proBAMr

proBAMr maps peptide-spectrum matches (PSMs) from shotgun proteomics to the genome and generates proBAM and SAM files for genome-based representation and analysis of proteomics data.

Key Features:

• Protein BAM (proBAM) file format: Organizes PSMs relative to the genome to provide a structured, genome-based representation of proteomics data.
• R package - probamr: Generates proBAM files from shotgun proteomics by mapping PSMs back to the genome and constructing SAM files for downstream analysis.
• R package - proBAMtools: Provides functions for analyzing proBAM files.
• Annotation preparation from GTF: Includes functions to prepare genomic annotations from GTF files for incorporation into proteomics analyses.

Scientific Applications:

• Enhanced data interpretation: Integrates genomic annotation information to improve interpretation of proteomics datasets.
• Reannotation and assembly: Enables reannotation of PSMs using custom gene annotation schemes to facilitate protein and gene identification.
• Data integration: Uses the genome as a common reference to integrate proteomics and proteogenomics data.
• Visualization in genome browsers: Produces proBAM files compatible with genome browsers for genomic-context visualization of proteomics data.

Methodology:

Maps PSMs to the genome, constructs SAM files and produces proBAM files; prepares annotations from GTF files; and provides analytical functions for proBAM file analysis via proBAMtools.