For label-free quantification, the Quantification Spectrum chart displays the precursor isotope distribution for a selected PSM, LCMS feature, or MS/MS spectrum input. The abundances are measured by calculating either the height or the area of the extracted ion chromatogram of the most abundant isotope in the pattern. When you select a PSM or LCMS peak, the peaks of the selected isotope cluster are colored in blue with a filled blue circle above it. Other isotope distributions that coelute display diamonds in different colors above them, with peaks from the same isotope clusters having the same color of diamond.
Procedure
- Select the PSMs, MS/MS Spectrum Info, or LCMS tab in the result file.
- Select the row of the PSM that interests you.
- Choose View > Quantification Spectrum, or select the Quantification Spectrum icon,
. Quantification Spectrum chart for label-free quantification
The x axis of the chart displays the mass-to-charge ratio of the isotopes, and the y axis displays the area of the extracted ion chromatogram for the isotopes.
The colors and symbols on the chart are the same as those for precursor ion quantification.