firststeps
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firststeps [2009/03/05 14:20] 132.168.73.124 |
firststeps [2009/04/16 09:39] (current) 132.168.73.247 |
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| ====== Getting Started ====== | ====== Getting Started ====== | ||
| - | This tutorial will show you how to validate a Mascot identification result with IRMa. A sample Mascot result file is available int the IRMa distribution (''<IRMA_HOME>/samples/result_sample.dat''). But the same operation could be executed with any Mascot MS/MS Ion Search result. | + | This tutorial will show you how to validate a Mascot identification result with IRMa. A sample Mascot result file is available in the [[ftp://ftp.cea.fr/pub/edyp/irma|download section]] : ''result_sample.dat''. But the same operation could be executed with any Mascot MS/MS Ion Search result. |
| + | |||
| + | **Note**: The ''.dat'' file should not be stored in a directory containing accent or blank. | ||
| ===== Step 1 : Run IRMa ===== | ===== Step 1 : Run IRMa ===== | ||
| Line 18: | Line 20: | ||
| ===== Step 2 : Open and Parse a result file ===== | ===== Step 2 : Open and Parse a result file ===== | ||
| + | **Note**: The ''.dat'' file should not be stored in a directory containing accent or blank. | ||
| - | Select Menu File --> Open --> Mascot Identification. In the //open dialog// go to the <IRMa_HOME>/samples directory and select result_sample.dat file. | ||
| - | In the first dialog, specify same parameters for Matrix Science parser (Almost, the same parameters as those proposed on mascot server search form are available here) : | + | Select Menu File --> Open --> Mascot Identification. In the //open dialog// select the ''result_sample.dat'' file. |
| + | |||
| + | In this first dialog, you must specify the parameters that will be used to generate the result (almost, the same parameters as those proposed on mascot server result view): | ||
| * Report Settings | * Report Settings | ||
| * Report top (absolute or auto) : select Auto with p value < 0.05 | * Report top (absolute or auto) : select Auto with p value < 0.05 | ||
| * peptides cut-off : score = 20 | * peptides cut-off : score = 20 | ||
| - | * subsets threashold = 1, to consider all sub sets | + | * subsets threshold = 1, to consider all sub sets |
| * Parser Properties | * Parser Properties | ||
| * Select "Never read sequence" (The result has been generated on our mascot server, so it sequence can't be retrieve in this case !) | * Select "Never read sequence" (The result has been generated on our mascot server, so it sequence can't be retrieve in this case !) | ||
| + | |||
| + | {{ parser_settings.png?300 | Parser settings}} | ||
| ===== Step 3 : Filter results ===== | ===== Step 3 : Filter results ===== | ||
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| * rank threshold = 1 | * rank threshold = 1 | ||
| + | {{ filter_settings.png?300 | Filter settings}} | ||
| - | ===== Step 4 : Browse result ===== | + | ===== Step 4 : Result validation ===== |
| From Protein Centric Navigation Panel, you can select any identified protein hit to view its property (see User Guide Description...FIXME) | From Protein Centric Navigation Panel, you can select any identified protein hit to view its property (see User Guide Description...FIXME) | ||
| - | |||
| - | ===== Step 5 : Result curation ===== | ||
| They can be identified in the Protein Centric Navigation Panel, they are grayed | They can be identified in the Protein Centric Navigation Panel, they are grayed | ||
| + | |||
| + | {{ hit_search.png?500 | Hit search}} | ||
| For example, | For example, | ||
| Line 58: | Line 65: | ||
| * In Protein Hit Tab, clik on first icon : <IMG> | * In Protein Hit Tab, clik on first icon : <IMG> | ||
| - | It is also possible to delete all protein hits with no relevant peptides bu clicking on <IMG_ALL_DEL> in general toolbox. | + | It is also possible to delete all protein hits with no relevant peptides by clicking on <IMG_ALL_DEL> in general toolbox. |
| - | + | ||
| - | ===== Step 6 : Export validated result ===== | + | |
| + | ===== Step 5 : Export validated result ===== | ||
| + | Once validated, the identification result can be exported into various formats. Click File -->Export --> Identification result --> to Excel. Choose the name of the file that will be generated and click Save | ||
firststeps.1236259200.txt.gz · Last modified: 2009/03/05 14:20 by 132.168.73.124
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