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Abstract
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.
Keywords
PEFF, Proteomics Standards Initiative, PSI, file formats, standards, mass spectrometry, PASTA, proteomics, proteogenomics, TANDEM MASS-SPECTROMETRY, PROTEIN, REPRESENTATION, SEARCH, IDENTIFICATION, ORGANIZATION, PROTEOFORM, TOOLS

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Citation

Please use this url to cite or link to this publication:

MLA
Binz, Pierre-Alain et al. “Proteomics Standards Initiative Extended FASTA Format.” JOURNAL OF PROTEOME RESEARCH 18.6 (2019): 2686–2692. Print.
APA
Binz, P.-A., Shofstahl, J., Vizcaíno, J. A., Barsnes, H., Chalkley, R. J., Menschaert, G., Alpi, E., et al. (2019). Proteomics Standards Initiative extended FASTA format. JOURNAL OF PROTEOME RESEARCH, 18(6), 2686–2692.
Chicago author-date
Binz, Pierre-Alain, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Gerben Menschaert, Emanuele Alpi, et al. 2019. “Proteomics Standards Initiative Extended FASTA Format.” Journal of Proteome Research 18 (6): 2686–2692.
Chicago author-date (all authors)
Binz, Pierre-Alain, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Gerben Menschaert, Emanuele Alpi, Karl Clauser, Jimmy K Eng, Lydie Lane, Sean L Seymour, Luis Francisco Hernández Sánchez, Gerhard Mayer, Martin Eisenacher, Yasset Perez-Riverol, Eugene A Kapp, Luis Mendoza, Peter R Baker, Andrew Collins, Tim Van Den Bossche, and Eric W Deutsch. 2019. “Proteomics Standards Initiative Extended FASTA Format.” Journal of Proteome Research 18 (6): 2686–2692.
Vancouver
1.
Binz P-A, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, et al. Proteomics Standards Initiative extended FASTA format. JOURNAL OF PROTEOME RESEARCH. 2019;18(6):2686–92.
IEEE
[1]
P.-A. Binz et al., “Proteomics Standards Initiative extended FASTA format,” JOURNAL OF PROTEOME RESEARCH, vol. 18, no. 6, pp. 2686–2692, 2019.
@article{8614708,
  abstract     = {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.},
  author       = {Binz, Pierre-Alain and Shofstahl, Jim and Vizcaíno, Juan Antonio and Barsnes, Harald and Chalkley, Robert J and Menschaert, Gerben and Alpi, Emanuele and Clauser, Karl and Eng, Jimmy K and Lane, Lydie and Seymour, Sean L and Hernández Sánchez, Luis Francisco and Mayer, Gerhard and Eisenacher, Martin and Perez-Riverol, Yasset and Kapp, Eugene A and Mendoza, Luis and Baker, Peter R and Collins, Andrew and Van Den Bossche, Tim and Deutsch, Eric W},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keywords     = {PEFF,Proteomics Standards Initiative,PSI,file formats,standards,mass spectrometry,PASTA,proteomics,proteogenomics,TANDEM MASS-SPECTROMETRY,PROTEIN,REPRESENTATION,SEARCH,IDENTIFICATION,ORGANIZATION,PROTEOFORM,TOOLS},
  language     = {eng},
  number       = {6},
  pages        = {2686--2692},
  title        = {Proteomics Standards Initiative extended FASTA format},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.9b00064},
  volume       = {18},
  year         = {2019},
}

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