Protein Group Parsimony

Greedily select a parsimonious protein group covering peptide evidence.

Description

Protein parsimony summarizes a peptide-evidence graph with a small covering set of proteins.

Protein parsimony summarizes a peptide-evidence graph with a small covering set of proteins. A greedy cover offers a deterministic procedure without guaranteeing the globally smallest set.^[1]

Greedily select a parsimonious protein group covering peptide evidence.

When to use Protein Group Parsimony

Use this tool to greedily select a parsimonious protein group covering peptide evidence.

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 Protein Group Parsimony 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 selectedProteinIds, coveredPeptides, uncoveredPeptides. 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 exact protein/peptide IDs. Deduplicate edges, choose greatest new coverage and break ties by protein ID localeCompare. Return selected protein order, covered peptides in first-occurrence order and any uncovered peptides.

repeat: choose protein covering most remaining distinct peptides; remove its covered peptides

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

Output field	Meaning	Value type
selectedProteinIds	Selected protein ids	list of string
coveredPeptides	Covered peptides	list of string
uncoveredPeptides	Uncovered peptides	list of string

json

{
  "input": {
    "proteinIds": [
      "A",
      "A",
      "B",
      "B"
    ],
    "peptideIds": [
      "x",
      "y",
      "y",
      "z"
    ]
  },
  "output": {
    "selectedProteinIds": [
      "A",
      "B"
    ],
    "coveredPeptides": [
      "x",
      "y",
      "z"
    ],
    "uncoveredPeptides": []
  }
}

Limitations and assumptions

The tool uses only supplied assignments and may choose among biologically ambiguous proteins. Exact IDs are not normalized and greedy selection is not exhaustive optimization.

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 Unique Peptide Tally: Count peptides unique to each protein in the observed evidence graph. For a complementary task, use Protein Sequence Coverage: Measure protein sequence coverage as the union of peptide intervals.

References

Protein Group Parsimony — tool.io

Similar or alternative tools

Unique Peptide Tally
Count peptides unique to each protein in the observed evidence graph.
Protein Sequence Coverage
Measure protein sequence coverage as the union of peptide intervals.