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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. |
===== Step 1 : Run IRMa ===== | ===== Step 1 : Run IRMa ===== | ||
- | To start IRMa, simply double clic on the batch file ''run.bat'' or launch it from the command prompt. If the application didn't start, please check your java installation (see [[instalguide#Requirements]]) The first time IRMa is launched, it will ask for some preferences properties. Mandatory values are | + | To start IRMa, simply double clic on the batch file ''run.bat'' or launch it from the command prompt. If the application didn't start, check your java installation (see [[instalguide#Requirements]]). The first time IRMa is launched, it will ask for some preferences properties. Mandatory values are |
* Mascot Server | * Mascot Server | ||
- | * Mascot URL : URL of your mascot server | + | * Mascot URL : URL of your mascot server. If you don't have a local mascot server, you can use http://www.matrixscience.com/. |
* Mascot Server Version : 2.0 and 2.1 data were formated differently. 2.1 could be choose for 2.1 and above version | * Mascot Server Version : 2.0 and 2.1 data were formated differently. 2.1 could be choose for 2.1 and above version | ||
- | * Mascot data path : path where result files are saved, specified in Mascot configuration. Default is ../data/and may be right for most installation | + | * Mascot data path : path where result files are saved, specified in Mascot configuration. Default is ''../data/'' and may be right for most installation |
- | If you don't have a local mascot server, you can specify http://www.matrixscience.com/ in order to pass the preference dialog. | + | {{ config_irma.png?400 | IRMa configuration}} |
Other preferences are not needed to run IRMa and can be changed later. | Other preferences are not needed to run IRMa and can be changed later. | ||
- | ==== Open result file ==== | + | ===== Step 2 : Open and Parse a result file ===== |
- | Select Menu File --> Open --> Mascot Identification. In the //open dialog// go to the <IRMa_HOME>/samples directory and select result_sample.dat file. | + | Select Menu File --> Open --> Mascot Identification. In the //open dialog// select the ''result_sample.dat'' file. |
- | === Parser === | + | 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): |
- | + | ||
- | 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) : | + | |
* 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 ===== | ||
In the filter dialog, the second one, parameters specified are used to classify PSM (Peptide Spectra Matches) to significants, duplicated or ambiguous groups. | In the filter dialog, the second one, parameters specified are used to classify PSM (Peptide Spectra Matches) to significants, duplicated or ambiguous groups. | ||
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* rank threshold = 1 | * rank threshold = 1 | ||
+ | {{ filter_settings.png?300 | Filter settings}} | ||
- | ==== Browse result ==== | + | ===== Step 4 : Browse result ===== |
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) | ||
- | === Hit with no relevant peptides === | + | ===== Step 5 : Result validation ===== |
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 | ||
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* 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 ===== | ||