Trypsin Cleavage Sites

Locate trypsin cut positions at K/R not followed by proline.

Description

Trypsin-site enumeration identifies internal peptide-bond boundaries after K/R, with proline blocking the next position.

Trypsin-site enumeration identifies internal peptide-bond boundaries after K/R, with proline blocking the next position. Boundary coordinates differ from residue indexes.^[1]

Locate trypsin cut positions at K/R not followed by proline.

When to use Trypsin Cleavage Sites

Use this tool to locate trypsin cut positions at K/R not followed by proline.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Trypsin Cleavage Sites and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence using the field table and calculation rules, then run the tool.
Read cleavagePositions, cleavageCount. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required

Enter a canonical sequence. Return ascending zero-based slice boundaries and their count; the last residue is never included as an internal cut.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

cutPosition=i+1 for internal K/R at residue index i when sequence[i+1]≠P

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
cleavagePositions	Cleavage positions	list of number
cleavageCount	Cleavage count	number

json

{
  "input": {
    "sequence": "AKRPA"
  },
  "output": {
    "cleavagePositions": [
      2
    ],
    "cleavageCount": 1
  }
}

Limitations and assumptions

This applies the stated simplified specificity only. Digestion efficiency, modifications and missed cleavage must be addressed separately.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Tryptic Peptides: Generate fully tryptic peptides with K/R cleavage blocked before proline. For a complementary task, use Protease Digest: Simulate sequence digestion from caller-specified cut and blocking residues.

References

Trypsin Cleavage Sites — tool.io

Similar or alternative tools

Tryptic Peptides
Generate fully tryptic peptides with K/R cleavage blocked before proline.
Protease Digest
Simulate sequence digestion from caller-specified cut and blocking residues.