PSM Qvalue Gate

Gate peptide-spectrum matches by supplied q-value threshold.

Description

A PSM q-value gate filters already computed peptide-spectrum-match confidence values.

A PSM q-value gate filters already computed peptide-spectrum-match confidence values. It applies a threshold rather than estimating q-values from search scores.^[1]

Gate peptide-spectrum matches by supplied q-value threshold.

When to use PSM Qvalue Gate

Use this tool to gate peptide-spectrum matches by supplied q-value threshold.

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 PSM Qvalue Gate 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 psmQValues, maximumQValue using the field table and calculation rules, then run the tool.
Read acceptedIndexes, rejectedIndexes, acceptedPercent. 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
psmQValues	Psm q values	list of number	Required
maximumQValue	Maximum q value	number	Required

Enter a nonempty q-value list and maximum, all in 0–1. Return zero-based accepted/rejected indexes in input order and acceptance percentage. Equality is accepted.

accepted={i:q_i≤maximum}; accepted%=100 acceptedCount/totalCount

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

Output field	Meaning	Value type
acceptedIndexes	Accepted indexes	list of number
rejectedIndexes	Rejected indexes	list of number
acceptedPercent	Accepted percent	number

json

{
  "input": {
    "psmQValues": [
      0.01,
      0.04,
      0.1
    ],
    "maximumQValue": 0.05
  },
  "output": {
    "acceptedIndexes": [
      0,
      1
    ],
    "rejectedIndexes": [
      2
    ],
    "acceptedPercent": 66.66666666666666
  }
}

Limitations and assumptions

Upstream q-value estimation, calibration and protein-level confidence are outside the gate. No spectra are read.

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 Target Decoy FDR: Estimate target-decoy PSM false discovery rate using caller database-size ratio. For a complementary task, use Protein Volcano Coordinates: Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.

References

PSM Qvalue Gate — tool.io

Similar or alternative tools

Target Decoy FDR
Estimate target-decoy PSM false discovery rate using caller database-size ratio.
Protein Volcano Coordinates
Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.