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prolineconcepts:rs

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.

Content of a Search Result

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

Mascot result importation

FIXME : todo : Mascot specificities

The peptide matches score correspond to Mascot ion score

OMSSA result importation

FIXME : todo : OMSSA specificities

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

  • Score = -log10(E-value)

X! Tandem result importation

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 (FIXME: 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 (FIXME: 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)

prolineconcepts/rs.txt · Last modified: 2016/07/07 14:19 by 132.168.72.225