Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control

Data-dependent acquisition of full MS/MS spectra from all detectable (or, alternatively, preselected) lipid precursors produces a rich data set, whose subsequent interpretation by the dedicated software LipidInspector emulates the simultaneous acquisition of an unlimited number of precursor and neutral loss scans in a single analysis. Using logical operations, emulated scans can be combined into highly specific data interpretation routines (termed Boolean scans) enabling in-depth structural characterization of fragmented precursors. Alternatively, a small number of preselected precursors can be fragmented regardless of their relative intensities in survey spectra, hence emulating selected reaction monitoring (SRM) analysis that attains both high detection specificity and sensitivity. Although the data-dependent acquisition approach is, in principle, cross-platform, it benefits from the high mass resolution capacity of hybrid tandem mass spectrometers with time-of-flight and, especially, Fourier transform or Orbitrap analyzers.