In spite of a significant contribution of nitrogen and spectroscopic indications for proteinic material in natural organic matter, only a limited number of amino acids could be recognised in pyrolysates of organic matter from soil, waters and sediments. Due to the relatively high polarity of this type of macromolecular material, pyrolysis in the presence of TMAH appears as a suitable tool for its study. So as to build a database for further studies, the present paper thoroughly investigates the mechanisms undergone by the 20 protein amino acids upon TMAH pyrolysis. As expected, methylation is the major process for all but four amino acids, three of them mainly yielding cyclisation products and one undergoing deamination. Although TMAH is commonly considered as preventing decarboxylation, the latter mechanism is dominating in the case of phenylalanine, tyrosine, tryptophan and histidine. In the case of the first three amino acids, homolysis of the side chain also occurs, favoured by the presence of an aromatic ring. Elimination of the side chain is also observed for threonine resulting in the formation of the same product as the methylated glycine. Dimerisation to diketopiperazines occurs with several amino acids. Dimerisation without cyclisation is the major process occurring for glycine A specific mechanism, dehydration, is observed with serine due to the presence of a hydroxyl group on its side chain. Comparison with literature data on conventional pyrolysis, i.e. without TMAH, highlights the role of TMAH. The similar involvement of cyclisation and side chain homolysis confirms that they are thermal processes. Due to the complexity of pyrochromatograms of natural samples, the present study constitutes a database that can be used to define diagnostic signals for amino acids in studies of natural samples.