To detect missing proteins and protein isoforms in the human proteome, shotgun proteomics experiments are usually conducted, in which proteins are first proteolytically digested into peptides. It is desirable to use a protease that can yield more unique peptides with properties amenable for mass spectrometry analysis. Though trypsin is currently the most widely used protease, some proteins can yield only a limited number of unique peptides by trypsin digestion due to some hindering effect on cleavage activity. For example, trypsin does not cleave at a lysine or arginine residue when a negatively charged amino acid, such as aspartic acid and glutamic acid, or phosphorylated serine or threonine, is located nearby. Moreover, it has been reported that 19 types of PTMs occurring at lysine may hinder trypsin cleavage efficiency.
Other protease and multiple proteases have been applied in reported studies to increase the number of identified proteins and protein sequence coverage. To facilitate the selection of protease, we have developed a web server, called in silico Human Proteome Digestion Map (iHPDM), which contains a comprehensive proteolytic peptide database constructed from human proteins including isoforms in neXtProt digested by 15 protease combinations of single or two proteases. iHPDM provides convenient functions, including Protein Query, Multi-protease Comparison and Isoform Digestion, and graphical visualizations for users to examine and compare the digestion results of different proteases. Notably, it also supports users to input filtering criteria on digested peptides, e.g., peptide length and uniqueness, in consideration of MS detectability to select suitable proteases.
In summary, with the capability to compare and examine different combinations of proteases for protein digestion in MS experiments, iHPDM can facilitate the selection of proteases for shotgun proteomics experiments to identify missing proteins, protein isoforms and single amino acid variant peptides.