Open a GC/MS analysis and you see a percentage column. Almost everyone reads it as: how much of the sample’s mass this compound makes up.
Not quite.
What the machine measures
When a compound leaves the chromatography column, the detector records a peak. The area under the peak is proportional to the amount of signal the detector receives, not to the mass of the compound.
The percentage on the analysis is the area of one peak divided by the total area of all peaks. So it is properly called area percentage, and a decent analysis will say so explicitly.
Why the two differ
The detector does not respond equally to every kind of molecule.
With a flame ionisation detector, the signal depends mainly on the number of carbon atoms that can burn. Oxygen-rich molecules give a weaker signal for their mass, because some of their carbon is already oxidised.
With mass spectrometry, the signal depends on how the molecule ionises and breaks apart — which varies a great deal between groups of compounds.
The result: a sample rich in alcohols and esters will report proportions slightly different from the true masses.
How large the error is
With the familiar hydrocarbon terpenes of essential oils, the error is usually small — a few per cent in relative terms. Small enough to ignore for most practical purposes.
With groups of compounds that differ a lot in how oxidised they are, the error can be more significant.
A serious laboratory can correct for this with response factors for each compound, but that requires a reference standard for each compound and is rarely done in routine testing.
What this changes in how you read
Don’t treat the number as an absolute measurement. It is a good estimate, not a constant.
Comparing the same compound between samples can be trusted. If linalool is 30% in one lot and 34% in another, the detector error almost cancels out because it is the same compound and the same detector.
Comparing different compounds within one sample is less reliable. Saying compound A is twice as abundant as compound B on the basis of peak areas is a statement with an error margin.
And as the next lesson shows, even if the number were perfectly accurate by mass, it still could not tell you which compound decides the smell.