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

Bottom-up proteomics is currently
the dominant strategy for proteome
analysis. It relies critically upon the use of a protease to digest
proteins into peptides, which are then identified by liquid chromatography–mass
spectrometry (LC-MS). The choice of protease(s) has a substantial
impact upon the utility of the bottom-up results obtained. Protease
selection determines the nature of the peptides produced, which in
turn affects the ability to infer the presence and quantities of the
parent proteins and post-translational modifications in the sample.
We present here the software tool ProteaseGuru, which provides in
silico digestions by candidate proteases, allowing evaluation of their
utility for bottom-up proteomic experiments. This information is useful
for both studies focused on a single or small number of proteins,
and for analysis of entire complex proteomes. ProteaseGuru provides
a convenient user interface, valuable peptide information, and data
visualizations enabling the comparison of digestion results of different
proteases. The information provided includes data tables of theoretical
peptide sequences and their biophysical properties, results summaries
outlining the numbers of shared and unique peptides per protease,
histograms facilitating the comparison of proteome-wide proteolytic
data, protein-specific summaries, and sequence coverage maps. Examples
are provided of its use to inform analysis of variant-containing proteins
in the human proteome, as well as for studies requiring the use of
multiple proteomic databases such as a human:mouse xenograft model,
and microbiome metaproteomics.