NSAF Abundance

Normalize spectral abundance factors by protein length and cohort total.

Description

NSAF first adjusts spectral counts for protein length, then normalizes those values within a cohort.

NSAF first adjusts spectral counts for protein length, then normalizes those values within a cohort. Length correction changes the relative shares compared with raw spectral counts.^[1]

Normalize spectral abundance factors by protein length and cohort total.

When to use NSAF Abundance

Use this tool to normalize spectral abundance factors by protein length and cohort total.

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 NSAF 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 spectralCounts, proteinLengths using the field table and calculation rules, then run the tool.
Read nsaf, totalLengthAdjustedCounts. 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
spectralCounts	Spectral counts	list of number	Required
proteinLengths	Protein lengths	list of number	Required

Enter aligned nonempty nonnegative counts and strictly positive lengths with positive adjusted total. Return ordered NSAF fractions and the length-adjusted total.

adjusted_i=count_i/length_i; NSAF_i=adjusted_i/Σadjusted

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

Output field	Meaning	Value type
nsaf	Nsaf	list of number
totalLengthAdjustedCounts	Total length adjusted counts	number

json

{
  "input": {
    "spectralCounts": [
      10,
      20
    ],
    "proteinLengths": [
      100,
      200
    ]
  },
  "output": {
    "nsaf": [
      0.5,
      0.5
    ],
    "totalLengthAdjustedCounts": 0.2
  }
}

Limitations and assumptions

Fractional counts and lengths are accepted. Detectability, response factors, shared peptide assignments and absolute concentration are not determined.

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 Spectral Count Share: Normalize spectral counts to within-run protein abundance shares. For a complementary task, use IBAQ Abundance: Compute intensity-based absolute quantification per theoretical peptide.

References

NSAF Abundance — tool.io

Similar or alternative tools

Spectral Count Share
Normalize spectral counts to within-run protein abundance shares.
IBAQ Abundance
Compute intensity-based absolute quantification per theoretical peptide.