Isolated sulfoquinovosyl-diacylglycerol (SQD) from spinach and the purple bacterium Rhodobacter sphaeroides provide two sources of very different molecular species of SQD. We were able to demonstrate by fast atom bombardment-collisionally activated dissociation tandem mass spectrometry in the negative ion mode that the sulfoquinovosyl head group of the plant and bacterial lipids can be characterized by the common fragmentation pattern found in the spectra of both samples. Differences in the acyl functions from the two sources were also identified by this technique. SQD specific fragments are found at m/z 299, 283, 241, 225, 165 and 80 which indicate the presence of the sulfoquinovosyl moiety. The two predominant molecular species found in spinach contain palmitic and linolenic ([M-H]- at m/z 815) or two linolenic acids ([M-H]- at m/z 837) in the sn-1 and sn-2 positions, while the two major species, of the bacterial lipid contain palmitic and 18:1 (vaccenic) acids ([M-H]- at m/z 819) or stearic and 18:1 (vaccenic) acids, ([M-H]- at m/z 847), respectively.