Cargando…
proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data
To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs) within the context of the genome. proBAMsuite also...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The American Society for Biochemistry and Molecular Biology
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813696/ https://www.ncbi.nlm.nih.gov/pubmed/26657539 http://dx.doi.org/10.1074/mcp.M115.052860 |
_version_ | 1782424316364718080 |
---|---|
author | Wang, Xiaojing Slebos, Robbert J. C. Chambers, Matthew C. Tabb, David L. Liebler, Daniel C. Zhang, Bing |
author_facet | Wang, Xiaojing Slebos, Robbert J. C. Chambers, Matthew C. Tabb, David L. Liebler, Daniel C. Zhang, Bing |
author_sort | Wang, Xiaojing |
collection | PubMed |
description | To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs) within the context of the genome. proBAMsuite also includes two R packages, proBAMr and proBAMtools, for generating and analyzing proBAM files, respectively. Applying proBAMsuite to three recently published proteomics datasets, we demonstrated its utility in facilitating efficient genome-based sharing, interpretation, and integration of proteomics data. First, the interpretation of proteomics data is significantly enhanced with the rich genomic annotation information. Second, PSMs can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. Third, using the genome as a common reference, proBAMsuite facilitates seamless proteomics and proteogenomics data integration. Finally, proBAM files can be readily visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the proteomics community. Results from this study establish proBAMsuite as a useful bioinformatics framework for proteomics and proteogenomics research. |
format | Online Article Text |
id | pubmed-4813696 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | The American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-48136962016-04-11 proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data Wang, Xiaojing Slebos, Robbert J. C. Chambers, Matthew C. Tabb, David L. Liebler, Daniel C. Zhang, Bing Mol Cell Proteomics Regular Articles To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs) within the context of the genome. proBAMsuite also includes two R packages, proBAMr and proBAMtools, for generating and analyzing proBAM files, respectively. Applying proBAMsuite to three recently published proteomics datasets, we demonstrated its utility in facilitating efficient genome-based sharing, interpretation, and integration of proteomics data. First, the interpretation of proteomics data is significantly enhanced with the rich genomic annotation information. Second, PSMs can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. Third, using the genome as a common reference, proBAMsuite facilitates seamless proteomics and proteogenomics data integration. Finally, proBAM files can be readily visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the proteomics community. Results from this study establish proBAMsuite as a useful bioinformatics framework for proteomics and proteogenomics research. The American Society for Biochemistry and Molecular Biology 2016-03 2015-12-11 /pmc/articles/PMC4813696/ /pubmed/26657539 http://dx.doi.org/10.1074/mcp.M115.052860 Text en © 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Author's Choice—Final version free via Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0) . |
spellingShingle | Regular Articles Wang, Xiaojing Slebos, Robbert J. C. Chambers, Matthew C. Tabb, David L. Liebler, Daniel C. Zhang, Bing proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title | proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title_full | proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title_fullStr | proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title_full_unstemmed | proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title_short | proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data |
title_sort | probamsuite, a bioinformatics framework for genome-based representation and analysis of proteomics data |
topic | Regular Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813696/ https://www.ncbi.nlm.nih.gov/pubmed/26657539 http://dx.doi.org/10.1074/mcp.M115.052860 |
work_keys_str_mv | AT wangxiaojing probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata AT slebosrobbertjc probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata AT chambersmatthewc probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata AT tabbdavidl probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata AT lieblerdanielc probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata AT zhangbing probamsuiteabioinformaticsframeworkforgenomebasedrepresentationandanalysisofproteomicsdata |