====== Search Result ======

A **Search Result** (aka [[:msidb_documentation#result_set|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 [[prolineconcepts: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 [[prolineconcepts: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)