Gas chromatography/mass spectrometry: Can I use peak ratios and molecular mass to derive quantity?
Is this even how GC/MS results work?



As cbeleites said the method you described is a proper technique but not likely to be appropriate given the information you cited.

In GC/MS you should have two sets of information. The first is the GC Total Ion Chromatograph (TIC) which will have time as the x-axis and response (abundance) as the y-axis. For each retention time on the TIC there will be a corresponding Mass Spectra (MS). In the MS the x-axis is m/z (ion) and y-axis is also response (abundance).

Different compounds have different responses so if you inject the exact same amount of two different compounds you could get a much larger response from one compared to the other. For example tramadol gives much higher response compared to hydrocodone. This is why you want your internal standard to be structurally similar to your analyte. 

Quantification of a compound is often done by running 3 - 5 calibrators at known concentrations in order to make a calibration curve. Once an acceptable calibration curve is made the sample along with controls can be fit onto the curve to calculate the amount of the compound of interest in the sample and controls. If the controls are correct then the sample value can be used.

To make a calibration curve you need an internal standard in each calibrator, control and sample. You can then make the curve either with ion ratios between paired internal standard and analyte ions OR if your internal standard response is consistent in all the calibrators, controls and sample you can use the GC peak response.

In conclusion if you only have one GC/MS run with the two dissimilar compounds in it you will not be able to easily calculate the quantity of the second compound based on the GC response of the first unless you have additional information that was not listed in this question.