Electrospray Ionization (ESI) mass spectrometer with liquid chromatography for proteome analysis

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This application is for an electrospray ionization mass spectrometer including chromatography with excellent sensitivity, resolution and mass accuracy, which is able to carry out different types of scans. This includes different fragmentations, data-dependent and data-independent acquisitions, mass window scans, targeted analyses and robust quantifications using label-free and isotope-labeled methods. This device is primarily intended to be used for research at the “Plant Biochemistry” department, where the existing mass spectrometers are out of date. Research topics are the chloroplast quality control system and regulation of chloroplast biogenesis via the ubiquitin-proteasome system, proteome analyses of different plastid type differentiation and the operational control of chloroplast functions via phosphorylation. In all cases, highly sensitive proteome analysis is required, e.g. to characterize mutants of components of the chloroplast quality control system and to understand the crosstalk of its different functions. Since these processes take effect post-transcriptionally, the analyses must be carried out at the proteome level. The same applies to the differentiation of plastids, especially when it comes to analyze the functionality of the protein import system, and to the analysis of post-translational modifications and their function. The device should be suitable to identify post-translational modifications of very low abundant peptides and to quantify them robustly. Analytical depth must be high, because e.g. the N-terminal peptides of plastid precursor proteins in the cytosol are subject to a high turnover and, in addition to their already very low abundance, are also highly unstable. The device is to be set up in a facility in the future, and around 30% of it’s time will be made available for commissioned work. This means that it has to be robust, relatively easy to operate and have low maintenance requirements.