You need a linear curve of peak area versus mass or concentration of the pure analyte reference standard (detector response curve) for comparison. You cannot determine yield from %area alone!
1. Ideally, you need 2 kinds of standards: a) standard (S) at varying concentrations, and b) an internal standard (IS) at constant concentration. The IS needs to be chemically related to S but should be different by mass (generally heavy N or similar). If S and IS are volatile then no derivatization will be required. However, if they are not volatile then they have to be derivatized with a suitable agent to render them volatile, so that they can be separable from other molecules on the GC column.
2. Run the standard solutions, comprising varying concentrations of desired standard and constant concentration of internal standard on your GC/MS.
3. Measure both signals (S(S), S(IS)) and calculate the ratios (S(S))/(S(IS)) for each [S].
4. Plot the (S(S))/(S(IS)) vs [S]/[IS] to obtain the standard curve. If this curve is linear then the line can be used directly. If it is non-linear, then there are 3 possibilities: a) [S] is exceeding saturation (convex curve), b) [S] is near limits of detection (concave curve), or c) [S] range is too great (curve is concave at low end and convex at upper end. To avoid saturation effects, reduce the upper end of [S]. If you need to push quantitation limits, then you may need to use non-linear regression or log/log transformation.
5. Make sure to add IS (at the same concentration as with the standards above) in all your samples.
6. Process the samples the same way as you did with the standards. If derivatization is needed to ensure volatility then the same procedures need to be followed for samples as well as standards.
7. Measure the S(S), S(IS) from the sample. The S(S) represents the presence of S in the sample. Calculate the (S(S))/(S(IS)) for all samples. If this ratio is outside of the range of the standard curve, then you may need to dilute the sample (before adding the IS) prior to further processing and running.
8. Use the standard curve from step 4 to calculate the [S] in samples.
9. The above steps may need further optimization after an initial samples run.
Weight Percentage = (Area Percentage * Compound Molecular Weight) / Sum of (Area Percentage * Molecular Weight of all compounds)
Suppose you have a GC-MS analysis of a mixture containing three compounds: A, B, and C. The area percentages obtained are as follows: Compound A (40%), Compound B (30%), and Compound C (30%).
Let's assume the molecular weights for these compounds are: Molecular Weight of A (100 g/mol), Molecular Weight of B (150 g/mol), and Molecular Weight of C (200 g/mol).