The analytical method for the global profiling of molecular lipids in biological samples, with particular emphasis on the plasmalogen lipids is described. The global profiling method is based on ultrahigh-performance liquid chromatography combined with quadrupole time-of-flight-mass spectrometry (UHPLC-QTOF-MS). The profiling approach is complemented by UHPLC-LTQ-Orbitrap mass spectrometry in MSn mode for de novo lipid identification.