Reporter ions, also called reporters, are produced from the MS/MS of the labels affixed to peptide samples in reporter ion quantification. You can use the quantification value intensity to calculate the relative ratio of a peptide. You might also want to view the absolute quantification value intensity to verify that the peptide ratio calculation is correct.

Procedure

  1. Select the PSMs, MS/MS Spectrum Info, or Quan Spectra tab in the result file.
  2. Select the row of the PSM or quantification spectrum that interests you.
  3. Choose View > Quan Channel Values, or select Quan Channel Values .

The following figure shows the Quantification Channel Values chart created by the Show Quan Channel Values command for a selected PSM quantified using a TMT 10plex method.

Quantification Channel Values chart showing the reporter ion raw S/N values for a selected PSM

The x axis of the chart shows the names of the quantification channels, and the y axis shows the intensity of the reporter ions, in counts.

A legend is not available in the Quantification Channel Values chart when you display PSMs and quantification spectra.