Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows
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Updated: Jun 16, 2026

Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics
Published on: June 23, 2022
Leander Roeland van der Hoeven1, Maico Lechner1, Cristina Hernandez-Rollan1,2
1Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, Building 6.1, Copenhagen N DK-2200, Denmark.
Abstract:
This study presents a comparative analysis of three LysC endopeptidase homologues from Achromobacter lyticus (A. lyticus),Pseudomonas aeruginosa and Lysobacter enzymogenes for mass spectrometry-based proteomics. Utilizing a protein aggregation capture workflow with HeLa cell lysates, we assessed the enzymes' cleavage specificity, digestion efficiency, and performance across various experimental conditions. Results showed that while all three LysC homologues exhibited high cleavage specificity at lysine residues, A. lyticus LysC outperformed the two others with superior peptide identification, digestion efficiency, and protein coverage, especially at shorter digestion times. Our experiments using a combination ofA. lyticusLysC and trypsin demonstrated the importance of employing LysC for significantly minimizing missed cleavage rates in tryptic digests, especially with regard to lysine-containing peptides. This study underscores A. lyticus LysC's potential as an optimal choice for enhancing mass spectrometry-based proteomics.
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