[esloomis]

I am attempting to derivatize a suite of different plant metabolites through a two step process of Methoximation (1) (with Methoxyamine HCL) and silylation (2) with MSTFA.  They are then analyzed by GC/MS.  At the present, we are still working on analyzing standards and building a library for further testing of actual samples.  We have found that Amino acids are not getting derivatized with this process.  When the methoximation step is removed, the expected derivatized product appears.  I am not an expert in chemistry, and neither is anyone else in my lab.  We are trying to understand why the MEOX step is causing this problem and how (or if) it might be fixed.  If anyone knows anything about derivatizations of this type, or if they could point me towards more information, I would appreciate it.

[sjb]

Do you have conditions for N-silylation? I haven't seen this transformation anywhere. It's possible the silylation that you see when the methoxyamine step is not carried out is actually occuring on the carboxyl group, instead?

S

[esloomis]

The Methoxymation step is carried out at 30C for 90 min with Pyridine as the solvent.
Silylation is carried out at 37C for 30 min with MSTFA. 
I assume that is what you mean by "conditions for N-silylation?" 
When a large enough amount of AA is added to the above reaction, you can see the underivatized Amino acid peak on the GC, even though it looks really bad.  This is what makes me think that somehow derivatization is not happening for the Amino acids.