prolineconcepts:rs
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prolineconcepts:rs [2015/07/09 14:42] 130.79.67.200 [OMSSA result importation] |
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, OMSSA ''.omx'' or a 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. | + | 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 information: | + | 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 | ||
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| ==== X! Tandem result importation ==== | ==== X! Tandem result importation ==== | ||
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| + | **Note 0:** X! Tandem file should respect XML markup structure. | ||
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| + | **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 : | ||
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| + | ''<group id="581" mh="1840.926000" z="1" rt="25.5" type="model">'' | ||
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| + | **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.1436445722.txt.gz · Last modified: 2015/07/09 14:42 by 130.79.67.200
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