A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

Lipidomics, an emerging scientific discipline, aims at the quantitative molecular characterization of the full lipid complement of cells, tissues or whole organisms (reviewed in [1-4]). Eukaryotic lipidomes comprise over a hundred lipid classes, each of which is represented by a large number of individual yet structurally related molecules. According to different estimates, a eukaryotic lipidome might contain from 9,000 to 100,000 individual molecular lipid species in total [2,5]. Due to the enormous compositional complexity and diversity of physicochemical properties of individual lipid molecules, lipidomic analyses rely heavily on mass spectrometry. A shotgun lipidomics methodology implies that total lipid extracts from cells or tissues are directly infused into a tandem mass spectrometer and the identification of individual species relies on their accurately determined masses and/or MS/MS spectra acquired from corresponding precursor ions [6-8].The apparent technical simplicity of shotgun lipidomics is appealing; indeed, molecular species from many lipid classes are determined in parallel in a single analysis with no chromatographic separation required. Species quantification is simplified because in direct infusion experiments the composition of electrosprayed analytes does not change over time. Adjusting the solvent composition (organic phase content, basic or acidic pH, buffer concentration) and ionization conditions (polarity mode, declustering energy, interface temperature, etc.) enhances the detection sensitivity by several orders of magnitude [8,9]. In shotgun tandem mass spectrometry (MS/MS) analysis, all detectable precursors (or, alternatively, all plausible precursors from a pre-defined inclusion list) could be fragmented [10]. Given enough time, the shotgun analysis would ultimately produce a comprehensive dataset of MS and MS/MS spectra comprising all fragment ions obtained from all ionizable lipid precursors.While methods of acquiring shotgun mass s