title: 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.
authors.affiliation: Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Côté
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.forename: José A
authors.initials: JA
authors.lastname: Dianes
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: James C
authors.initials: JC
authors.lastname: Wright
authors.forename: Henk W P
authors.initials: HW
authors.lastname: van den Toorn
authors.forename: Bas
authors.initials: B
authors.lastname: van Breukelen
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
authors.forename: Niels
authors.initials: N
authors.lastname: Hulstaert
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.forename: David
authors.initials: D
authors.lastname: Ovelleiro
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Rivevol
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D030562:Databases, Protein; D001330:Electronic Data Processing; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis; D040901:Proteomics; D012984:Software; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D020543:Proteome