iHPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations

Abstract

When conducting proteomics experiments to detect missing proteins and protein isoforms in the human proteome, 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. Other proteases 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 proteases, we developed a web-based resource, 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 one or two proteases. iHPDM provides convenient functions 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, to select suitable proteases. iHPDM can facilitate protease selection for shotgun proteomics experiments to identify missing proteins, protein isoforms, and single amino acid variant peptides.

DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning

“…For instance, digestion prediction can facilitate the selection of proteases for shotgun proteomic experiments to identify missing proteins, proteoforms, etc. It is critical to choose the suitable protease(s) in order to obtain more unique peptides divergent among proteoforms. , Besides, the peptide digestibility has been utilized to improve the accuracy of peptide detectability prediction …”

“…It is critical to choose the suitable protease(s) in order to obtain more unique peptides divergent among proteoforms. 4,52 Besides, the peptide digestibility has been utilized to improve the accuracy of peptide detectability prediction. 10 ■ ASSOCIATED CONTENT * sı Supporting Information…”

“…Until now, trypsin has been the most popular and widely used protease, because of its high specificity, ease of use, and low cost. , Furthermore, the sole use of trypsin may hinder our ability to explore the full proteome, missing particular cleavage sites or protein segments . For this reason, some alternative proteases are used to be complementary solutions, such as ArgC, chymotrypsin, GluC, etc . However, regardless of which protease is used, proteolytic digestion can hardly be complete.…”

“…2 For this reason, some alternative proteases are used to be complementary solutions, such as ArgC, chymotrypsin, GluC, etc. 4 However, regardless of which protease is used, proteolytic digestion can hardly be complete. In fact, it was reported that about 40% of unique identified peptides digested by trypsin contained one or more missed cleavages.…”

ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics

“…A comparison of features between ProteaseGuru and other existing in silico digestion tools is provided in Table 2. iHDPM 24 is a great tool, with many wonderful visualization features, but lacks customizability. iHDPM is limited to analysis of the human proteome, with a predetermined set of proteolytic digests.…”