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).

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

1. Select Mascot DAT Files
2. Next >

1. 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)
2. Next >

1. Keep default settings
2. Next >

• 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)

• 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

If the experiment is part of a published manuscript it is highly recommended to include a reference to the paper.

• 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 >

• 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

• Select the appropriate technology 2D Gel or Other
• Next >

• 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

• 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 >

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)

• 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.