We encounter significant side products or contamination issues when trying this method. The contamination/side products aren't aromatic in nature so we have no idea where they're coming from but they are associated with this reagent. The contamination appears to be a homologous series of whatever the heck it is (evenly spaced apart on the chromatogram and having the same type of spectra). I don't think it's column bleed since we're using a Rt-5 and this would also be aromatic column bleed.
Jonathan,
My experience has been with 14% methanolic BF3 and it worked just fine. I will say that plasticizers in any plastics are something to watch out for. also used only acid washed glassware as detergents can contaminate.
Dan
Have you run a PFB blank, i.e. carried out the derivatisation protocol on a blank sample, even if to confirm the contaminants are not present in the derivatisation agents?
Assuming the contaminant peaks are a product of the derivatisation reaction with your samples, based on your description it sounds like the reaction results in decarboxylation of some of the fatty acids resulting in homologuous alkanes (alkenes) as by-products.
As mentioned by Daniel, standard method for derivatisation of fatty acids is indeed MeOH/BF3 to yield FAMEs; best run on medium-polar (DB-1701) or polar (DB-23) GC columns.
Thank you all for your comments and suggestions. Yes, we were using this reagent to boost sensitivity in our analytical method. After 2 weeks of trouble shooting we finally discovered that the contamination was originating from our 10-100 ul size pipette tips! Who knew, right? Well we know now. By switching to a different brand the peaks reduced close to the noise floor of the detector. That, as they say, is research. Thank you all once again.
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