Comprehensive mass spectrometry (MS)-based proteomics and phosphoproteomics is now feasible, but typically requires mg of starting material per sample condition and several days of instrument time. Moreover, reproducible quantification remains challenging especially for analysis of post-translational modifications (PTMs), such as phosphorylation. I will present how we benchmarked the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). I will also present our efforts to optimize and apply sensitive proteome and phosphoproteomics workflows based on a Q Exactive HF-X mass spectrometer using the phase-constrained spectrum deconvolution method (ΦSDM) for fast and deep analysis of samples labeled with TMT10-plex.
Jesper Olsen studied analytical chemistry at the University of Southern Denmark in Odense, and obtained his PhD in biochemistry and molecular biology in the laboratory of Matthias Mann. During his PhD he was involved in developing high-resolution mass spectrometry-based proteomics. He spent 4 years as a post-doctoral fellow at the Max Planck Institute for Biochemistry in Munich, where he developed a quantitative phosphoproteomics technology that was applied to global time-resolved analyses of cell signaling pathways in human cells. In 2009, Jesper was recruited back to Denmark to head a group at the newly established Novo Nordisk Foundation Center for Protein Research (CPR) at University of Copenhagen. In 2012, he was promoted to vice director of CPR and in 2014 full professor. Jesper has received a number of research awards including the Max Planck Institute for Biochemistry Junior Research Award and HUPO Young Investigator Award in Proteomic Sciences.