One source for the protein diversity in higher eukaryotes are (post-translational) protein modifications like phosphorylation, glycosylation, acetylation, methylation, nitrosylation, sulfonation, ubiquitinylation, SUMOyltation. In collaboration with several research groups we set out methods for the enrichment and/or detection of post-translationally modified peptides by MS (e.g. an efficient semi-high-throughput approach for enrichment of phosphopeptide prior to MS (collaboration with the Department of Cellular Biochemistry, Mol. Cell. Immunologie and other) or a computational approach for the detection of SUMO acceptor sites (collaboration with F. Melchior Dept. Biochemistry I) by high-end MS that implements the commonly used search engines MASCOT or SEQUEST. We also developed a novel method in MS, called pseudo-neutral-loss scan, for selective detection of phosphopeptides and N-glycopeptides.