TMT Channel Normalization

Equalize TMT reporter channels to caller-supplied reference totals.

Description

Channel normalization scales each supplied intensity to its paired reference total.

Channel normalization scales each supplied intensity to its paired reference total. Here the normalized output consequently reproduces that reference value up to floating-point precision.^[1]

Equalize TMT reporter channels to caller-supplied reference totals.

When to use TMT Channel Normalization

Use this tool to equalize TMT reporter channels to caller-supplied reference totals.

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 TMT Channel Normalization 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 channelIntensities, referenceChannelTotals using the field table and calculation rules, then run the tool.
Read normalizedIntensities, factors. 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
channelIntensities	Channel intensities	list of number	Required
referenceChannelTotals	Reference channel totals	list of number	Required

Enter aligned nonempty strictly positive channel intensities and reference totals. Return factors and their products in input order.

factor_i=reference_i/intensity_i; normalized_i=intensity_i×factor_i

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

Output field	Meaning	Value type
normalizedIntensities	Normalized intensities	list of number
factors	Factors	list of number

json

{
  "input": {
    "channelIntensities": [
      10,
      20
    ],
    "referenceChannelTotals": [
      20,
      20
    ]
  },
  "output": {
    "normalizedIntensities": [
      20,
      20
    ],
    "factors": [
      2,
      1
    ]
  }
}

Limitations and assumptions

This is independent per-channel scaling, not cohort median normalization. Reference totals must be established separately and biological differences can be affected by their choice.

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 TMT Isotope Matrix Audit: Solve a multichannel TMT isotope-crosstalk correction matrix. For a complementary task, use SILAC Heavy Light Ratio: Calculate an impurity-adjusted SILAC heavy-to-light protein ratio.

References

TMT Channel Normalization — tool.io

Similar or alternative tools

TMT Isotope Matrix Audit
Solve a multichannel TMT isotope-crosstalk correction matrix.
SILAC Heavy Light Ratio
Calculate an impurity-adjusted SILAC heavy-to-light protein ratio.