It is possible that these are not GC-amenable and they are either not volatilising or decompose upon heating. It will depend on their composition, what conditions you used for GC, and how you derivatised. You would need to give more detail.

Multiple modes of analysis are required to obtain a rough number of possible compounds present in a natural product. You stated that you only used GC, which is specific for use with volatile samples only. IOW: You will miss many other sample types by limiting your analytical technique to one that is for use with volatile samples only. Please include other techniques to gain more information. No single technique or mode is "universal" (even if the sales brochure says it is).

For a more scientific and comprehensive analysis include other analytical techniques suitable to natural products such as HPLC with UV/VIS scanning (DAD) or HPLC with DAD and MS inline for even more information.

@ A S M Ali Reza Can I assume that from the plant fraction you isolated 2 pure active compounds detectable by GC-MS but not detected in the initial GC-MS analysis of the fraction? If this is true, the possible reasons may include:

1. The isolated pure compounds were formed during isolation process;

2. The concentrations of the two compounds in the initial fraction sample (possibly still a complex mixture) were below the LODs and thus the two compounds could not be found in the initial fraction analysis. However, when samples for the isolated pure compounds were prepared at much higher concentration, those compounds could be detected.

Isolation and identification do not act apart from generally but the concentration of fractions created is very important. In fact, the pure compounds of the sample in comparison with its compound identified in the certain level of different concentration would not be same results. It is important to several analytical techniques are done and the made results in different treatment of concentration are compared together.

Kindly visit..

https://www.nature.com/articles/s41598-020-73442-0

Dear Dr A S M Ali Reza . May be they are not detected because they are of high molecular weight. See the following useful link: https://www.technologynetworks.com/analysis/articles/gas-chromatography-how-a-gas-chromatography-machine-works-how-to-read-a-chromatograph-and-gcxgc-335168

Kindly see also the following useful RG link: Article GC-MS analysis of bioactive compounds present in different e...

Also check please the following useful RG link: Article GC–MS analysis of volatile organic compounds from Bambara gr...

The following link is also very useful: https://www.omicsonline.org/open-access/gc-ms-technique-and-its-analytical-applications-in-science-and-technology-2155-9872.1000222.php?aid=33334

Compounds can decompose in the hot GC injector, or they may be too large or too polar to go through a GC column. Here's an example where the active sulfur-containing compounds from Mimosa pudica volatiles were found to decompose in the GC, producing only CS2 instead of the intact molecules.

Musah, R.A., Lesiak, A.D., Maron, M.J., Cody, R.B., Edwards, D., Fowble, K.L., Dane, A.J., Long, M.C.: Mechanosensitivity Below Ground: Touch-Sensitive Smell-Producing Roots in the "Shy Plant," Mimosa pudica L. Plant Physiology. 170, 1075-1089 (2015)

In GC we can identify only the organic volatile compounds (mostly). The pressure and temperature of gas (mobile phase) helps to detect volatile compounds. On contrast to LC, there is a scope of identify the non volatile (mostly non volatile; depends on the concentration of the sample). Besides, in TLC, both types of element (volatile and non volatie) can be isolated.