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/.
Highlights
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
Design and Implementation—The PRoteomics IDEntifications (PRIDE) Inspector Toolsuite is written in Java, ensuring that can be used in different operating systems such as Microsoft Windows, Mac OS, and Linux
The Toolsuite is divided in two main groups of libraries: (i) PRIDE-Utilities, which contains the set of algorithms and libraries for data handling, validation, and quality assessment, and (ii) PRIDE-Toolsuite, containing the set of graphical user interface components and tools (Table I)
Summary
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. The ProteomeXchange (PX) Consortium was formally started in 2011 to overcome the challenges in MS proteomics data sharing and dissemination [3, 4] by implementing standard pipelines and promoting collaboration, developing an international consortium of major stakeholders in the domain. At present, it includes the PRoteomics IDEntifications (PRIDE) database [5], PeptideAtlas [6] and the related resource PeptideAtlas SRM Experiment Library (PASSEL) [7] and the Mass Spectrometry Interactive Virtual Environment (MassIVE, http://massive.ucsd.edu/). In the context of bottom-up MS/MS approaches, the most adopted XML-based standards are: mzML [8] to store the “primary” MS data (the mass spectra and chromatograms) and mzIdentML [9] to report peptide identifications as well as the inferred protein identifications, including post-
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