Protein Volcano Coordinates

Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.

Description

Volcano coordinates combine an already-log2 effect with negative-log10 adjusted p-values.

Volcano coordinates combine an already-log2 effect with negative-log10 adjusted p-values. A positive floor makes zero or tiny p-values finite for plotting.^[1]

Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.

When to use Protein Volcano Coordinates

Use this tool to build protein volcano-plot log2 effect and negative-log10 FDR coordinates.

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 Volcano Coordinates 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 log2FoldChanges, adjustedPValues, pValueFloor using the field table and calculation rules, then run the tool.
Read xCoordinates, yCoordinates. 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
log2FoldChanges	Log 2 fold changes	list of number	Required
adjustedPValues	Adjusted p values	list of number	Required
pValueFloor	P value floor	number	Required

Enter equal-length effect and adjusted-p-value lists, with p-values in 0–1 and floor in (0,1]. Copy effects and transform adjusted p-values in input order. Two empty lists are permitted.

x_i=log2FoldChange_i; y_i=−log10(max(adjustedP_i,pValueFloor))

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

Output field	Meaning	Value type
xCoordinates	X coordinates	list of number
yCoordinates	Y coordinates	list of number

json

{
  "input": {
    "log2FoldChanges": [
      1,
      -2
    ],
    "adjustedPValues": [
      0.01,
      0.001
    ],
    "pValueFloor": 0.000001
  },
  "output": {
    "xCoordinates": [
      1,
      -2
    ],
    "yCoordinates": [
      2,
      3
    ]
  }
}

Limitations and assumptions

The tool returns coordinates without rendering a plot, testing hypotheses or adjusting raw p-values. Values below the chosen floor share the same height.

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 PSM Qvalue Gate: Gate peptide-spectrum matches by supplied q-value threshold. For a complementary task, use Target Decoy FDR: Estimate target-decoy PSM false discovery rate using caller database-size ratio.

References

Protein Volcano Coordinates — tool.io

Similar or alternative tools

PSM Qvalue Gate
Gate peptide-spectrum matches by supplied q-value threshold.
Target Decoy FDR
Estimate target-decoy PSM false discovery rate using caller database-size ratio.