Heavy isotopes are incorporated into proteins in precursor ion quantification. You can use the quantification value area to calculate the relative ratio of a peptide. You might also want to view the quantification value area to verify that the peptide ratio calculation is correct.
Procedure
- Select the PSMs tab in the result file.
- Select the row of the PSM or quantification spectrum that interests you.
- Choose View > Quan Channel Values, or select Quan Channel Values
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The following figure shows the chart created by the Show Quan Channel Values command for a PSM quantified using the SILAC 2plex method. It shows the relative peak area for the samples with the Light and Heavy isotope labels. The sample labeled Light is the sample with the greatest area.
The x axis of the chart shows the quantification channels, and the y axis shows the detected area for the given quantification channel, defined by counts Χ seconds.
A legend is not available in the Quantification Channel Values chart when you display PSMs and quantification spectra. You also cannot display grouped and ungrouped abundances.