Tryptic Peptides

Generate fully tryptic peptides with K/R cleavage blocked before proline.

Description

A fully tryptic sequence digest splits after internal lysine or arginine unless proline follows.

A fully tryptic sequence digest splits after internal lysine or arginine unless proline follows. Cleavage boundaries describe where the sequence is sliced.^[1]

Generate fully tryptic peptides with K/R cleavage blocked before proline.

When to use Tryptic Peptides

Use this tool to generate fully tryptic peptides with K/R cleavage blocked before 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 Tryptic Peptides 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 trypticPeptides, cleavagePositions. 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. Find internal cut positions as zero-based exclusive slice ends, split from the N terminus and include the final segment. Return ordered peptides and cut positions.

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.

cut after K/R when next residue≠P; peptide segments end at those cut positions

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

Output field	Meaning	Value type
trypticPeptides	Tryptic peptides	list of string
cleavagePositions	Cleavage positions	list of number

json

{
  "input": {
    "sequence": "AKRA"
  },
  "output": {
    "trypticPeptides": [
      "AK",
      "R",
      "A"
    ],
    "cleavagePositions": [
      2,
      3
    ]
  }
}

Limitations and assumptions

No missed cleavage, kinetic yield or modifications are modeled. A terminal K/R does not create an extra empty peptide.

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 Trypsin Cleavage Sites: Locate trypsin cut positions at K/R not followed by proline. For a complementary task, use Missed Cleavage Peptide Count: Count fully and partially tryptic peptide candidates up to missed-cleavage limit.

References

Tryptic Peptides — tool.io

Similar or alternative tools

Trypsin Cleavage Sites
Locate trypsin cut positions at K/R not followed by proline.
Missed Cleavage Peptide Count
Count fully and partially tryptic peptide candidates up to missed-cleavage limit.