how_to:studio:importmascot
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| Both sides previous revision Previous revision Next revision | Previous revision | ||
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how_to:studio:importmascot [2014/09/29 10:18] 130.79.67.121 [Import in All Imported] |
how_to:studio:importmascot [2015/10/28 15:04] (current) 132.168.72.237 [Import directly in a Dataset] |
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| - select the file(s) you want to import thanks to the file button (the Parser will be automatically selected according to the type of file selected) | - select the file(s) you want to import thanks to the file button (the Parser will be automatically selected according to the type of file selected) | ||
| - | - select the different parameters | + | - select the different parameters (see description below) |
| - click on OK button | - click on OK button | ||
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| **Note 3** : Proline is able to import OMSSA files compressed with BZip2. | **Note 3** : Proline is able to import OMSSA files compressed with BZip2. | ||
| + | |||
| + | **__Parameters description__ :** | ||
| + | |||
| + | * Software Engine: the software which generated your interrogation file | ||
| + | * Instrument: mass-spectrometer used for sample analysis | ||
| + | * Peaklist Software: the software used for the peaklist creation | ||
| + | |||
| + | * Decoy Strategy: The type of decoy search which was performed. | ||
| + | * "No Decoy Database": if the search was performed against a target database only. | ||
| + | * "Concatenated Decoy Database": if target and decoy sequences were merged into a single database. | ||
| + | * "Software Decoy": if the "Decoy" sequences were generated on-the-fly by your search engine. | ||
| + | * Protein Match Decoy Rule: for concatenated searches only. Select the rule to apply for the discrimination of target and decoy protein matches. | ||
| + | |||
| + | * Parser Parameters: according to your Software Engine, this will display some extra-parameters. | ||
| + | * Mascot: | ||
| + | * Ion Score Cutoff: peptide matches with a score lower than this value won't be imported | ||
| + | * Subset Threshold: the percentage of score between a given protein match and the master protein match (superset). Protein matches with a relative score lower than <code>Master_protein_score * (1-subset threshold)</code> won't be imported. | ||
| + | * Mascot Server URL : URL of the local Mascot server from where some information would be retrieve. | ||
| + | * Omssa: | ||
| + | * User mod file: TODO | ||
| + | * PTM Composition File: TODO | ||
| + | |||
| {{:how_to:studio:importidentificationdialogV3.png|}} | {{:how_to:studio:importidentificationdialogV3.png|}} | ||
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| ===== Import directly in a Dataset ===== | ===== Import directly in a Dataset ===== | ||
| - | It is possible to import a Search Result directly in an Dataset. In this case, the Search Result is avaible in "All Imported" too. | + | It is possible to import a Search Result directly in a Dataset. In this case, the Search Result is available in "All Imported" too. |
| + | |||
| + | To import a Search Result in a Dataset, right click on a dataset and then click on "Import Search Result..." menu. | ||
| - | To import a Search Result in a Dataset, right click on a dataset and then click on "Add > Search Result..." menu. | ||
| - | {{:how_to:studio:importidentificationinaggregatev3.png|}} | + | {{:how_to:studio:importsearchresultpopup.png|}} |
how_to/studio/importmascot.1411978700.txt.gz · Last modified: 2014/09/29 10:18 by 130.79.67.121
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