MS/MS spectra showing the characteristic fragmentation patterns of the precursor ions of the major lipids, providing the identifications of these lipids in the CcO crystals from CL(+) (169WT) and CL(−) (169CL3) R. sphaeroides using CID MS/MS in positive and negative ion modes on a MALDI-linear ion trap mass spectrometer. Representative lipids in the crystals include A) PG 18:1/18:1 at m/z 773 (−ve), B) SQDG 16:0/18:1 at m/z 819 (−ve), C) SQDG 18:0/18:1 at m/z 847 (−ve) and D) OL 3-OH 20:1/19:1 at m/z 719 (+ve). In panels B and C, the fragment ion at m/z 225 is determined by MS3 to represent the sulfoquinovosyl head group of SQDG, and the peaks in the middle of the spectra are generated by the neutral loss of either one of the two fatty acid chains respectively.