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Lab Demichev:
Quantitative Proteomics



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Recently, mass spectrometry (MS)-based proteomics has taken a major leap in terms of speed, sensitivity and depth of proteome coverage. Novel fast workflows can measure hundreds of proteomes per day and thus facilitate robust and cost-effective large-scale experiments, from perturbation screens in cell culture to biomarker discovery studies. At the same time, proteomic profiling of sub-nanogram sample amounts has become a reality, resulting in a rapid rise of single-cell proteomics. These advances have been driven by the introduction of fast and sensitive mass spectrometers, development of novel acquisition modes and the emergence of sophisticated data processing strategies. Proteomics can now facilitate large-scale studies of a wide range of clinical samples, allowing information-rich characterisation of disease trajectories and prediction of outcomes. Nevertheless, its speed and data quality can still be improved significantly, paving the road for new applications.

Demichev lab works in collaborations with industry partners to increase the speed, quantitative accuracy and proteomic depth of MS-based methods, with the ultimate vision of bringing MS-based proteomics to the clinical environment as a routine measurement method. Our primary focus is on the development of novel acquisition techniques and data analysis methods, and their application to clinical samples profiling as well as basic science. We also place special emphasis on establishing fast and robust methods for proteome-wide profiling of phosphorylation and ubiquitination, and using these to take an in depth look at protein turnover, its regulation and its link to metabolism and ageing. We work within the MSTARS consortium, wherein the primary goal is to use high-throughput multi-omics methods to identify biomarkers as well as establish machine learning predictors of treatment success in cancer patients.