The characterization of lipids is performed by mass spectrometry based on structure specific fragments or by accurate mass measurements of intact precursor ions. The latter method, termed ’top-down lipidomics’, is due to its robustness, simplicity and speed a valuable tool for medical research to elucidate the molecular background of lipid metabolic disorders. The current thesis aims to improve the established lipidomics methods. Therefore, a new top-down lipidomics method was introduced that increased the analysis throughput, lipidome coverage and accuracy of quantification, compared to previous approaches, by rapid successive acquisition of high resolution Fourier transform mass spectra in positive and negative ion modes. Furthermore, the characterization of molecular lipid species by utilizing high energy collisional dissociation was achieved on Orbitrap instruments. The mass accuracy of acquired MS/MS spectra increased the confidence in identification for unusual very-long chain polyunsaturated phosphatidylcholine species and a new lipid class, the maradolipids. Beyond that, effort was made to enhance the accuracy and comparability of MS/MS based bottom-up lipidomics data. In this respect, lipids with varying degree of unsaturation were analyzed and revealed discrete fragmentation properties. The technical refined lipidomics methods allowed insight into the lipid composition of lipoproteins and changes of the blood plasma induced by apheresis. Lipidomics screening of blood plasma uncovered an altered lipid pattern in consequence of impaired glucose metabolism and type 2 diabetes. The lipidomics characterization of islet allowed their quality assessment.

The characterization of lipids is performed by mass spectrometry based on structure specific fragments or by accurate mass measurements of intact precursor ions. The latter method, termed ’top-down lipidomics’, is due to its robustness, simplicity and speed a valuable tool for medical research to elucidate the molecular background of lipid metabolic disorders. The current thesis aims to improve the established lipidomics methods. Therefore, a new top-down lipidomics method was introduced that increased the analysis throughput, lipidome coverage and accuracy of quantification, compared to previous approaches, by rapid successive acquisition of high resolution Fourier transform mass spectra in positive and negative ion modes. Furthermore, the characterization of molecular lipid species by utilizing high energy collisional dissociation was achieved on Orbitrap instruments. The mass accuracy of acquired MS/MS spectra increased the confidence in identification for unusual very-long chain polyunsaturated phosphatidylcholine species and a new lipid class, the maradolipids. Beyond that, effort was made to enhance the accuracy and comparability of MS/MS based bottom-up lipidomics data. In this respect, lipids with varying degree of unsaturation were analyzed and revealed discrete fragmentation properties. The technical refined lipidomics methods allowed insight into the lipid composition of lipoproteins and changes of the blood plasma induced by apheresis. Lipidomics screening of blood plasma uncovered an altered lipid pattern in consequence of impaired glucose metabolism and type 2 diabetes. The lipidomics characterization of islet allowed their quality assessment.