KB000444: Why do the Ion Ratios Not Change when Using QEDIT? - MS ChemStation 

The Subtraction Method must be set to Extended Area Quant. In both Enhanced and EnviroQuant mode of G1701xx, it is possible to integrate each of the extracted ion chromatograms used for quant and qualifier signals independently of one another. To do this, the compound must be set for extended area quant by selecting Extended Area Quant as the Subtraction Method for the compound(s) on page one under Edit Compounds. To edit individual ion chromatograms, select Qedit, then Display and then select Qualifiers. Ion chromatograms are then displayed in a separated format, rather than merged. It is possible to manually integrate any and all of the ion chromatograms displayed. Updated quant ion areas are displayed in the report, along with corrected ion ratios.