Your Protein Digestion Is Finished.
How Do You Remove the Trypsin?

Trypsin is widely used for protein digestion and peptide mapping, but residual protease can remain after the desired digestion period. Affinity-removable trypsin adds a purification handle to the enzyme itself, allowing the protease to be captured and removed after processing.

Why Trypsin?

Trypsin preferentially cleaves peptide bonds on the C-terminal side of lysine and arginine residues.

Its predictable cleavage behavior makes trypsin useful for protein characterization, controlled proteolysis and peptide-mapping workflows.

But digestion efficiency is only part of the workflow. Once the desired processing period is complete, researchers may also need a reliable way to stop further proteolysis.

Inactivation Is Not the Same as Removal

Changes in pH or temperature and the addition of protease inhibitors can reduce proteolytic activity.

However, these approaches do not necessarily remove the protease molecule from the processed sample.

For workflows where residual enzyme is undesirable, physical removal of the protease may provide a useful alternative.

What If the Trypsin Has Its Own Affinity Tag?

MEDNA Bio's Affinity-Removable Recombinant Trypsin contains a C-terminal polyhistidine affinity tag.

Polyhistidine tags bind immobilized metal ions such as nickel or cobalt, forming the basis of immobilized metal affinity chromatography (IMAC).

Following digestion, the His-tagged protease can therefore be captured using Ni-NTA or another compatible IMAC matrix.

Digest → Capture → Remove

STEP 1 — Digest
Process the target protein with affinity-removable recombinant trypsin.

STEP 2 — Capture
Contact the processed sample with Ni-NTA or another compatible IMAC medium.

STEP 3 — Bind
The C-terminal polyhistidine tag on the trypsin binds the immobilized metal matrix.

STEP 4 — Recover
Collect the processed protein or peptide fraction for downstream analysis.

Why Could This Be Useful for Peptide Mapping?

Digestion reproducibility can influence peptide-mapping performance. Variables include enzyme-to-substrate ratio, incubation time, temperature, buffer conditions and the method used to terminate proteolysis.

An affinity-removable protease introduces another workflow option: physically separate the digestion enzyme once the desired reaction period is complete.

MEDNA Bio therefore lists peptide-mapping method development and controlled proteolysis among the intended applications for the enzyme.

Affinity-Removable Recombinant Trypsin

The enzyme is recombinantly produced in Pichia pastoris and contains a C-terminal polyhistidine tag.

It is compatible with Ni-NTA and other IMAC matrices and can be used in soluble or immobilized proteolysis workflows.

Current configurations include 100 µg, 500 µg, 1 mg and custom bulk quantities.

Potential Applications

✓ Recombinant protein processing

✓ Controlled proteolysis

✓ Protein characterization

✓ Peptide-mapping method development

✓ Protease immobilization studies

✓ Protein purification workflow development

✓ Workflows requiring post-digestion protease removal

One Important Workflow Consideration

If the protein of interest is itself His-tagged, it may also interact with the same IMAC matrix used to capture the protease. The affinity tags on the target protein and the downstream purification strategy should therefore be considered when designing the workflow.

Developing a Protein Digestion or Peptide-Mapping Workflow?

Dana Bioscience can help evaluate recombinant proteases, protein purification products, IMAC media and reagents for protein characterization.

Share your target protein, digestion objective, sample amount, current protease and downstream analysis, and we can help identify appropriate research products and workflow options.