Project description:The ionization conditions necessary for intact protein characterization in Orbitrap mass analyzers can be highly variable. To more rapidly characterize intact proteins we have developed a method where multiple sets of conditions can be used within a single experiment. These 3 scan events contain generic parameters for: 1) Proteins that do not require additional in-source collision energy for efficient ionization, 2) Proteins that require some additional energy, 3) Proteins that require substantial in source energy. We test this method with a commercial intact protein standard containing proteins between 10kDa and 90kDa with and without the addition of the NIST monoclonal antibody standard.
Project description:It was crucial to choose the appropriate dissociation method and collision energy for large-scale glycoproteomics studies. HCD has been successfully applied to large-scale glycoproteomics experiments31. We know that TMT-labelled glycopeptides require higher collision energies for identification and quantitative accuracy because glycosidic bonds can absorb part of the energy32. Therefore, we systematically evaluated the performance of different HCD collision energies in characterizing TMT-labelled intact N-glycopeptides based on the StrucGP high HCD energy identification of peptides, and low HCD energy identification of glycans by fragmentation strategy.
Project description:Optimising the parameters for cross-link analysis using a QToF mass spectrometer. We performed triplicate analysis of 6 different collision energy ramps to determine the optimal energy for cross-link fragmentation.