Proteomics Standards Initiative Extended FASTA Format
Autor: | 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 |
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Jazyk: | angličtina |
Rok vydání: | 2019 |
Předmět: |
0301 basic medicine
Proteomics Biochemistry & Molecular Biology Computer science Information Storage and Retrieval PEFF Biochemistry Mass Spectrometry Article Proteomics Standards Initiative 03 medical and health sciences Controlled vocabulary Humans PSI FASTA ddc:616 Information retrieval 030102 biochemistry & molecular biology NeXtProt file formats FASTA format General Chemistry Biological Sciences File format Metadata PASTA 030104 developmental biology Validator proteogenomics Chemical Sciences standards Generic health relevance UniProt Software Biotechnology |
Zdroj: | Journal of Proteome Research Journal of Proteome Research, Vol. 18, No 6 (2019) pp. 2686-2692 Journal of proteome research, vol 18, iss 6 |
ISSN: | 1535-3893 |
Popis: | 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 |
Databáze: | OpenAIRE |
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