ORCID Profile
0000-0002-1767-2343
Current Organisations
Ruhr-Universität Bochum
,
HITS gGmbH
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Publisher: Cold Spring Harbor Laboratory
Date: 02-05-2019
DOI: 10.1101/624494
Abstract: Mass spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs), in biological s les. 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 in idual 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 ex le 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 ex le files, are available at eff .
No related grants have been discovered for Gerhard Mayer.