Assignment of unknown proteins based on mass spectrometric peptide fragmentationSimone König, Andreas Herrmann, Andreas Henselpp 61-75Abstract:Mass spectrometry-based identification of proteins not yet sequenced and available in public databases is challenging. This tutorial advises in approaches to match experimental data obtained by peptide fragmentation with collision-induced dissociation to homologuous proteins with the goal of generating a valid hypothesis for the unknown protein sequence. Preparatory steps, manual fragment spectrum analysis and tools such as sequence pattern search as well as alignments are discussed. The example of the identification of a Boswellia basic secretory protease is used.Introduction to protein structure visualisation and simple manipulationSimone Königpp 77-84Abstract:The visualization of the tertiary structure of a protein allows insights with respect to protein binding and interaction, which would be difficult to obtain otherwise. Not for every protein an experimentally determined 3D-structure is however available. A number of bioinformatics tools have therefore been developed to simulate protein folding based on templates or amino acid properties. In this primer a workflow is described to generate appropriate 3D-structures from primary sequences. Moreover, it is demonstrated, how protein heterodimers can be modeled, possibly including experimentally determined restrains such as cross-links.Protein aeroallergensSimone Königpp 85-93Abstract:Protein contaminants in the ambient air such as pollen or dandruff may cause human disease. Well known examples are pet allergies as response to animal hair or seasonal hayfever. This review summarizes the current knowledge with respect to the type of airborne protein allergens as well as collection and detection methods.Synthetic phosphorylation of histidine residues in the myoglobin-heme complexUlli Martin Hohenester, Katrin Ludwig, Simone Königpp 95-101Abstract:The study of acid-labile histidine protein phosphorylation is of increasing interest in proteomics. We use synthetic peptide and protein phosphorylation with potassium phosphoramidate (PPA) to generate model substance for analytical purposess. In addition to the modification of unfolded proteins PPA is also of interest for the investigation of protein tertiary structure as was demonstrated for the myoglobin-heme complex.P-soyatose supplemented nutrition affects metabolism in silkworm Bombyx moriUlli Martin Hohenester, Anna Maria Mehlich, Nitin Kumar Singh, Muthukalingan Krishnan, Simone Königpp 103-107Abstract:Nutrition affects larval growth and silk production in silkworm Bombyx mori. Hydrolyzed soy protein (P-soyatose) is highly nutritive, shortens the larval growth phase and increases silk production. Fat body proteomes of larvae supplemented with P-soyatose were compared with a control group delivering experimental evidence that metabolism is increased with protein-enriched nutrition. Enzymes from glycolysis, the citric acid cycle and fatty acid metabolism were detected in the treated group on day 6 V instar.