TY - JOUR T1 - Proteomics Standards Initiative Extended FASTA Format (PEFF) JF - bioRxiv DO - 10.1101/624494 SP - 624494 AU - Pierre-Alain Binz AU - Jim Shofstahl AU - Juan Antonio Vizcaíno AU - Harald Barsnes AU - Robert J. Chalkley AU - Gerben Menschaert AU - Emanuele Alpi AU - Karl Clauser AU - Jimmy K. Eng AU - Lydie Lane AU - Sean L. Seymour AU - Luis Francisco Hernández Sánchez AU - Gerhard Mayer AU - Martin Eisenacher AU - Yasset Perez-Riverol AU - Eugene A. Kapp AU - Luis Mendoza AU - Peter R. Baker AU - Andrew Collins AU - Tim Van Den Bossche AU - Eric W. Deutsch Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/05/02/624494.abstract N2 - 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. ER -