Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs.

ABSTRACT: In bottom-up proteomics, proteins are enzymatically digested into peptides before measurement with mass spectrometry. The relationship between proteins and their corresponding peptides can be represented by bipartite graphs. We conduct a comprehensive analysis of bipartite graphs using quantified peptides from measured data sets as well as theoretical peptides from an in silico digestion of the corresponding complete taxonomic protein sequence databases. The aim of this study is to characterize and structure the different types of graphs that occur and to compare them between data sets. We observed a large influence of the accepted minimum peptide length during in silico digestion. When changing from theoretical peptides to measured ones, the graph structures are subject to two opposite ef

SUBMITTER: Schork K 

PROVIDER: S-EPMC9586388 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature