Proteomics has become one of the most exciting and dynamic research areas. Since the genomes sequenced failed to answer several questions, systems biology research started to target other biomolecules. Proteomic studies aim to decipher structural changes of proteins and protein complexes, their role in different interactions, biological functions and processes by characterizing the qualitative and quantitative changes in protein mixtures of varied complexity: up to cellular organelles, cell lines, tissues, or even individuals. Mass spectrometry has become the method of choice for such research. It is equally well suited for protein identification, de novo sequencing, for the characterization of post-translational modifications, or other covalent labeling. It can also be used for probing the 3D structure of proteins, the spatial organization of protein complexes, or studying intact protein populations. Last but not least, mass spectrometry can also deliver quantitative results. We have extensive collaborations within the HUN-REN BRC and with academic organizations in Hungary and abroad. Biological samples are provided by our partners. Our tasks are the analytical sample preparation, chromatographic fractionation if necessary, mass spectrometry analysis as well as data interpretation. However, an ideal collaboration starts at the planning stage, designing the experiments together. Obviously our goal is to assure that the samples will be compatible with the following analyses, but the number of biological and technical replicates or the selection of proper controls is also discussed whenever it is necessary. We developed and routinely use a reliable protocol for the isolation of protein complexes. We also regularly perform the qualitative and (semi)quantitative characterization of the resulting mixtures, as well as other protein samples of different complexity. Such analysis may include the characterization of certain posttranslational modifications. We are experienced in the characterization of disulfide-bridges, proteolytic cleavage sites, ubiquitination, phosphorylation and glycosylation. For about a decade we have been successfully developing new methods for the characterization of mucin-type O-glycosylation.