ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets

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 data sets. We, therefore, developed ProteoSushi, a software tool tailored to analysis of each modified site in peptide-centric proteomic data sets 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 for each modified site, merging overlapping peptide charge states, missed cleavages, spectral matches, and variable modifications into a single value. ProteoSushi also 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 protein’s subcellular location and function, and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushi’s flexibility and combination of analysis features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics data sets.

In Silico Analysis of Individual Fractions of Bovine Casein as Precursors of Bioactive Peptides—Influence of Post-Translational Modifications

“…2 Value of parameter A computed from Equation (1). 3 Complete list of activities of fragments found in proteins and released upon in silico proteolysis is presented in Tables S2-S9 in the Supplementary Materials. 4 Values of parameter A E computed according to Equation (2).…”

“…Given the importance of modifications of amino acid residues, contemporarily-developed computer programs take account of such modifications in protein sequences [1][2][3][4][5]. Databases annotating modified amino acid residues in proteins have recently been established as well [6][7][8].…”

An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells

“…7c ). Considering the above challenges and the substantial P-site-specific differences we identified between distinct illumination regimes, the field will benefit from site-specific PTM annotation databases 80 , 81 and bioinformatic framework incorporating new phosphoproteomic results 57 , 82 – 84 . We believe that both comprehensive P-site-specific annotation and high-quality phosphoproteomic studies are necessary to deeply understand the complexities of cell signaling.…”