Unique Peptide Tally
Count peptides unique to each protein in the observed evidence graph.
Description
Unique-peptide evidence distinguishes assignments exclusive to one observed protein from shared peptides.
Unique-peptide evidence distinguishes assignments exclusive to one observed protein from shared peptides. Uniqueness depends on the evidence graph supplied to the tool.1
Count peptides unique to each protein in the observed evidence graph.
When to use Unique Peptide Tally
Use this tool to count peptides unique to each protein in the observed evidence graph.
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 Unique Peptide Tally 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 proteinIds, peptideIds using the field table and calculation rules, then run the tool.
- Read uniquePeptideCounts, distinctPeptideCount. 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 |
|---|---|---|---|
| proteinIds | Protein ids | list of string | Required |
| peptideIds | Peptide ids | list of string | Required |
Enter aligned nonempty protein/peptide ID lists, one assignment per row. Build sets of proteins for each exact peptide ID, deduplicate repeated edges and return counts for distinct proteins in first-occurrence order plus distinct peptide total.
uniqueCount(protein)=number of distinct peptides assigned only to that protein Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| uniquePeptideCounts | Unique peptide counts | list of number |
| distinctPeptideCount | Distinct peptide count | number |
{
"input": {
"proteinIds": [
"A",
"A",
"B",
"B"
],
"peptideIds": [
"x",
"y",
"y",
"z"
]
},
"output": {
"uniquePeptideCounts": [
1,
1
],
"distinctPeptideCount": 3
}
}Limitations and assumptions
IDs are matched exactly without trimming or case normalization. Output counts have no protein-ID list, so retain input-derived protein order. Uniqueness is not checked against an external proteome.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Protein Group Parsimony: Greedily select a parsimonious protein group covering peptide evidence. For a complementary task, use Protein Sequence Coverage: Measure protein sequence coverage as the union of peptide intervals.
References
-
Unique Peptide Tally — tool.io
Similar or alternative tools
- Protein Group Parsimony
Greedily select a parsimonious protein group covering peptide evidence.
- Protein Sequence Coverage
Measure protein sequence coverage as the union of peptide intervals.