EMPAI Abundance
Calculate exponentially modified protein abundance index from peptide counts.
Description
emPAI applies an exponential transformation to the observed-versus-observable peptide ratio.
emPAI applies an exponential transformation to the observed-versus-observable peptide ratio. The supplied observable count defines what evidence is expected.1
Calculate exponentially modified protein abundance index from peptide counts.
When to use EMPAI Abundance
Use this tool to calculate exponentially modified protein abundance index from peptide counts.
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 EMPAI 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 observedPeptides, observablePeptides using the field table and calculation rules, then run the tool.
- Read pai, empai. 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 |
|---|---|---|---|
| observedPeptides | Observed peptides | number | Required |
| observablePeptides | Observable peptides | number | Required |
Enter nonnegative safe-integer observed count and positive safe-integer observable count, with observed no greater than observable. Return ratio and exponential index.
PAI=observed/observable; emPAI=10^PAI−1 Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| pai | Pai | number |
| empai | Empai | number |
{
"input": {
"observedPeptides": 3,
"observablePeptides": 6
},
"output": {
"pai": 0.5,
"empai": 2.1622776601683795
}
}Limitations and assumptions
The observable count is supplied, not generated from digestion or detection limits. This is an abundance index rather than a calibrated absolute concentration.
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 IBAQ Abundance: Compute intensity-based absolute quantification per theoretical peptide. For a complementary task, use Missed Cleavage Peptide Count: Count fully and partially tryptic peptide candidates up to missed-cleavage limit.
References
-
EMPAI Abundance — tool.io
Similar or alternative tools
- IBAQ Abundance
Compute intensity-based absolute quantification per theoretical peptide.
- Missed Cleavage Peptide Count
Count fully and partially tryptic peptide candidates up to missed-cleavage limit.