PRIDE Toolsuite

The PRIDE Toolsuite consists of a selection of tools and libraries for Mass Spectrometry:
pride-asa-pipeline: Uniform annotation of identified spectra.
ols-dialog: Java front end to the ontology lookup service (OLS 3.0)
PGConverter: ProteoGenomics Converter tool
PoGo: Mapping of peptides identified through mass spectrometry to a reference genome using annotation.
pride-inspector: Java desktop application for visualization and Quality Assessment on Mass Spectrometry data and Proteomics.
PRIDEParametersExtractor: Retrieves the search parameters from Complete Submissions in PRIDE.
searchgui: Graphical user interface for proteomics identification search engines.
peptide-shaker: Interprets proteomics identification results.
denovogui: Graphical user interface for de novo sequencing of tandem mass spectra.
pladipus: Platform for Distributed Proteomics Software.
inspector-quality-chart: PRIDE Quality Chart library provides a Java Swing API that for assessment of the quality of MS experiments.
inspector-mzgraph-browser: A library for visualization and annotatation of MS spectrum and chromatogram.
inspector-swing-utils: A library with various classes and utility functions for PRIDE Inspector.
inspector-example-files: Pride Inspector example files for testing purposes.
pride-converter-2: Automatically exports from code.google.com/p/pride-converter-2.

Topic

Proteomics;Proteomics experiment;Data submission, annotation and curation

Detail

  • Operation: Deposition

  • Software interface: Graphical user interface;Suite

  • Language: Java

  • License: BSD

  • Cost: Free

  • Version name: -

  • Credit: The BBSRC, the Wellcome Trust, the EU FP7, EMBL core funding, the Natural Science Foundation of the Hubei Province (China), Educational Commission of the Hubei Province, Protein Unit for Research in Europe (PURE), a project of North Rhine-Westphalia, Germany.

  • Input: -

  • Output: -

  • Contact: juan@ebi.ac.uk

  • Collection: -

  • Maturity: Mature

Publications

  • PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
  • Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229.
  • https://doi.org/10.1074/mcp.O115.050229
  • PMID: 26545397
  • PMC: PMC4762524

Download and documentation

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