Hello,

I assume you're talking about derivatization for GC/GC-MS analysis? If yes, then you can definitely use BSTFA + TMCS! The silylation potential of BSTFA is the same as for MSTFA. However, keep in mind that for carbohydrates/polyhydroxy compounds you might need a longer silylation time (whereas organic acids mostly are silylated "at the drop of a hat").

We routinely use both BSTFA + TMCS and HMDS + TMCS in pyridine (dried with KOH pellets) for silylation. The latter silylation method will give precipitation (NH4Cl), but it's much cheaper and more selective than BSTFA. This makes it an attractive alternative for carbohydrate analysis when you have, say, 50-60 samples.

If you're interested in various silylation methods, many chemical suppliers (e.g., Sigma-Aldrich) have overviews/fact sheets.

Best regards,

JR

Great answers above, and in addition you must consult some of the following resources such as:

Mass spectral fragmentation of trimethylsilylated small molecules: http://onlinelibrary.wiley.com/doi/10.1002/mas.21518/full by Professor Oliver Fiehn, and his excellent book chapter on GC-MS Derivatization protocols:

UNIT 30.4 Metabolomics by Gas Chromatography–Mass Spectrometry: Combined Targeted and Untargeted Profiling: http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb3004s114/abstract

More derivatization options, as you are possibly looking for Natural Products and Phytochemistry applications, then Sigma resource: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/migrationresource4/Derivatization%20Rgts%20brochure.pdf would be very useful in selecting your reagents!

For Carbohydrate derivatization only, I have always found this one very useful: Derivatization of carbohydrates for GC and GC–MS analyses: http://www.sciencedirect.com/science/article/pii/S1570023210007063

whereas, if you have already zeroed on BSTFA and MSTFA then this one would be useful: http://www.sciencedirect.com/science/article/pii/S0039914008006966

Thanks,

Biswa

Thank you for the brilliant answers and the recommended resources. 

Thank you for these ansewers. what about dichloromethane used with MSTFA? there is any recommandations?