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

Area of Science:

• Proteomics
• Bioinformatics
• Mass Spectrometry

Background:

• Trypsin is the standard protease for proteomics, but it has limitations in identifying all proteins and isoforms.
• Identifying unique peptides is crucial for accurate protein identification in mass spectrometry.

Purpose of the Study:

• To develop a web-based resource, the in silico Human Proteome Digestion Map (iHPDM), to aid in protease selection for proteomics experiments.
• To provide a comprehensive database of in silico digested human proteome peptides using various protease combinations.

Main Methods:

• Constructed a proteolytic peptide database from human proteins and isoforms in neXtProt.
• Utilized 15 combinations of one or two proteases for in silico digestion.
• Developed user-friendly functions for examining, comparing, and filtering digestion results based on peptide properties.

Main Results:

• Created a comprehensive database of in silico digested human proteome peptides.
• The iHPDM allows users to compare digestion outcomes from different protease combinations.
• Users can apply filters for peptide length and uniqueness to optimize protease selection.

Conclusions:

• The iHPDM facilitates informed protease selection for shotgun proteomics.
• This resource aids in the identification of missing proteins, protein isoforms, and single amino acid variant peptides.
• iHPDM enhances the efficiency and scope of human proteome analysis.