title: proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.
abstract: 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)(1) 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.
authors.affiliation: From the ‡Department of Biomedical Informatics.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Wang
authors.affiliation: §Department of Biochemistry, ¶Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232.
authors.forename: Robbert J C
authors.initials: RJ
authors.lastname: Slebos
authors.affiliation: From the ‡Department of Biomedical Informatics.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.affiliation: From the ‡Department of Biomedical Informatics, §Department of Biochemistry.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: From the ‡Department of Biomedical Informatics, §Department of Biochemistry, ¶Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
authors.affiliation: From the ‡Department of Biomedical Informatics, ‖Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232; bing.zhang@vanderbilt.edu.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
mesh_terms: D000072224:Bcl-2-Like Protein 11 / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D064878:Web Browser
chemical_list: D000072224:Bcl-2-Like Protein 11; D010455:Peptides