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proteases for mass spectrometry

Proteases for Mass Spectrometry

Proteins are generally digested with proteases to generate peptides for mass spectrometry analysis followed by sequencing (tandem MS). We offer a range of proteases qualified for use in mass spectrometry sample prep.

Available proteases for optimal digestion of proteins in mass spectrometry include Trypsin, Trypsin/Lys-C, rLys-C, Lys-C, rAsp-N and more. We also offer ProteaseMAX™ Surfactant for improved in-gel digestion and protein solubilization.

Learn about Proteases and Surfactants
Shop Protease and Surfactant products

24 Products

Product Type

Sample Type

Shop all Proteases for Mass Spectrometry

Lys-C, Mass Spec Grade, and Lys-N, Mass Spec Grade

Cleavage site: C-terminal or N-terminal of Lys. Optimal pH: 7–9.

VA1170, VA1180

rAsp-N, Mass Spec Grade

Cleavage site: N-terminal of Asp. Optimal pH: 6–9.


AccuMAP™ Low pH Protein Digestion Kits

Protein digestion at low (mildly acidic) pH to suppress deamidation and disulfide bond scrambling.

VA1040, VA1050

Rapid Digestion-Trypsin and -Trypsin/Lys-C Kits

Minimize protein digestion time, maximize data output.

VA1060, VA1061

Sequencing Grade Modified Trypsin

Cleavage sites: C-terminal of Arg and Lys. Optimal pH: 7–9.

V5111, V5117, V5113

Mass Spec-Compatible Yeast and Human Protein Extracts

Yeast and human protein extracts for mass spec applications such as instrument monitoring.

V7461, V7341, V6951, V6941

IdeS and IdeZ Proteases

IgG-degrading enzymes that cleave at a single site below the hinge region.

V7511, V7515, V8341, V8345, V8342

Trypsin/Lys-C Mix, Mass Spec Grade

Cleavage sites: C-terminal of Arg and Lys. Optimal pH: 8.

V5071, V5072, V5073

PNGase F

Catalyzes cleavage of N-linked oligosaccharides between the innermost GlcNAc and asparagine residues.


Endoglycosidase H

Characterize protein glycosylation in applications such as monitoring protein trafficking and determining glycan location and structure by mass spectrometry.

V4871, V4875


Cleavage sites: N-terminal of Leu, Phe, Val, Ala, Met, Ile. Optimal pH: 5–8.5.



Cleavage sites: C-terminal of Phe, Leu, Tyr and Trp. Optimal pH: 1–3.



Cleavage sites: C-terminal of Ala, Val, Ser, Gly, Leu and Ile. Optimal pH: 9.


Arg-C, Sequencing Grade

Cleavage site: C-terminal of Arg. Optimal pH: 7.6–7.9.


rLys-C, Mass Spec Grade

Cleavage site: C-terminal of Lys. Optimal pH: 8–9.


Showing 24 of 24 Products

What Are Proteases and Surfactants?

Bottom-up proteomics focuses on the analysis of protein mixtures after enzymatic digestion of the proteins into peptides. The resulting complex mixture of peptides is analyzed by reverse-phase liquid chromatography (RP-LC) coupled to tandem mass spectrometry (MS/MS). Identifying peptides, and subsequently proteins, is completed by matching peptide fragment ion spectra to theoretical spectra generated from protein databases.

Trypsin is the most widely used protease in mass spectrometry sample preparation. It is a highly specific serine protease, which cleaves at the carboxylic side of lysine and arginine residues. Protein digestion with trypsin generates peptides of optimal sizes for mass spec analysis.

There are certain proteins and protein mixtures where trypsin digestion alone is not efficient enough. Examples include digestion of membrane proteins and analysis of histone post-translational modifications (PTMs). Digestion with an alternative protease, individually or in combination with trypsin, creates a unique peptide map that may include sequences not seen with trypsin digestion alone. Overlaying peptides obtained with alternative proteases and trypsin increases protein coverage and overall confidence in protein identification.

We offer a complete portfolio of protein analysis products supported by a growing library of educational resources, including technology guides, on-demand webinars, scientific articles and protocols.

Use the links below to learn more about protein analysis products, or to explore learning resources covering topics such as in vitro protein expression, protein purification methods and live-cell protein interaction analysis.