The Research Group for Computational Systems Biochemistry at the Max Planck Institute of Biochemistry in Martinsried, near Munich (Germany), invites Early Stage Researchers to apply for a PhD position that is part of the European training Network “PUSHH: Palaeoproteomics to Unleash Studies on Human History”, funded by the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No 861389).
As part of the PUSHH network, ESR12 will work on developing computational proteomics software and algorithms to better identify peptides and proteins from ancient samples. Building on the expertise in the lab compiled in the GrandPep software which is based on the MaxQuant software for computational proteomics, the candidate will work on the design, implementation and improvement of algorithms relevant for the computational analysis of ancient samples. These include method development in data-dependent acquisition (DDA) and data-independent acquisition (DIA) proteomics. The candidate will apply machine learning algorithms including deep learning to proteomics data by utilizing TensorFlow and other frameworks. In addition to peptide database search engine approaches (Andromeda) development of de-novo identification algorithms to identify heavily modified peptides in DDA and DIA samples will be part of the duties. Furthermore, the top-down proteomics algorithm developed in the lab will be adapted to the application to ancient samples. All algorithms will be developed in order to be broadly applicable to different mass spectrometer types, including Orbitrap and time-of-flight technologies coupled to ion mobility spectrometry.
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