Spectral Count Share

Normalize spectral counts to within-run protein abundance shares.

Description

Spectral-count shares normalize supplied counts within one run.

Spectral-count shares normalize supplied counts within one run. They are fractions of that run’s total rather than concentration measurements.^[1]

Normalize spectral counts to within-run protein abundance shares.

When to use Spectral Count Share

Use this tool to normalize spectral counts to within-run protein abundance shares.

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 Spectral Count Share 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 using the field table and calculation rules, then run the tool.
Read relativeAbundances, totalSpectra. 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

Enter a nonempty nonnegative count list with positive total. Return shares in input order and total spectra. Fractional numeric counts are accepted.

share_i=count_i/Σcounts

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

Output field	Meaning	Value type
relativeAbundances	Relative abundances	list of number
totalSpectra	Total spectra	number

json

{
  "input": {
    "spectralCounts": [
      2,
      3,
      5
    ]
  },
  "output": {
    "relativeAbundances": [
      0.2,
      0.3,
      0.5
    ],
    "totalSpectra": 10
  }
}

Limitations and assumptions

No protein-length correction, uncertainty or between-run scaling is applied. Counts and protein order must already be prepared.

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 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

Spectral Count Share — 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.