standards > model/format > DOI:10.25504/FAIRsharing.v033mj

in development proBed

General Information
The Proteomics Informatics Working Group is developing standards for describing the results of identification and quantification processes for proteins, peptides, small molecules and protein modifications from mass spectrometry. This working group is developing proBed, a tab delimited text file format to report “proteogenomics” results, i.e. the identification and mapping of peptide/protein sequences back against a genome, to assist in annotation efforts. The original BED format is used to describe genome coordinate data across lines, for use on annotation tracks. In BED, data lines are defined as tab-separated plain text with 12 mandatory fields (columns). Of those, only the first three fields are required, and the other 9 are optional. The proBed format builds upon this original structure by extending the 12 original BED fields to include a further 13 fields to describe information primarily on peptide-spectrum matches (PSMs). The format can also accommodate peptides (as groups of PSMs).

How to cite this record proBed; proBed; DOI:; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Dec 12 2019 11:14 a.m.

This record is maintained by HUPO PSI  (HUPOPSI)

Record added: March 2, 2017, 11:31 a.m.
Record updated: Nov. 21, 2018, 10:06 a.m. by The FAIRsharing Team.

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Implementing Databases (1)
The Ensembl project is based at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). It provides one of the most comprehensive and integrated resources of genomic data, which can be accessed through the web ( and through BioMart, FTP, Perl APIs, REST API and MySQL queries.

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