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

SUBMITTER: Wang X 

PROVIDER: S-EPMC4813696 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature