The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

Abstract

The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.

ProCon — PROteomics CONversion tool

“…PRIDE Converter 2 [17] and ProteoWizard [25]. But these tools don't support the conversion of ProteomeDiscoverer ® and ProteinScape ® result at the moment and also the M2Lite converter [50] has still its weaknesses.…”

“…Furthermore the use of such standardized CV (Controlled Vocabulary) terms allows additional semantic correctness checks by validator software [12] and makes the file formats more flexible and thereby more stable, because it suffices to add new CV annotations, so that one must not always change the underlying XML schema in order to support new upcoming technologies or MS instruments. To augment the adoption of this standard formats [13][14][15][16], some converter tools [17], libraries for Java [18][19][20][21][22][23] and other programming languages [24,25] for accessing data stored in these standard formats, and upload tools [26] have been developed and described in detail in [2,27]. There are also already some tools available, which read in such standard formats.…”

Proteogenomics Dashboard for the Human Proteome Project

“…This is a standard format developed by members of the Proteomics Informatics working group of the HUPO-PSI, which is stored in a simple tabulated way in line with the results we currently display in dasHPPboard and will facilitate us to include proteomics results in an easier way because of the increasingly better integration of standards in protein-related programs and the simple conversion between these formats through programs such as PRIDE Converter 2. 51 Also, in this direction, we want to add more metadata to the panel of experiments and to the results of the search section, including information coming from databases like PeptideAtlas 46 or the GPMDB 47 to display a more complete panel, giving them the possibility to easily access to full data sets with raw data.…”

Exploring the potential of public proteomics data

“…This ongoing endeavor, led by the HUPO‐PSI (Human Proteome Organization−Proteomics Standards Initiative−http://www.psidev.info), has resulted in key data standards for the field, including mzML (for MS data), mzIdentML (for peptide/protein identification data), mzTab (for peptide/protein identification and quantification data), mzQuantML (for peptide/protein quantification data), and TraML (for transition lists in targeted proteomics approaches) 18, 19, 20, 21, 22. Importantly, support for these standards is provided through software libraries or tools such as ProteoWizard 23, PRIDE Converter 24, 25, mzidLibrary 26, and PRIDE Inspector 27. Successful adoption of these standards is moreover demonstrated by the existence of import and/or export capabilities in many of the most popular software in the field.…”