Vis enkel innførsel

dc.contributor.authorBinz, Pierre-Alainen_US
dc.contributor.authorShofstahl, Jimen_US
dc.contributor.authorVizcaino, Juan Antonioen_US
dc.contributor.authorBarsnes, Haralden_US
dc.contributor.authorChalkley, Robert J.en_US
dc.contributor.authorMenschaert, Gerbenen_US
dc.contributor.authorAlpi, Emanueleen_US
dc.contributor.authorClauser, Karlen_US
dc.contributor.authorEng, Jimmy K.en_US
dc.contributor.authorLane, Lydieen_US
dc.contributor.authorSeymour, Sean L.en_US
dc.contributor.authorHernández Sánchez, Luis Franciscoen_US
dc.contributor.authorMayer, Gerharden_US
dc.contributor.authorEisenacher, Martinen_US
dc.contributor.authorPerez-Riverol, Yasseten_US
dc.contributor.authorKapp, Eugene A.en_US
dc.contributor.authorMendoza, Luisen_US
dc.contributor.authorBaker, Peter R.en_US
dc.contributor.authorCollins, Andrewen_US
dc.contributor.authorVan Den Bossche, Timen_US
dc.contributor.authorDeutsch, Eric W.en_US
dc.date.accessioned2020-05-07T12:58:45Z
dc.date.available2020-05-07T12:58:45Z
dc.date.issued2019
dc.PublishedBinz, Shofstahl, Vizcaino, Barsnes H, Chalkley RJ, Menschaert G, Alpi, Clauser K, Eng, Lane, Seymour, Hernández Sánchez LF, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp, Mendoza, Baker, Collins A, Van Den Bossche, Deutsch EW. Proteomics Standards Initiative Extended FASTA Format. Journal of Proteome Research. 2019;18(6):2686-2692eng
dc.identifier.issn1535-3907
dc.identifier.issn1535-3893
dc.identifier.urihttps://hdl.handle.net/1956/22127
dc.description.abstractMass-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.en_US
dc.language.isoengeng
dc.publisherACSeng
dc.titleProteomics Standards Initiative Extended FASTA Formaten_US
dc.typePeer reviewed
dc.typeJournal article
dc.date.updated2019-11-11T15:28:45Z
dc.description.versionacceptedVersionen_US
dc.rights.holderCopyright 2019 American Chemical Society
dc.identifier.doihttps://doi.org/10.1021/acs.jproteome.9b00064
dc.identifier.cristin1713731
dc.source.journalJournal of Proteome Research
dc.relation.projectBergens forskningsstiftelse: BFS2016REK02
dc.relation.projectNorges forskningsråd: 251235


Tilhørende fil(er)

Thumbnail

Denne innførselen finnes i følgende samling(er)

Vis enkel innførsel