The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Posted on 2018-01-31 - 05:00
Abstract On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here 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 of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several widely used genome browsers, can already be used to manipulate and visualize these formats “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, including the detailed file format specifications and example files, are accessible at http://www.psidev.info/probam and at http://www.psidev.info/probed .
CITE THIS COLLECTION
Menschaert, Gerben; Wang, Xiaojing; Jones, Andrew; Ghali, Fawaz; Fenyö, David; Olexiouk, Volodimir; et al. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.3992754.v1
Select your citation style and then place your mouse over the citation text to select it.
Read the peer-reviewed publication
data formatsgenome browsersproBAMtranscriptomics informationProteomics Standards Initiativeproteomics informationsoftware toolsSAMproBedHUPOformat specificationsexample filesHuman Proteome Organizationdata analysisproteogenomics studiesgenomics toolsproteomics dataproteomics data Abstractmass spectrometry-based proteomics data