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The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

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 transcriptomi...

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Autores principales: Menschaert, Gerben, Wang, Xiaojing, Jones, Andrew R., Ghali, Fawaz, Fenyö, David, Olexiouk, Volodimir, Zhang, Bing, Deutsch, Eric W., Ternent, Tobias, Vizcaíno, Juan Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793360/
https://www.ncbi.nlm.nih.gov/pubmed/29386051
http://dx.doi.org/10.1186/s13059-017-1377-x
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author Menschaert, Gerben
Wang, Xiaojing
Jones, Andrew R.
Ghali, Fawaz
Fenyö, David
Olexiouk, Volodimir
Zhang, Bing
Deutsch, Eric W.
Ternent, Tobias
Vizcaíno, Juan Antonio
author_facet Menschaert, Gerben
Wang, Xiaojing
Jones, Andrew R.
Ghali, Fawaz
Fenyö, David
Olexiouk, Volodimir
Zhang, Bing
Deutsch, Eric W.
Ternent, Tobias
Vizcaíno, Juan Antonio
author_sort Menschaert, Gerben
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-017-1377-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-57933602018-02-12 The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data Menschaert, Gerben Wang, Xiaojing Jones, Andrew R. Ghali, Fawaz Fenyö, David Olexiouk, Volodimir Zhang, Bing Deutsch, Eric W. Ternent, Tobias Vizcaíno, Juan Antonio Genome Biol Open Letter 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-017-1377-x) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-31 /pmc/articles/PMC5793360/ /pubmed/29386051 http://dx.doi.org/10.1186/s13059-017-1377-x Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Open Letter
Menschaert, Gerben
Wang, Xiaojing
Jones, Andrew R.
Ghali, Fawaz
Fenyö, David
Olexiouk, Volodimir
Zhang, Bing
Deutsch, Eric W.
Ternent, Tobias
Vizcaíno, Juan Antonio
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title_full The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title_fullStr The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title_full_unstemmed The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title_short The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
title_sort probam and probed standard formats: enabling a seamless integration of genomics and proteomics data
topic Open Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793360/
https://www.ncbi.nlm.nih.gov/pubmed/29386051
http://dx.doi.org/10.1186/s13059-017-1377-x
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