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Alternative Proteases

Figure 9356CA
  • Improve protein sequence coverage by combining digestion with trypsin and an alternative protease.
  • Enhance digestion of tightly folded proteins by using proteases that tolerate denaturing conditions.
  • Identify post-translational modifications (PTM) that are resistant to trypsin digestion by using an alternative protease.

Increase Protein Sequence Coverage

Digestion with alternative proteases individually or in combination will create a unique peptide map that may include sequences not seen with trypsin digestion alone. Overlaying these peptides with those obtained with trypsin increases protein coverage and overall confidence in protein identification.

Increase in protein coverage with use of chymotrypsin + trypsin compared to trypsin alone.

Increase Protein Sequence Coverage With:

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Lys-C/Chymotrypsin

Both Lys-C and Chymotrypsin, when used as alternative proteases with trypsin, have shown their value in extending proteomics coverage for bottom-up protein identification and for mapping of post-translational modification.

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Asp-N/Glu-C

Endoproteinases Asp-N and Glu-C have been used for protein characterization for over 30 years and due to their specific cleavage sites, these proteinases create unique peptide fragments available for mass spectrometry analysis.

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Pepsin/Thermolysin

Thermolysin and pepsin are distinct from other proteases because they tolerate extreme conditions: high temperatures and low pH, respectively. These properties make them ideal proteases for digestion of proteolytically resistant, tightly folded proteins.

Enhance Digestion of Difficult Proteins with Thermolysin and Pepsin

Thermolysin and pepsin are unique because they tolerate conditions that can be used to denature difficult to digest and tightly folded proteins, high temperatures and low pH, respectively. Because they remain active under these conditions, these proteases can cleave previously inaccessible sites.

Figure 10693MA

Enhance Digestion of Difficult Proteins With:

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Pepsin/Thermolysin

Thermolysin and pepsin are distinct from other proteases because they tolerate extreme conditions: high temperatures and low pH, respectively. These properties make them ideal proteases for digestion of proteolytically resistant, tightly folded proteins.

Characterize Post-translation Modifications with Arg-C

Some Post-translation Modifications (PTM), such as acetylation and methylation, prevent trypsin digestion. As a result, digesting with trypsin alone can miss certain PTMs. Including digestion with Arg-C can identify more PTMs, including mono-, dimethylated and acetylated lysine and arginine residues.

Figure 10691MA

Improve Data for PTM Analysis With:

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Arg-C

In recent experiments, we have shown a parallel Arg-C digestion complemented the trypsin digestion by recovering an additional 2,653 peptides and providing a 37.4% increase in the number of identified peptides. In this same experiment, this also resulted in an increase in the number of identified proteins.

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