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Proteomics Standards Initiative Extended FASTA Format

Authors :
Peter R. Baker
Martin Eisenacher
Eric W. Deutsch
Tim Van Den Bossche
Robert J. Chalkley
Jim Shofstahl
Juan Antonio Vizcaíno
Luis Francisco Hernández Sánchez
Karl R. Clauser
Lydie Lane
Andrew Collins
Eugene A. Kapp
Sean L. Seymour
Gerhard Mayer
Pierre-Alain Binz
Luis Mendoza
Jimmy K. Eng
Gerben Menschaert
Yasset Perez-Riverol
Harald Barsnes
Emanuele Alpi
Source :
Journal of Proteome Research, Journal of Proteome Research, Vol. 18, No 6 (2019) pp. 2686-2692, Journal of proteome research, vol 18, iss 6
Publication Year :
2019
Publisher :
ACS, 2019.

Abstract

Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI extended FASTA format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backward compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available at http://www.psidev.info/peff. acceptedVersion

Details

Language :
English
ISSN :
15353893
Database :
OpenAIRE
Journal :
Journal of Proteome Research, Journal of Proteome Research, Vol. 18, No 6 (2019) pp. 2686-2692, Journal of proteome research, vol 18, iss 6
Accession number :
edsair.doi.dedup.....86d4945481669057e35224f38ac49916