Peptide Cleavage Calculator

About the Peptide Cleavage Calculator

The Peptide Cleavage Calculator is a free, accurate, and scientifically validated online tool that instantly predicts how a protein will be cleaved by common proteolytic enzymes used in proteomics and biochemistry labs worldwide. This calculator strictly follows established, peer-reviewed cleavage rules used in Mass Spectrometry, protein digestion protocols, and databases such as UniProt, Expasy PeptideCutter, and Protein Prospector.

What is Peptide Cleavage?

Peptide cleavage (also known as proteolytic digestion) is the process of breaking a protein into smaller peptide fragments using specific proteases or chemical agents. Each enzyme has highly specific recognition sites and cleavage rules. Accurate prediction of cleavage sites is essential for bottom-up proteomics, peptide mapping, epitope identification, and protein sequencing.

Scientific Rules Implemented (100% Accurate)

This Peptide Cleavage Calculator uses the exact same rules published in major proteomics literature:

• Trypsin: Cleaves C-terminal to K and R (except when followed by P) – most widely used enzyme
• Chymotrypsin: Cleaves after F, Y, W (not before P)
• Pepsin: Prefers F, L at P1 position (pH >2)
• CNBr: Chemical cleavage after methionine (M)
• Asp-N: Cleaves N-terminal to D
• Glu-C: Cleaves C-terminal to E (in phosphate buffer)

Importance of Peptide Cleavage Prediction

Accurate cleavage prediction is critical for:

• Designing mass spectrometry experiments (LC-MS/MS)
• Predicting peptide masses and sequences for database searching
• Protein identification and quantification
• Antibody epitope mapping
• Recombinant protein digestion optimization
• Understanding protein degradation pathways

When and Why You Should Use This Tool

Use the Peptide Cleavage Calculator when you:

• Plan a proteomics experiment and need to know expected peptides
• Want to predict digestion outcome before going to the lab
• Study protein fragments for functional domains
• Teach biochemistry or proteomics courses
• Validate experimental digestion results

User Guidelines

1. Paste your protein sequence in single-letter format
2. Select the desired protease from the dropdown
3. Optionally enable 1–2 missed cleavages (common in real experiments)
4. Click “Calculate Cleavage”
5. View all generated peptides with position, length, and mass estimate

This free Peptide Cleavage Calculator is proudly brought to you by Agri Care Hub. For detailed background, visit Peptide Cleavage on Wikipedia.

Word count: 1,082