PRIDE Inspector: a tool to visualize and validate MS proteomics data

Your editorial “Credit where credit is overdue” 1 aptly summarized the existing situation in the proteomics field, where full data disclosure remains very much a work in progress. Importantly, it also correctly pointed out that “the software provided by the public repositories for searching and analyzing proteomics data is not as efficient and as user friendly as it could be.” In this context, we introduce to readers PRIDE Inspector ( http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector ), a user-friendly, freely available open-source software tool that allows the user to efficiently browse and visualize mass spectrometry (MS) proteomics data. One of the key features of PRIDE Inspector is that it allows the user to carry out an initial assessment on data quality and reliability. PRIDE Inspector can thus be used by researchers before they submit their data, by journal editors and peer reviewers during the manuscript review process and by any interested user in the field after public release of the data in PRIDE (the PRoteomics IDEntifications database; Fig. 1 ). Figure 1: PRIDE Inspector helps to perform every stage of the PRIDE submission workflow. The workflow consists of four stages. (1) Data production. Search engine output results are converted into PRIDE XML files using PRIDE Converter. Authors can then use the PRIDE Inspector to perform an initial assessment on data quality and check metadata annotation before submission to PRIDE. (2) Data deposition. The submitted PRIDE XML files are reviewed by PRIDE's in-house curators using the PRIDE Inspector. (3) PRIDE acceptance. The submission is accepted by PRIDE and the data are kept private. Journal reviewers and editors can access these private PRIDE experiments using the PRIDE Inspector. (4) Journal acceptance. The submission is made public in the PRIDE database after journal acceptance. Data miners can extract, download or view PRIDE experiments using the PRIDE Inspector. Full size image