Yes, GC-MS can detect compounds with functional groups that FTIR might miss due to its greater sensitivity and compound separation capabilities. Overall, GC-MS is more precise and advanced for identifying compounds in complex mixtures, while FTIR provides broad functional group information.

FTIR technique is primarily limited to the qualitative identification of functional groups within a molecule. In contrast, GC-MS requires your analyte to be a volatile compound, irrespective of its functional group, from which you obtain the molecular weight of the compound or its fragments. Based on the fragmentation pattern, you can identify the compound. GC-MS is the most precise and advanced technique for the identification of complex mixtures.

Both techniques are complementary.

FTIR detect funcional groups of all the molecules that you put in the cell or over probe. But your limit of detection could be microg but your limit of quantification is tens of ppm.

GC-MS use the GC to separate the different compounds that your sample has and because of that it gives you mass spectra of each peak with the fragmentation information with a normal LOD of less than ng/ml (ppb) and a LOQ in the order of ng/ml.

So GC-MS allow to have more precise information of each compounds present in the sample and with a better LOD and LOQ.

For that reason GC-MS is better than FTIR for the identification of compounds in a complex sample.

best

This is probably not relevant to the question, but there is also a GC/FTIR technique which may identify compounds separated by GC by they FTIR spectrum. The sensitivity is less than MS for the detection because FTIR is less sensitive than MS. The technique is seldom available in analytical facilities.

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