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Related Experiment Video

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Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics

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Published on: June 23, 2022

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows.

Leander Roeland van der Hoeven¹, Maico Lechner¹, Cristina Hernandez-Rollan^1,2

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.

Journal of Proteome Research

|December 22, 2025

Summary

Achromobacter lyticus LysC enhances mass spectrometry proteomics by improving peptide identification and digestion efficiency. This LysC endopeptidase homologue offers superior performance compared to others, minimizing missed cleavages for better protein coverage.

Keywords:

LC-MS/MS bottom-up proteomics endoproteinase LysC label-free quantitation method development proteolytic enzymes proteomics workflow

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Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays

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Published on: November 29, 2014

Area of Science:

Proteomics
Enzymology
Mass Spectrometry

Background:

LysC endopeptidases are crucial for protein digestion in mass spectrometry-based proteomics.
Comparative analysis of LysC homologues is needed to identify optimal enzymes for enhanced proteomic workflows.

Purpose of the Study:

To comparatively analyze three LysC endopeptidase homologues from *Achromobacter lyticus*, *Pseudomonas aeruginosa*, and *Lysobacter enzymogenes*.
To evaluate their performance in mass spectrometry-based proteomics using a protein aggregation capture workflow.

Main Methods:

Comparative analysis of LysC homologues' cleavage specificity and digestion efficiency.
Utilized a protein aggregation capture workflow with HeLa cell lysates.
Assessed enzyme performance across various experimental conditions, including digestion times.

Main Results:

All three LysC homologues showed high specificity for lysine residues.
*Achromobacter lyticus* LysC demonstrated superior peptide identification, digestion efficiency, and protein coverage, particularly at shorter digestion times.
Combining *A. lyticus* LysC with trypsin significantly reduced missed cleavage rates, especially for lysine-containing peptides.

Conclusions:

Achromobacter lyticus LysC is a highly effective endopeptidase for mass spectrometry-based proteomics.
Its superior performance enhances peptide identification and protein coverage, making it an optimal choice for proteomic studies.
Employing LysC enzymes, particularly *A. lyticus* LysC, is crucial for minimizing missed cleavages in tryptic digests.