Lysyl Endopeptidase® (Lys-C) for Peptide Mapping
Application and Function
Lysyl Endopeptidase (also known as Lys-C): This is a serine protease (peptidase). It targets proteins by cleaving peptide bonds internally (endopeptidase), specifically cutting on the carboxy-terminal side of lysine residues. Because it cuts strictly at lysine residues, scientists use it to digest proteins into predictable peptide fragments for mass spectrometry mapping.
Preparation and Solubility
The enzyme presents as a stable powder configuration. For laboratory preparations, it dissolves clearly in aquaeous buffers at a concentration of 10 mg/mL, ensuring uniform distribution and predictable activity metrics across standard enzymatic assays.
| Parameter | Specification |
| Source | Native (derived from Lysobacter Enzymogenes) |
| Cleavage Specificity | C-terminal side of lysine residues |
| Activity | 0.03 ~ 0.07 AU/vial |
| Appearance | Lyophilized, containing 2 mmol/L Tris-HCl buffer, pH 8.0 |
| Grade | Proteome Research |
| Storage Temperature | -20°C |
| Article Number | Description | Pack Size |
| 125-05061 | Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) | 5x 20 µg/vial |
| 121-05063 | Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) | 20 µg/vial |
Resources
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Core Target Applications
Biopharma Characterization
Critical structural evaluation of therapeutic proteins and biosimilars across early-stage development, optimization, and scale-up routines.
Monoclonal Antibody Profiling
Production of highly reproducible peptide digests for rigorous mAb sequence verification, chain mapping, and PTM profiling.
High-Resolution Proteomics
Robust sample preparation for complex biological matrices, utilizing specific digestion patterns to enhance downstream peptide identification rates.
Structural Characterization Challenges
Overcoming Intact Mass Limitations in Biologics Analysis
Intact large proteins, including monoclonal antibodies, fusion proteins, and complex recombinant therapeutics, present significant analytical hurdles when injected directly into mass spectrometers. Their sheer size and structural complexity often mask minor sequence variants, post-translational modifications (PTMs), or processing variations.
To achieve the single-amino-acid resolution necessary for quality confirmation, these macromolecular complexes must be systematically fragmented into predictable peptide mixtures. Cleaving intact targets prior to LC-MS/MS analysis generates a highly reproducible molecular fingerprint, enabling precise sequence validation and batch-to-batch structural auditing.
Analytical Workflow
The Peptide Mapping Pipeline
1. Sample Denaturation
Target protein samples are prepared, denatured, or reduced to expose specific internal cleavage sites.
2. Lys-C Proteolysis
Incubation with Lysyl Endopeptidase selectively cleaves the sequence cleanly on the carboxyl side of lysine residues.
3. LC-MS/MS Analysis
Generated peptide fragments undergo high-resolution liquid chromatography separation followed by tandem mass spectrometry.
4. Sequence Verification
Resulting peptide maps are compared to theoretical sequences to identify modifications, variants, or structural anomalies.
Maximizing Sequence Coverage
Lysyl Endopeptidase (Lys-C) provides exceptional cleavage specificity, significantly lowering the frequency of missed cleavages compared to multi-site proteases. It performs reliably under challenging conditions, and can be applied either as an independent standalone enzyme or as a targeted preliminary digestion step prior to trypsin exposure. This dual-capability ensures complete, predictable sequence maps for intricate biologics.
Specificity Rate
Technical FAQ
Review answers to common scientific inquiries regarding Lys-C digestion protocols.
Lys-C is an exceptionally precise endopeptidase that specifically cuts peptide bonds exclusively at the C-terminal side of lysine residues. This rigorous constraint yields highly uniform, predictable fragment sizes that simplify subsequent spectral matching and sequence alignments.
It minimizes missed-cleavage rates and improves overall sequence coverage. By rendering clear, reproducible molecular fragments, it allows analytical labs to confidently declare the absolute identity and absolute purity of therapeutic components.
Yes. Used in many monoclonal antibody characterisation and quality control workflows, an initial digestion with Lys-C is deployed to partially fragment tightly folded proteins, followed by a secondary trypsin digestion. This combined method drastically increases sequence depth in complex or hidden structural domains.