Full details of the analytical procedures are presented in Sturt et al. (2004) and Biddle et al. (2006). Briefly, sediments were extracted using a modified Bligh and Dyer procedure, and sample cleanup was effected by open-column chromatography using silica adsorbent and 10 increasingly polar mixtures of solvents giving eight fractions containing various classes of compounds (Rütters et al., 2002b). Fractions 7 (glycolipids) and 8 (phospholipids) were analyzed using the high-performance liquid chromatography/electrospray ionization multistage mass spectrometry (HPLC-MSn) procedures described by Sturt et al. (2004).
The softly ionizing electrospray procedure produces almost exclusively molecular ions, which is of great benefit when complex samples are analyzed. For clarity, results are presented as chromatograms in density map form, where mass to charge ratio (m/z) is plotted on the y-axis and time on the x-axis. Increasing relative intensity is plotted in darker shades of gray to black, causing eluting compounds to show up as distinct spots against a pale background. Archaeal lipids with their relatively simple system of core lipids (mainly archaeols and glyceroldialkylglyceroltetraethers [GDGTs]) generally show up as single signals, whereas bacterial lipids with a variety of fatty acid chain lengths show up as a series of closely eluting signals but with molecular ions varying by 14 Da (i.e., a CH2 unit). The density map represents one "layer" of data, the base peak from each full scan (500–2000 m/z) is isolated and fragmented giving MS2 spectral data, and the base peak from that MS2 spectrum is further isolated and fragmented giving MS3 spectral data. Also, data are recorded in both positive and negative ion modes (as two separate chromatographic runs) giving complimentary structural information. Only the positive ion density maps are shown here.
With the exception of one sample from Hole 1257C, all studied samples are from Hole 1258B (Table T1). Samples from both organic-rich black shales and organic-lean nannofossil chalks and clays have been analyzed.