standards > model/format > DOI:10.25504/FAIRsharing.v033mj
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in development proBed


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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 FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Aug 14 2020 midnight


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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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Ensembl
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.

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