SILAC Heavy Light Ratio

Calculate an impurity-adjusted SILAC heavy-to-light protein ratio.

Description

A SILAC ratio compares modeled corrected heavy signal with light signal.

A SILAC ratio compares modeled corrected heavy signal with light signal. This implementation removes a supplied fraction from heavy intensity without reallocating it to light.^[1]

Calculate an impurity-adjusted SILAC heavy-to-light protein ratio.

When to use SILAC Heavy Light Ratio

Use this tool to calculate an impurity-adjusted SILAC heavy-to-light protein ratio.

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 SILAC Heavy Light Ratio 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 heavyIntensity, lightIntensity, heavyImpurityFraction using the field table and calculation rules, then run the tool.
Read correctedHeavyIntensity, heavyToLightRatio. 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
heavyIntensity	Heavy intensity	number	Required
lightIntensity	Light intensity	number	Required
heavyImpurityFraction	Heavy impurity fraction	number	Required

Enter nonnegative heavy intensity, positive light intensity and impurity fraction from zero to below one. Return corrected heavy signal and heavy/light ratio.

correctedHeavy=heavy×(1−impurityFraction); ratio=correctedHeavy/light

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

Output field	Meaning	Value type
correctedHeavyIntensity	Corrected heavy intensity	number
heavyToLightRatio	Heavy to light ratio	number

json

{
  "input": {
    "heavyIntensity": 120,
    "lightIntensity": 40,
    "heavyImpurityFraction": 0.1
  },
  "output": {
    "correctedHeavyIntensity": 108,
    "heavyToLightRatio": 2.7
  }
}

Limitations and assumptions

The correction is a one-sided scaling model. Isotopic envelopes, cross-channel transfer, labeling efficiency and peptide interference are not fitted.

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 TMT Channel Normalization: Equalize TMT reporter channels to caller-supplied reference totals. For a complementary task, use Western Total Protein Normalization: Normalize a western target band to total-lane protein and a reference lane.

References

SILAC Heavy Light Ratio — tool.io

Similar or alternative tools

TMT Channel Normalization
Equalize TMT reporter channels to caller-supplied reference totals.
Western Total Protein Normalization
Normalize a western target band to total-lane protein and a reference lane.