What type of sample and/or compounds are you assessing in this experiment? What reagent are you using? I assume these are being converted to a TMS analog (+SI(CH3)3). The derivatization should not affect the results of your analysis from a qualitative perspective as long as you are still able to identify the compounds after derivatization. Commercial libraries have many of these, but not all. From a quantiative perspective, the results won't be impacted if you account for the response factor difference (non-derivatized versus derivatized) using an authentic standard.

Hi,

I would highly recommend you to go for reading a Book Chapter by Professor Oliver Fiehn

Metabolomics by Gas Chromatography–Mass Spectrometry: Combined Targeted and Untargeted Profiling: Article Metabolomics by Gas Chromatography-Mass Spectrometry: Combin...

Also, do consult his website, for a lot of educational resources on "silylation" strategies and interpretation.

Thanks,

Hi Hicham,

There are some examples where silylation also can affect the result qualitatively (One reported compound can arise from different compounds). So in any Case you should do additional bibliographic research on this issue!

I have to ask a follow-up question to your question: How are your results effected? What are you comparing them to when you say the results are effected? Are you accounting for the additional silyl group(s) that are being added to your sample before GC/MS?