期刊
JOURNAL OF PROTEOME RESEARCH
卷 18, 期 6, 页码 2686-2692出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.9b00064
关键词
PEFF; Proteomics Standards Initiative; PSI; file formats; standards; mass spectrometry; PASTA; proteomics; proteogenomics
资金
- National Institutes of Health (NIH) [R24GM127667, R01GM087221, U19AG023122, U54EB020406]
- European Research Council
- Research Council of Norway
- Bergen Research Foundation
- SIB Swiss Institute of Bioinformatics
- NIH under the UniProt Grant [U24HG007822]
- European Molecular Biology Laboratory (EMBL)
- BMBF [FKZ 031 A 534A]
- PURE project of Northrhine-Westphalia
- VALIBIO project of Northrhine-Westphalia
- Wellcome Trust [WT101477MA, 208391/Z/17/Z]
- NIH [R24GM127667]
- Adelson Medical Research Foundation
- EMBL
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据