The basic fragment rules are based on published results8 ,21 (link). They were adapted and extended by visual inspection of spectra from control experiment 1 and biological data. We determined detectable fragments, identified mandatory fragments, derived intensity rules, and extracted decisive differences for many isobaric/isomeric subclasses/adducts. Further, we determined intensity relationships characteristic for sn-position assignment. Finally, we found novel fragment ion relationships, such as the relative intensity of the sodiated form of a carboxylated chain fragment that allowed for differentiation between 1,2- and 1,3-diacylglycerols at optimal collision energies, and demonstrated the software’s capability to distinguish regio-isomers under certain chromatographic conditions (Supplementary Fig. 4 and Supplementary Table 14).
We defined more than 1,000 decision rule sets for lipid subclasses/adducts for various MS platforms and experimental conditions. These decision rule sets cover the major lipid subclasses and mass spectrometers commonly used today and will serve as a point of entry for investigators unfamiliar with lipid data analysis. The direct visual feedback particularly provides an easy introduction to fragmentation patterns of lipids. Importantly, decision rule sets developed are provided along with software for the algorithm, which can be downloaded from http://genome.tugraz.at/lda2. In addition, raw data, results of detailed analysis, comments about information content that can be derived from the various adduct ions, and suggestions about optimal collision energies for subclasses/adducts are available.