RT Journal Article
SR Electronic
T1 The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 152579
DO 10.1101/152579
A1 Gerben Menschaert
A1 Xiaojing Wang
A1 Andrew R. Jones
A1 Fawaz Ghali
A1 David Fenyö
A1 Volodimir Olexiouk
A1 Bing Zhang
A1 Eric W. Deutsch
A1 Tobias Ternent
A1 Juan Antonio Vizcaíno
YR 2017
UL http://biorxiv.org/content/early/2017/06/20/152579.abstract
AB On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI), we are here introducing two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations from the well-defined, widely used file formats SAM/BAM and BED respectively, and both have been extended to meet specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several very popular genome browsers, can be used to manipulate and visualize these formats already out-of-the-box. We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation to the formats, including the detailed file format specifications, and example files are accessible at http://www.psidev.info/probam and http://www.psidev.info/probed.