Mass spectrometry has undergone an impressive development during the past decade. New and improved ion sources and mass analyzers have opened new horizons in terms of sensitivity, specificity, resolution, mass accuracy, controlled fragmentation and available structure information. The present habilitation thesis comprises 15 original papers and one review. In the chapter natural products the focus is on the analysis of stratum corneum lipids. New methods are described allowing the separation and quantification of the lipid classes and in particular the ceramides. Mass spectra give insights into the structure, particularly in terms of fatty acid and sphingoid base chain lengths. A normal phase LC/APCI-MS method is applied to investigate the lipid composition in healthy test persons and patients suffering from psoriasis and atopic dermatitis, resp. It turned out that non-lesionated areas do not show significant changes in lipid composition. An LC/APCI-MS method for the analysis of cholesterol oxidation products is presented. In the carbohydrate section, new LC/MS and CE/MS methods for the determination of hyaluronic acid fragments are reported. In the section dealing with peptides and proteins, new results concerning the analysis of phytochelatins, elastin crosslinks, as well as the characterization of peptic β-casein digests by means of MALDI-TOF PSD and ESI tandem mass spectrometry are described. Novel aspects of bioinformatic processing of MS raw data are presented. In the section about alkaloids, tandem MS studies on morphinans and benzylisoquinolines are shown. In the chapter drugs, a study on bufexamac and its degradation products is described. In the chapter pharmaceutical excipients, new results on the analysis of polyvinylpyrrolidone products as well as a comprehensive study on polyethoxylated surfactants are presented. It can be expected that the use of mass spectrometric methods in pharmacy will gain importance in the future.