TMT Isotope Matrix Audit

Solve a multichannel TMT isotope-crosstalk correction matrix.

Description

TMT isotope correction treats observed channels as mixtures of underlying signals.

TMT isotope correction treats observed channels as mixtures of underlying signals. Solving the supplied linear system separates those signals under the stated matrix model.^[1]

Solve a multichannel TMT isotope-crosstalk correction matrix.

When to use TMT Isotope Matrix Audit

Use this tool to solve a multichannel TMT isotope-crosstalk correction matrix.

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 Isotope Matrix Audit 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 reporterSignals, isotopeMixingMatrix using the field table and calculation rules, then run the tool.
Read correctedSignals, matrixInvertible. 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
reporterSignals	Reporter signals	list of number	Required
isotopeMixingMatrix	Isotope mixing matrix	list of list of number	Required

Enter a nonempty nonnegative signal vector and an aligned square finite matrix. Solve by Gauss–Jordan elimination with partial pivoting. Pivots below 1e−12 are rejected; results below 1e−12 in absolute value are set to zero. Reject remaining negative corrected signals.

mixingMatrix×correctedSignals=reporterSignals

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

Output field	Meaning	Value type
correctedSignals	Corrected signals	list of number
matrixInvertible	Matrix invertible	boolean

json

{
  "input": {
    "reporterSignals": [
      90,
      10
    ],
    "isotopeMixingMatrix": [
      [
        0.9,
        0.1
      ],
      [
        0.1,
        0.9
      ]
    ]
  },
  "output": {
    "correctedSignals": [
      100,
      0
    ],
    "matrixInvertible": true
  }
}

Limitations and assumptions

Successful results always return matrixInvertible=true; singular matrices are input errors. Matrix orientation and calibration are caller responsibilities; no condition number or nonnegative constrained fit is provided.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Matrices are limited to 128 rows and 128 entries per row; other lists are limited to 100,000 entries. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use TMT Channel Normalization: Equalize TMT reporter channels to caller-supplied reference totals. For a complementary task, use Target Decoy FDR: Estimate target-decoy PSM false discovery rate using caller database-size ratio.

References

TMT Isotope Matrix Audit — tool.io

Similar or alternative tools

TMT Channel Normalization
Equalize TMT reporter channels to caller-supplied reference totals.
Target Decoy FDR
Estimate target-decoy PSM false discovery rate using caller database-size ratio.