Pride Inspector

Introduction

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/.

Publications

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Cite this
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, 2016-01-01 - Molecular & cellular proteomics : MCP

Credits

Yasset Perez-Riverol
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Qing-Wei Xu
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Rui Wang
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Julian Uszkoreit
Developer
§Ruhr-Universität Bochum, Medizinisches Proteom-Zenter
Johannes Griss
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Aniel Sanchez
Developer
‖Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cuba
Florian Reisinger
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Attila Csordas
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Tobias Ternent
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Noemi Del-Toro
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Jose A Dianes
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Martin Eisenacher
Developer
§Ruhr-Universität Bochum, Medizinisches Proteom-Zenter
Henning Hermjakob
Developer
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
Juan Antonio Vizcaíno
Investigator
From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)

Community Ratings

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Summary

Accession	BT000503
Tool Type	Application
Category
Platforms	Linux/Unix
Technologies
User Interface	Terminal Command Line
Download Count	0
Submitted By	Juan Antonio Vizcaíno

Pride Inspector

Introduction

Publications

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. Cite this

Credits

Community Ratings

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Cite this