The core technology in proteomics is mass spectrometry, by which thousands of proteins can be identified and quantified and that has hugely impacted life sciences research over the past two decades. The Proteomics Center develops mass spectrometry-based proteomics methodologies for the qualitative and quantitative analysis of proteomes and provides proteomics services for fundamental, translational and clinical application in the biomedical research field. The ultimate mission is to provide state-of-the-art technology to better understand how cellular processes are controlled at the molecular level during homeostasis and the diseased state.
The Proteomics Center is supported by Erasmus MC central funds and ‘Rijksbijdrage’ (~800 k€ /year), customer fees (~250 k€ / year) and externally acquired funding (variable amount). The core facility acts as an independent organizational unit within Erasmus MC, is run by one director/associate professor, and employs one scientist, two technicians and one bioinformaticians. Within the next half-year, the total number of fte will increase to 7. The Center runs and maintains about 7 M€ worth of state-of-the art mass spectrometry equipment, which has largely been funded from external grants.
The Proteomics Center has been part of national and international consortia such as the Netherlands Proteomics Centre I (2004-2008), Netherlands Proteomics Centre II (2009-2013), EuTRACC (2007-2011) and Protein@work (2014-2019). The embedment within (inter)national infrastructure vehicles illustrates that the Proteomics Center is recognized as a leading player in the field. It fulfills a central role within the Erasmus MC research community and trains researchers in the field of proteomics. Strong connections in the field, nationally and internationally, guarantee the use of cutting edge methodology and technology in this rapidly evolving research area.
Currently, the Proteomics Center mostly hosts Orbitrap based (hybrid) mass spectrometers, all coupled to nanoLC equipment: a Q Exactive Plus (Thermo), an Orbitrap Fusion (Thermo) and an Orbitrap Fusion Lumos (Thermo). In January 2020, an Eclipse Orbitrap (Thermo) will be installed. That instrument is the fastest, most sensitive and most versatile instrument for proteomics that is currently on the market. Older equipment (an LTQ Orbitrap (Thermo), an LTQ Orbitrap XL, a Xevo Triple Quad (Waters) and a Xevo Q-ToF (Waters)) is still in use, was donated to other departments at Erasmus MC or is kept for educational purposes.
Protein posttranslational modifications form an added layer of complexity that modulates protein function. The Center focuses on the development of mass spectrometry-based technology for the large-scale identification of posttranslational modifications, such as ubiquitination, phosphorylation, etc. This involves both improvements in sample preparation, bioanalytical chemistry and the analysis of large data sets. Another application of interest is the construction of protein interaction networks and study how these are affected during the cell cycle, cell differentiation, and upon external stimuli such as UV irradiation. Furthermore, these technologies are applied to patient material in order to look for prognostic protein biomarkers to diagnose diseases at early stages.
Over 140 scientific papers in the fields of proteomics, cell biology, biochemistry, genetics, oncology, neurosciences, etc. have been published in the past 13 years which were facilitated by the Proteomics Center. In fact, in many collaborative research projects the proteomics analyses formed the foundation of the scientific work and therefore usually take place in the first stage of a project. Many of these papers have appeared in leading journals including Nature (3x), Science (2x), Cell and associated journals. For a full list of publications please see www.proteomicscenter.nl.