Peptide cutter

What is Peptide Cutter?

Peptide Cutter maps protease and chemical cleavage sites across a protein sequence. Given one or more proteins, it tests up to 39 enzymes and chemical reagents simultaneously, reporting every position where each agent would cut. Systematic in silico cleavage mapping has been a foundational technique in proteomics for decades, enabling researchers to survey digestion patterns across an entire enzyme library before committing to a wet-lab protocol.

Where the related Peptide mass calculator answers "what fragments does one enzyme produce and what are their masses?", Peptide Cutter answers "which enzymes cut this protein, where, and how often?" The two tools complement each other: Peptide Cutter for surveying cleavage patterns, Peptide mass for quantitative fragment analysis.

How to use Peptide Cutter online

ProteinIQ runs Peptide Cutter entirely in the browser with instant results — no server round-trip or account required.

Input

Settings

Output

Each row represents one cleavage event — a specific enzyme cutting at a specific position.

Results can be downloaded as CSV or JSON.

Supported enzymes

The tool includes 39 proteases and chemical reagents organized by cleavage mechanism.

Serine proteases

Cysteine proteases

All caspases cleave after the terminal Asp and are blocked by Pro at P1'.

Aspartyl proteases

Metalloproteases

Endopeptidases

Chemical reagents

How Peptide Cutter works

Each enzyme is defined by a specificity rule in the Schechter-Berger nomenclature, which labels residues around the scissile bond as P4-P3-P2-P1 | P1'-P2'-P3'-P4'. Most proteases recognize a primary residue at the P1 position (C-terminal cleavage) or P1' position (N-terminal cleavage), with optional blocking rules for adjacent positions.

Three levels of specificity are supported:

1. Simple rules: A character class of cleavable residues plus optional exclusion at P1'. Covers most endopeptidases and chemical reagents (trypsin, Lys-C, CNBr, etc.).
2. Pattern rules: A regular expression matching multi-residue recognition motifs. Used for caspases, enterokinase, Factor Xa, and granzyme B, which require specific sequences upstream of the cleavage site.
3. Custom logic: Programmatic rules for enzymes whose specificity depends on multiple context positions simultaneously. Thrombin, for example, requires checking both the GRG motif and the [AFGILTVM]PR[^DE] motif, which cannot be captured in a single regex.

Cleavage is never predicted at the terminal residue — the enzyme must have a residue on both sides of the scissile bond.

Applications

• Proteomics experiment design: Surveying which enzymes produce useful fragmentation patterns before committing to a digestion protocol. Setting Max cuts filters out non-specific cutters, while Min cuts ensures the enzyme actually fragments the target protein.
• Recombinant protein engineering: Checking whether affinity tag removal sites (TEV, thrombin, Factor Xa, enterokinase) are unique to the tag linker and do not occur internally in the protein of interest. An unexpected internal thrombin site, for instance, would destroy the target during tag cleavage.
• Limited proteolysis studies: Identifying surface-accessible cleavage sites by correlating predicted sites with experimentally observed fragments. Buried residues are protected from proteolysis even if the enzyme has specificity for them.
• Caspase substrate screening: The caspase 1-10 panel can identify which caspases, if any, recognize motifs in a candidate substrate protein — relevant for apoptosis research and caspase inhibitor design.

Limitations

Specificity rules are based on primary sequence only. Protein tertiary structure, post-translational modifications, and local folding can all affect whether a theoretically predicted site is actually accessible to the protease in an experiment. Results represent the maximum possible cleavage pattern under denaturing conditions where all sites are fully exposed.

Related tools

• Peptide mass calculator: Digest a protein with one enzyme and compute fragment masses for mass spectrometry planning.
• Protein parameters: Comprehensive physicochemical characterization (molecular weight, pI, extinction coefficient, stability indices).
• Amino acid composition: Full residue breakdown and classification statistics.