biostudies-literatureMiller RMNational Institute of General Medical SciencesNIGMS NIH HHS1936-1942https://www.ebi.ac.uk/biostudies/studies/S-EPMC8366505biostudies-literatureUnknown20(4)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 singleJournal of proteome researchProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics.PMC8366505R35GM126914R35 GM126914T32 GM008505Ibrahim KMiller RMSmith LMfalseProteaseGuru: 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 single2021-01-01T00:00:00Z2021 Apr2026-04-08T08:44:16.284Z2025-02-18T23:32:10.553ZS-EPMC83665053366164110.1021/acs.jproteome.0c00954