title: PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
abstract: 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/.
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Qing-Wei
authors.initials: QW
authors.lastname: Xu
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: §Ruhr-Universität Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universitätsstr. 150, D-44801 Bochum, Germany;
authors.forename: Julian
authors.initials: J
authors.lastname: Uszkoreit
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; ¶Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria;
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.affiliation: ‖Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba.
authors.forename: Aniel
authors.initials: A
authors.lastname: Sanchez
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Tobias
authors.initials: T
authors.lastname: Ternent
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Noemi
authors.initials: N
authors.lastname: Del-Toro
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Jose A
authors.initials: JA
authors.lastname: Dianes
authors.affiliation: §Ruhr-Universität Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universitätsstr. 150, D-44801 Bochum, Germany;
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.affiliation: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; juan@ebi.ac.uk.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome