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

Rachel M Miller1, Khairina Ibrahim1, Lloyd M Smith1

  • 1Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States.

Journal of Proteome Research
|March 4, 2021
PubMed
Summary

Protease selection is crucial for bottom-up proteomics. ProteaseGuru software aids researchers by simulating protease digests in silico, optimizing proteomic experiment design and data analysis for various biological studies.

Keywords:
bottom-upexperiment planningin silico digestionmass spectrometrymultiple proteasesproteolytic peptides

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Bottom-up proteomics, a dominant proteome analysis strategy, relies on protease digestion for peptide generation.
  • The selection of proteases significantly impacts the quality and interpretability of proteomic data, affecting protein and post-translational modification identification.
  • Optimizing protease choice is essential for accurate and comprehensive proteomic studies.

Purpose of the Study:

  • To introduce ProteaseGuru, a novel software tool for in silico protease digestion.
  • To enable researchers to evaluate the utility of different proteases for bottom-up proteomic experiments.
  • To facilitate informed protease selection for diverse proteomic applications, from single proteins to complex proteomes.

Main Methods:

  • ProteaseGuru performs in silico digestion using various candidate proteases.
  • It generates theoretical peptide sequences and analyzes their biophysical properties.
  • The software offers data visualizations, including histograms and sequence coverage maps, for comparing digestion outcomes.

Main Results:

  • ProteaseGuru provides detailed peptide information and comparative digestion summaries.
  • It allows for the assessment of shared and unique peptides generated by different proteases.
  • The tool supports analysis across single proteins, complex proteomes, and multiple databases.

Conclusions:

  • ProteaseGuru is a valuable resource for optimizing bottom-up proteomic experimental design.
  • It enhances the ability to infer protein presence, quantity, and modifications.
  • The software supports a wide range of applications, including variant protein analysis, xenograft models, and metaproteomics.