proBed
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).
Description
More detailed information about this field from each metasource.
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).
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Webpage:
http://www.psidev.info/probedWebpage
More detailed information about this field from each metasource.
http://www.psidev.info/probed
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Tags:
Tags
More detailed information about this field from each metasource.
mass spectrometry spectra
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
peak matching
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
protein modification
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Tags
More detailed information about this field from each metasource.
mass spectrometry spectra
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
peak matching
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
protein modification
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: proBed; proBed; DOI: https://doi.org/10.25504/FAIRsharing.v033mj; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
mass spectrometry spectra peak matching protein protein modification small molecule polypeptide region
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