ProteoSushi

ProteoSushi annotates and quantifies modification-specific, peptide-centric proteomics datasets to produce site-centric PTM information for investigating post-translational modifications (PTMs) in cell signaling and disease.

Key Features:

• Peptide-Centric Analysis: Handles peptide-centric datasets enriched for PTMs and condenses results to individual modified sites.
• Compatibility and Flexibility: Supports any type of post-translational modification or chemical label.
• Redundancy Minimization: Assigns peptides to shared proteins and genes prioritizing UniProt annotation scores and accepts user-provided protein or gene lists to reduce redundancy.
• Simplified Quantitation: Sums or averages intensities across overlapping peptide charge states, missed cleavages, peptide spectral matches, and variable modifications to yield a single consolidated value per modified site.
• Comprehensive Annotation: Annotates each PTM site with UniProt-derived information including functional roles, known modifications, protein domains, subcellular locations, and functions.

Scientific Applications:

• Large-scale PTM profiling: Enables analysis of modification-specific datasets to elucidate regulatory roles of PTMs in cellular processes and cell signaling.
• Site-centric functional and disease analysis: Supports linking PTM site-level changes to protein function and disease pathogenesis.

Methodology:

Assigns peptides to proteins/genes with prioritization by UniProt annotation scores and optional input protein/gene lists; consolidates quantitation by summing or averaging intensities across charge states, missed cleavages, peptide spectral matches, and variable modifications to produce a single value per modified site; retrieves UniProt annotations (functional roles, known modifications, domains, subcellular locations, functions) for each PTM site.