proBed is one of the data standards developed by members of the Proteomics Informatics working group of the PSI.

For general information of the activities and the organization of this working group see HERE.

The original BED format (Browser Extensive Data, https://genome.ucsc.edu/FAQ/FAQformat.html - format1), developed by the UCSC (University of California, Santa Cruz) team, 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).

A manuscript describing this proBed format (together with the proBAM format) is available at Genome Biology.

Contents

1. proBed 1.0.0 (Final Version): Specification document and example files
2. proBed Tools and Implementations

proBed 1.0.0 (Final Version): Specification document and example files

The proBed file format is designed for storing and analyzing peptide spectrum matches (PSMs) within the context of the genome.

Direct links:

• proBed specification document (docx|PDF).
• Example documents:
  • PXD001524_reprocessed.pro.bed - example proBed file converted from the mzTab example file indicated below. This file has been further processed to only report upon chromosomes that are mentioned in the chrom_sizes.txt file.
  • Additional related files:
    • PXD001524_reprocessed.mzid – example mzIdentML file with genome annotation.
    • PXD001524_reprocessed.mztab – example mztab file converted from the mzidentML example file.
    • UCSC bed to big bed converter tool – v2.87.
    • chrom_sizes.txt – example chromosome sizes file.
    • proBed-1.0.0.as – proBed autoSQL file, supporting the file conversion to bigBed.
    • PXD001524_reprocessed.bb – example bigBed file converted using the example proBed file, aSQL file, chromosome sizes file, and converter tool.
  • proBed additional examples
    • PXD000656_reprocessed.pro.bed - 2nd example proBed file converted from the 2nd mzTab example file
    • PXD000656_reprocessed.mzid - 2nd example mzIdentML file with genome annotation.
    • PXD000656_reprocessed.mztab - 2nd example mztab file converted from the 2nd mzidentML example file.
    • PXD000656_reprocessed.bb - 2nd example bigBed file converted using the 2nd example proBed file
    • PXD000764_reprocessed.pro.bed - 3rd example proBed file converted from the 3rd mzTab example file
    • PXD000764_reprocessed.mzid - 3rd example mzIdentML file with genome annotation.
    • PXD000764_reprocessed.mztab - 3rd example mztab file converted from the 3rd mzidentML example file.
    • PXD000764_reprocessed.bb - 3rd example bigBed file converted using the 3rd example proBed file

proBed Tools and Implementations

• ms-data-core-api: A Java API to write and merge proBed files.
• PGConverter: A Java command line tool to convert and validate mzIdentML, mzTab, PRIDE XML and proBed files. Please see the README file for usage defails.
• bedToBigBed: Complied linux ELF executable UCSC Utility tool to convert from BED to to proBed.
• Ensembl genome browser: Able to visualize proBed data, example screenshot below.