userguide:pride_converter
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userguide:pride_converter [2011/03/02 15:12] 132.168.74.230 |
userguide:pride_converter [2011/03/04 18:17] (current) 132.168.74.230 |
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| It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS).\\ | It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS).\\ | ||
| - | ===== Generate a PRIDE XML file to only extract its detailled header ===== | + | ===== Generate a PRIDE XML file from a Mascot DAT File ===== |
| - | Below are the main steps to follow. For more details, see PRIDE Converter help which is accessible from each panel of the wizard. | + | :!:**Warning**:!: |
| + | * **The purpose here is to __create a PRIDE XML file from which we will only extract the header part__ (information about contact, experiment, sample, protocol, etc.). So, steps concerning the data itself (spectra selection, peptide and protein identification, etc.) are not described here.** | ||
| - | :!:**Tips:** | ||
| + | :!:**Tips**:!: | ||
| + | |||
| + | * PRIDE Converter help is accessible from each panel of the wizard | ||
| * If you don't know which ''CV Term'' to use, you can always ''Browse Ontology'' | * If you don't know which ''CV Term'' to use, you can always ''Browse Ontology'' | ||
| * To move up/down rows in tables (Protocol steps, etc.) right-click on a row and select ''Move Up'' or ''Move Down'' | * To move up/down rows in tables (Protocol steps, etc.) right-click on a row and select ''Move Up'' or ''Move Down'' | ||
| Line 72: | Line 75: | ||
| * Name: protocol name | * Name: protocol name | ||
| * Ok | * Ok | ||
| - | * Click on ''Add Protocol Step'' | + | * Click on ''Add Protocol Step'' (add as much protocol steps as needed) |
| * Click on ''Ontology Lookup Service'' | * Click on ''Ontology Lookup Service'' | ||
| * Select the appropriate ontology, for ex. PRIDE Controlled Vocabulary [PRIDE] | * Select the appropriate ontology, for ex. PRIDE Controlled Vocabulary [PRIDE] | ||
| Line 80: | Line 83: | ||
| * The CV Term you have selected appears now as a row in the ''Protocol Step'' table. Depending on the CV Term, it may be possible to specify a value. You can enter, for ex., ''Trypsin'' for the value of the ''Enzyme digestion'' CV Term (just double-click on the ''Value'' cell of this CV Term) | * The CV Term you have selected appears now as a row in the ''Protocol Step'' table. Depending on the CV Term, it may be possible to specify a value. You can enter, for ex., ''Trypsin'' for the value of the ''Enzyme digestion'' CV Term (just double-click on the ''Value'' cell of this CV Term) | ||
| * Ok | * Ok | ||
| - | * Add as much protocol steps as needed. | ||
| - | |||
| === Identification Type === | === Identification Type === | ||
| Line 87: | Line 88: | ||
| * Select the appropriate technology ''2D Gel'' or ''Other'' | * Select the appropriate technology ''2D Gel'' or ''Other'' | ||
| * Next > | * Next > | ||
| + | |||
| + | ==== Instrument Properties - Step 6 of 8 ==== | ||
| + | |||
| + | === Instrument === | ||
| + | |||
| + | * Click on ''Please Select an Instrument'' -> ''Create a New Instrument...'' | ||
| + | * Name: instrument name (for ex. LTQ-Orbitrap) | ||
| + | * Ok | ||
| + | * Source: click on the OLS button to find the appropriate CV term (for ex. in the ''Mass Spectroscopy CV (PSI-MS) [PSI]'' ontology, search the ''Electrospray Ionization'' Term Name) | ||
| + | * Detector: click on the OLS button to find the appropriate CV term (for ex. in the ''PRIDE Controlled Vocabulary [PRIDE]'' ontology, search the ''Microchannel Plate Detector'' Term Name) | ||
| + | * Click on ''Add Analyzer'' (at least one analyser) | ||
| + | * Click on ''Ontology Lookup Service'' to find the appropriate CV term (for ex. in the ''Mass Spectroscopy CV (PSI-MS) [PSI]'' ontology, search the ''LTQ Orbitrap'' Term Name) | ||
| + | * Click on ''Use Selected Item'' | ||
| + | |||
| + | === Processing === | ||
| + | |||
| + | * Software Name: ex. Mascot Distiller | ||
| + | * Software Version: ex. 2.2 | ||
| + | * Click on ''Add Processing Method'' (at least one processing method) | ||
| + | * Click on ''Ontology Lookup Service'' to find the appropriate CV term (for ex. in the ''Mass Spectroscopy CV (PSI-MS) [PSI]'' ontology, search the ''Peak Processing'' Term Name) | ||
| + | * Click on ''Use Selected Item'' | ||
| + | * If needed, provide information the ''Value'' cell (for ex. ''CentroidMassSpectrum'' for the ''Peak Processing'' CV Term) | ||
| + | * Next > | ||
| + | |||
| + | ==== User Parameters - Step 7 of 8 ==== | ||
| + | |||
| + | If there is anything else you would like to say about the experiment this is where you can do just that (a user parameter has a name and a value, for ex. ''ImportantComponent'' for the name, ''Cryptonite'' for the value) | ||
| + | |||
| + | ==== Output Properties - Step 8 of 8 ==== | ||
| + | |||
| + | * Select an output folder | ||
| + | * Click on ''Convert!'' | ||
| + | * Dialogs about | ||
| + | * modifications may appear. Click ''Ok'' for all. | ||
| + | * protein isoforms may appear. Select ''Always Select The First Isoform'', then ''Ok'' | ||
| + | |||
| + | A file ''mascotDatFile_MyLabel_to_PRIDE_YYYYMMDD_123456.xml.gz'' is created in your ouput folder (where ''myLabel'' is the label you specified in Step 3).\\ | ||
| + | Uncompress the file to obtain the ''mascotDatFile_MyLabel_to_PRIDE_YYYYMMDD_123456.xml'' file. | ||
userguide/pride_converter.1299075165.txt.gz · Last modified: 2011/03/02 15:12 by 132.168.74.230
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