Missed Cleavage Peptide Count
Count fully and partially tryptic peptide candidates up to missed-cleavage limit.
Description
Missed-cleavage candidates join consecutive fully tryptic segments.
Missed-cleavage candidates join consecutive fully tryptic segments. Counting those joins estimates candidate intervals without constructing peptide sequences.1
Count fully and partially tryptic peptide candidates up to missed-cleavage limit.
When to use Missed Cleavage Peptide Count
Use this tool to count fully and partially tryptic peptide candidates up to missed-cleavage limit.
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 Missed Cleavage Peptide Count 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, maximumMissedCleavages using the field table and calculation rules, then run the tool.
- Read basePeptides, candidatePeptides. 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 |
| maximumMissedCleavages | Maximum missed cleavages | number | Required |
Enter a canonical sequence and nonnegative safe-integer missed-cleavage limit. Use K/R cuts blocked before proline; return base-segment count and all contiguous interval candidates through the capped limit.
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.
base=cutCount+1; candidates=Σ(base−missed), missed=0…min(maximumMissed,base−1) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| basePeptides | Base peptides | number |
| candidatePeptides | Candidate peptides | number |
{
"input": {
"sequence": "AKRA",
"maximumMissedCleavages": 1
},
"output": {
"basePeptides": 3,
"candidatePeptides": 5
}
}Limitations and assumptions
Repeated sequences are counted as separate intervals. No mass, length filter, semi-specific cleavage or observed digestion yield is included.
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 Digest Mass Filter: Filter digest peptides by calculated monoisotopic neutral mass.
References
-
Missed Cleavage Peptide Count — tool.io
Similar or alternative tools
- Tryptic Peptides
Generate fully tryptic peptides with K/R cleavage blocked before proline.
- Digest Mass Filter
Filter digest peptides by calculated monoisotopic neutral mass.