proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data

摘要: To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs)(1) within context genome. proBAMsuite also includes two R packages, proBAMr proBAMtools, generating analyzing proBAM files, respectively. Applying to three recently published datasets, demonstrated its utility facilitating efficient sharing, interpretation, integration data. First, interpretation data significantly enhanced with rich genomic annotation information. Second, PSMs can be easily reannotated using user-specified gene schemes assembled into both identifications. Third, genome as common reference, facilitates seamless proteogenomics integration. Finally, files readily visualized browsers thus bring general audience beyond community. Results from this study establish useful framework research.