Protein Missing Fraction

Score per-protein missing measurement fractions in an abundance matrix.

Description

Protein missingness measures how often a chosen finite sentinel appears across each matrix row.

Protein missingness measures how often a chosen finite sentinel appears across each matrix row. Sentinel identity distinguishes absent measurements from ordinary abundance values.^[1]

Score per-protein missing measurement fractions in an abundance matrix.

When to use Protein Missing Fraction

Use this tool to score per-protein missing measurement fractions in an abundance matrix.

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 Missing Fraction 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, abundanceMatrix, missingSentinel using the field table and calculation rules, then run the tool.
Read missingFractions, mostMissingProteinId. 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
abundanceMatrix	Abundance matrix	list of list of number	Required
missingSentinel	Missing sentinel	number	Required

Enter nonempty protein IDs and an aligned rectangular numeric matrix with nonempty rows. Compare values exactly with the finite sentinel, return row fractions and the first protein ID tied for greatest missingness.

missingFraction_i=count(row_i values exactly equal to sentinel)/rowWidth

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

Output field	Meaning	Value type
missingFractions	Missing fractions	list of number
mostMissingProteinId	Most missing protein id	string

json

{
  "input": {
    "proteinIds": [
      "a",
      "b"
    ],
    "abundanceMatrix": [
      [
        1,
        0,
        2
      ],
      [
        0,
        0,
        3
      ]
    ],
    "missingSentinel": 0
  },
  "output": {
    "missingFractions": [
      0.3333333333333333,
      0.6666666666666666
    ],
    "mostMissingProteinId": "b"
  }
}

Limitations and assumptions

NaN and null are not accepted missing markers. A real abundance equal to the sentinel is counted as missing. No imputation or missingness mechanism is inferred.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Matrices are limited to 128 rows and 128 entries per row; other lists are limited to 100,000 entries. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Protein Volcano Coordinates: Build protein volcano-plot log2 effect and negative-log10 FDR coordinates. For a complementary task, use Spectral Count Share: Normalize spectral counts to within-run protein abundance shares.

References

Protein Missing Fraction — tool.io

Similar or alternative tools

Protein Volcano Coordinates
Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.
Spectral Count Share
Normalize spectral counts to within-run protein abundance shares.