prolineconcepts:rs
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prolineconcepts:rs [2013/11/08 18:05] 193.48.0.3 [Search Result] |
prolineconcepts:rs [2016/07/07 14:19] (current) 132.168.72.225 [X! Tandem result importation] |
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| 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** (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 or an OMSSA ''.omx'') 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. | + | 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 ===== | ===== Content of a Search Result ===== | ||
| - | Importing a [[prolineconcepts:resultfile|]] creates a new [[prolineconcepts:rs_rsm|Search Result]] in the database which contains the following informations: | + | 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 | + | * Search Settings: software name and version, parameters values |
| - | * Peak List and Spectrum information : file name, ms-level, precursor moz, ... | + | * Peak-List and Spectrum information: file name, MS level, precursor m/z, ... |
| * Search result data: | * Search result data: | ||
| - | * Proteins | + | * Protein sequences |
| - | * Peptide | + | * Peptide sequences |
| - | * Spectrum | + | * Spectra |
| - | * 2 type of Matches | + | * 2 kinds of Matches |
| - | * a Peptide Match is a match between a peptide and a spectrum, with score, fragment matches ... | + | * Peptide Spectrum Matches, i.e. the matching between a peptide and a spectrum, with some related data such as the score, fragment matches... |
| - | * a Protein Matches is a match between a peptide and a protein | + | * Protein Matches, i.e. the proteins in the databank corresponding to the PSMs identified by the search engine |
| ==== Mascot result importation ==== | ==== Mascot result importation ==== | ||
| Line 30: | Line 30: | ||
| FIXME : todo : OMSSA specificities | 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.1383930305.txt.gz · Last modified: 2013/11/08 18:05 by 193.48.0.3
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