A method is described for the liquid chromatography/tandem mass spectrometry analysis of free base porphyrins, which allows the routine and rapid recognition of alkyl substituents in the components of complex natural mixtures. The method overcomes difficulties associated with probe tandem mass spectrometry or liquid chromatography/mass spectrometry which can arise from the numerous isobaric ions present in the spectra and the associated uncertainty in assigning fragment ions to individual components. MS and MS/MS spectra of synthetic and natural free base porphyrin standards are compared to identify spectral patterns which allow recognition of extended alkyl chains. In natural mixtures, the identification of cycloalkano porphyrins with such chains is based on comparison of product ion spectra of a series of C 31 -C 35 standards and the presence of diagnostic ions which can be attributed to losses associated with bC 2 alkyl chains. Liquid chromatography/tandem mass spectrometry analysis of a free base porphyrin mixture from Serpiano oil shale is carried out to obtain MS/MS spectra of palaeoenvironmentally significant minor components. The results reveal the presence of cycloalkano porphyrins with bC 2 substituents in the shale, suggesting the occurrence of photic zone anoxia in the original depositional setting.