ProteoSushi: a software tool to biologically annotate and quantify modification-specific, peptide-centric proteomics datasets

Abstract

Large-scale proteomic profiling of protein post-translational modifications has provided important insights into the regulation of cell signaling and disease. These modification-specific proteomics workflows nearly universally enrich modified peptides prior to mass spectrometry analysis, but protein-centric proteomic software tools have many limitations evaluating and interpreting these peptide-centric datasets. We therefore developed ProteoSushi, a software tool tailored to the analysis of each modified site in peptide-centric proteomic datasets that is compatible with any post-translational modification or chemical label. ProteoSushi uses a unique approach to assign identified peptides to shared proteins and genes, minimizing redundancy by prioritizing shared assignments based on UniProt annotation score and optional user-supplied protein/gene lists. ProteoSushi simplifies quantitation by summing or averaging intensities, merging overlapping peptide charge states, missed cleavages, peptide spectral matches, and variable modifications into a single value for each modified site. ProteoSushi annotates each PTM site with the most up-to-date biological information available from UniProt, such as functional roles or known modifications, the protein domain in which the site resides, the proteins subcellular location and function and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushis flexibility and combination of features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics datasets.