value:

• Score = -log10(E-value)

Note 0: X! Tandem file should respect XML markup structure.

Note 1: regarding rt (retention time) label in <group> markup, it should be a real number. The current version of X! Tandem (Sledgehammer) generates a real number, which is not the case for (: some / all) previous versions. For exemple :

<group id=“581” mh=“1840.926000” z=“1” rt=“25.5” type=“model”>

Note 2: If all mark-ups and labels, needed for file import (: list them all) , are not existing in X! Tandem file, it'll generate error during import in ProlineStudio! The latest version, Sledgehammer, are supported in actual ProlineStudio (v.1.1)