The most likely method I'm looking at is the TCA precipitation method, however the majority of the papers on this that then use Kjeldahl are old and use filter paper as opposed to centrifugation which. Whereas the TCA method via centrifugation tends to measure the nitrogen content through SDS-PAGE (which I don't have access to). Would it be possible to centrifuge the substrate and then use the pellet in the kjeldahl method for a direct measure of amino acid nitrogen?
Free amino acids are not precipitated by TCA, only proteins. The protein pellet can be washed free of TCA with ether, dried and then used. However, instead of the classical diethyl ether I'd try methyl tert-butyl ether (MTBE), which is much less likely to form explosive peroxydes.
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