IBAQ Abundance
Compute intensity-based absolute quantification per theoretical peptide.
Description
iBAQ-style normalization divides summed peptide intensity by a supplied theoretical peptide count.
iBAQ-style normalization divides summed peptide intensity by a supplied theoretical peptide count. The count defines the normalization basis.1
Compute intensity-based absolute quantification per theoretical peptide.
When to use IBAQ Abundance
Use this tool to compute intensity-based absolute quantification per theoretical peptide.
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 IBAQ Abundance 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 summedPeptideIntensity, theoreticalPeptideCount using the field table and calculation rules, then run the tool.
- Read ibaq. 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 |
|---|---|---|---|
| summedPeptideIntensity | Summed peptide intensity | number | Required |
| theoreticalPeptideCount | Theoretical peptide count | number | Required |
Enter nonnegative intensity and positive safe-integer theoretical count. Return intensity per theoretical peptide.
iBAQ=summedPeptideIntensity/theoreticalPeptideCount Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| ibaq | Ibaq | number |
{
"input": {
"summedPeptideIntensity": 100,
"theoreticalPeptideCount": 5
},
"output": {
"ibaq": 20
}
}Limitations and assumptions
Theoretical digest filtering is not performed. No absolute molar calibration, peptide detectability correction or uncertainty is supplied.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use NSAF Abundance: Normalize spectral abundance factors by protein length and cohort total. For a complementary task, use EMPAI Abundance: Calculate exponentially modified protein abundance index from peptide counts.
References
-
IBAQ Abundance — tool.io
Similar or alternative tools
- NSAF Abundance
Normalize spectral abundance factors by protein length and cohort total.
- EMPAI Abundance
Calculate exponentially modified protein abundance index from peptide counts.