RT Journal Article SR Electronic T1 Proteomics Standards Initiative Extended FASTA Format (PEFF) JF bioRxiv FD Cold Spring Harbor Laboratory SP 624494 DO 10.1101/624494 A1 Pierre-Alain Binz A1 Jim Shofstahl A1 Juan Antonio Vizcaíno A1 Harald Barsnes A1 Robert J. Chalkley A1 Gerben Menschaert A1 Emanuele Alpi A1 Karl Clauser A1 Jimmy K. Eng A1 Lydie Lane A1 Sean L. Seymour A1 Luis Francisco Hernández Sánchez A1 Gerhard Mayer A1 Martin Eisenacher A1 Yasset Perez-Riverol A1 Eugene A. Kapp A1 Luis Mendoza A1 Peter R. Baker A1 Andrew Collins A1 Tim Van Den Bossche A1 Eric W. Deutsch YR 2019 UL http://biorxiv.org/content/early/2019/05/08/624494.abstract AB 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 backwards 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.