[kamiyu]

Do you think the intensity of the GC chromatograph is a reliable indication of relative concentration?

Linear relationship? or something?

[kriggy]

I would say yes but also suggest doing calibration curve

[Furanone]

In a general sense, yes, but each chemical compound will have a unique response factor that you would multiply by the area (or height) of that chemical's peak to obtain the true concentration, and these can be significantly different for different compounds. MS peak quantification is based on how well each type of molecule fragment when an electron beam hits them coming out the end of GC column into ionization chamber (and usually this is only a small percent), so compounds where a higher % of molecules fragment from the electron beam and also more fragments are created since each created ion that passes through quadrapole will hit the electron multiplier detector is counted will give a higher response (TIC).

In flame ionization detection (FID), quantification response is based on the combustion of organic material so there will be a higher relative response for molecules with more -C-C- or -C-H bonds so running fatty acid methyl esters will have a quantification bias for the longer chain fatty acids and a compound such as carbon dioxide would give virtually no response.

In my experience both GC-MS and GC-FID analyses I run in a food lab look similar to each other and have fairly good relative quantity responses (ie. there are no examples seen where a tiny peak has a massive quantity while a large peak works out to be a trace quantity).

Hope this helps