Introduction

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.

Publications

  1. proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.
    Cite this
    Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B, 2016-03-01 - Molecular & cellular proteomics : MCP

Credits

  1. Xiaojing Wang
    Developer

  2. Robbert J C Slebos
    Developer

    §Department of Biochemistry, ¶Jim Ayers Institute for Precancer Detection and Diagnosis

  3. Matthew C Chambers
    Developer

  4. David L Tabb
    Developer

  5. Daniel C Liebler
    Developer

    From the ‡Department of Biomedical Informatics, §Department of Biochemistry

  6. Bing Zhang
    Investigator

    From the ‡Department of Biomedical Informatics, ‖Department of Cancer Biology

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Summary
AccessionBT006437
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByBing Zhang