====== PRIDE Converter ======

PRIDE Converter is available at [[http://code.google.com/p/pride-converter/]]\\

  * Dowload the PRIDE_Converter_vX.Y.Z.zip file, then unzip.\\
  * To execute PRIDE Converter, double-click on PRIDEConverter-X.Y.Z.jar\\

PRIDE Converter converts mass spectrometry data from most common data formats (MASCOT .dat file for example) into PRIDE XML.\\
(PRIDE XML is the file format used for submission to the publicly available PRIDE database).\\
It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS).\\

===== Generate a PRIDE XML file from a Mascot DAT File =====

:!:**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**:!: 

  * 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''
  * To move up/down rows in tables (Protocol steps, etc.) right-click on a row and select ''Move Up'' or ''Move Down''

==== Data Source Selection ====
  - Select Mascot DAT Files
  - Next >

==== File Selection - Step 1 of 8 ====
  - Click on the button ''Select a File or a Folder'' and select a Mascot .dat file (the choice of this Mascot file is not very important as we will only keep the header of the generated PRIDE XML file)
  - Next >

==== Spectra Selection - Step 2 of 8 ====
  - Keep default settings
  - Next >


==== Experiment Properties - Step 3 of 8 ====

=== Experiment Properties ===

  * Title: title used to describe the experiment
  * Description: experiment description (optional)
  * Label: short label used to describe the experiment
  * Project: project name (allow several experiments to be grouped)

=== Contact Information ===

  * Click on ''Add Contact''
  * Click on ''Please Select a Contact'' -> ''Create a New Contact...'' (you can create as much as contacts as needed, at least one)
    * Name: first+last name of people that submitted the data and/or did the experiment. 
    * E-mail: 
    * Institution: full adress of the laboratory 
    * Ok

=== References (optional) ===
     
If the experiment is part of a published manuscript it is highly recommended to include a reference to the paper. 

==== Sample Properties - Step 4 of 8 ====

  * Click on ''Please Select a Sample Set'' -> ''Create a New Sample Set...'' (a sample set consists of one or multiple samples)
    * Name: sample set name
    * Ok
  * Select the ''Single sample'' or ''Multiple Samples'' tab (a Single Sample is most likely needed)
  * Click on ''Add Sample CV Term'' to add a sample
    * Select the appropriate Ontology: for ex. NEWT (species), BTO (tissue), CTO (cell type), GO and DO (disease state)
    * In the 'Term Name Search' enter for ex. ''Chlamydomonas'', select the appropriate row in the ''Search Results'' table, then click on ''Use Selected Term''.
  * Next >

==== Protocol Properties - Step 5 of 8 ====

=== Protocol ===

  * Click on ''Please Select a Protocol'' -> ''Create a New Protocol...''
    * Name: protocol name
    * Ok
  * Click on ''Add Protocol Step'' (add as much protocol steps as needed)
    * Click on ''Ontology Lookup Service''
      * Select the appropriate ontology, for ex. PRIDE Controlled Vocabulary [PRIDE]
      * Enter for ex. ''enzyme digestion'' as the ''Term Name''
      * Select the appropriate row in the ''Search Results'' table.
      * Click on ''Use Selected 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

=== Identification Type ===

  * Select the appropriate technology ''2D Gel'' or ''Other''
  * 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.