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PRIDE-Mod Library

PRIDE Modification library (PRIDE-Mod) is a Java API to handle post-translational modifications (PTMs) in proteomics experiments. The library provide a common representation between different PTMs databases such as UNIMOD , PSI-MOD and the PRIDE Modification Slim Ontology.

It also provide a the corresponding parsers for UNIMOD and PSI-MOD databases. It can be use to retrieve an specific modification using Accessions, Amino Acids, Delta Masses (monoisotopic or average).

License

pride-mod is a PRIDE API licensed under Apache License 2.0.

How to cite it:

Perez-Riverol, Yasset, Julian Uszkoreit, Aniel Sanchez, Tobias Ternent, Noemi del Toro, Henning Hermjakob, Juan Antonio Vizcaíno, and Rui Wang. "ms-data-core-api: an open-source, metadata-oriented library for computational proteomics." Bioinformatics 31, no. 17 (2015): 2903-2905. article

Main Features

  • Support UNIMOD and PSI-MOD databases
  • Common representation for all kind of modifications.
  • Common API to retrieve modifications based on: Accessions, Amino Acids, Delta Masses, etc.
  • Retrieve modifications by String patterns in Names or Descriptions.
  • Retrieve Group of Modifications based on common Names or Specificity Groups.

Availability and Version

Getting pride-mod

Maven Dependency If you wish to include pride-mod in your own Java projects, and you use Maven 2, the following snippets could be useful for you:

  • Maven 2 repository definition for pride-mod (and for a host of other EBI libraries):

      <repository>
      <id>nexus-ebi-release-repo</id>
      <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
  </repository>

  • pride-mod dependency snippet:

      <dependency>
      <groupId>uk.ac.ebi.pride.utilities</groupId>
      <artifactId>pride-mod</artifactId>
       <version>x.y.z</version>
  </dependency>

Getting Help

If you have questions or need additional help, please contact the PRIDE Helpdesk at the EBI: pride-support at ebi.ac.uk (replace at with @).

Please send us your feedback, including error reports, improvement suggestions, new feature requests and any other things you might want to suggest to the PRIDE team.

This library has been used in:

  • Côté, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W., ... & Vizcaíno, J. A. (2012). The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Molecular & Cellular Proteomics, 11(12), 1682-1689. PRIDE Converter 2

  • Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., ... & Hermjakob, H. (2013). The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic acids research, 41(D1), D1063-D1069. PRIDE-Archive

  • Perez-Riverol, Y., Xu, Q.W., Wang, R., Uszkoreit, J., Griss, J., Sanchez, A., Reisinger, F., Csordas, A., Ternent, T., del-Toro, N. and Dianes, J.A., 2016. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. Molecular & Cellular Proteomics, 15(1), pp.305-317. PRIDE Inspector Toolsuite

How to use pride-mod

Using pride-mod

Here we will show you how to use the PRIDE-Mod library:

  • How to retrieve all modifications in PSI-Mod and UNIMOD with 'phospho' pattern in the Description:

     ModReader modReader = ModReader.getInstance();
List<PTM> ptms = modReader.getPTMListByPatternDescription("Phospho");
assertTrue("Number of PTMs with Term 'Phospho' in name:", ptms.size() == 102);

  • Retrieve the the UNIMOD modification with Accession 1:

     File inputFile = new File("unimoddatabase.xml");
 unimodDataAccessController = new UnimodDataAccessController(inputFile);
 PTM ptm = unimodDataAccessController.getPTMbyAccession("UNIMOD:1");
 assertTrue("Difference mass for Average mass is:", ptm.getAveDeltaMass() == 42.0367);