proBAMr

proBAMr is an R package that is part of the proBAMsuite bioinformatics framework. It is designed to generate protein BAM (proBAM) files, which organize peptide spectrum matches (PSMs) within the context of the genome. proBAMr facilitates the efficient sharing, interpretation, and integration of proteomics data with genomic information using the genome as a reference. The package enables users to enhance the interpretation of proteomics data by incorporating rich genomic annotation information, reannotating PSMs using user-specified gene annotation schemes, and assembling PSMs into protein and gene identifications. proBAMr and the other components of proBAMsuite establish a valuable framework for proteomics and proteogenomics research, making data analysis more accessible to a broader audience beyond the proteomics community.