LC-MS User Meeting 2020 - Omics/Proteomics Morning Session

Proteomics and metabolomics have become widely adopted techniques, often multi-disciplinary, requiring the collaboration of biologists and medical doctors, of protein chemists, mass spectrometrists and bioinformaticians delivering the value of innovative applications and novel workflows as fresh knowledge on health, disease and biology. This field relies on the scientific community pushing the limits of mass spectrometry (MS) technology to gain understanding in various disease areas that can lead to effective diagnostics, treatments and vaccines. Over this day, we will highlight several of these cutting-edge developments and results in single cell analysis, spatial omics and clinical research deploying artificial intelligence for improved data acquisition and interpretation. Our specialists will also share their recommendations for achieving outmost performance with our instruments and software.

11:00 BST (12:00 CEST - Prague) | Optimal workflows for spatial proteomics on the Orbitrap Eclipse Tribrid Mass Spectrometer

• Speaker: Prof. Kathryn Lilley, Research Group Head, University of Cambridge, UK

11:30 BST (12:30 CEST - Prague) | Pushing the Limits of Sensitivity: Micropillar Array-Based Chromatography Coupled to a Quadrupole Orbitrap Mass Spectrometer and FAIMS for Low-Input Proteomics

• Speaker: Karl Mechtler, Head of Protein Chemistry Facility bei Research Institute of Molecular Pathology (IMP), Vienna Biocore Facilities, Austria

12:00 BST (13:00 CEST - Prague) | Mass spectrometry-based draft of the Arabidopsis proteome (Mergner et al Nature 2020)

• Speaker: Dr. Julia Mergner, Head of Proteomics, TU - Munich, Germany

12:30 BST (13:30 CEST - Prague) | MS Based Approach for Low Amount Tissue Proteome Profile

• Speaker: Alessandro Cuomo, Coordinator Mass Spectrometry Unit, IEO Research - Milano, Italy

Presenter: Prof. Kathryn Lilley (Research Group Head, University of Cambridge, UK)

Kathryn Lilley is a Professor in the Department of Biochemistry and a member of the Milner Therapeutics Institute.She is also Director of theCambridge Centre for Proteomics, and a Director of Studies at Jesus College.

Kathryn's research specialisesin the development of cutting edge proteomics technologies. Her research group is exploring waysto:

• Defineresidents of organelles and protein complexes within cells
• Usea combination of high throughput mass spectrometry and pattern recognition methods to define genuine residents of complexes and organelles
• Monitor concerted changes in location upon cellular perturbation such as drug treatment, mutation etc.

These methods are being used to locate proteins involved in stem cell pluripotency maintenance both in terms of sub cellular location and involvement in multi protein complexes.

She is also interested in what controls the location of proteins in cells and is developing methods to determine the spatial location of translation (where proteins are synthesised).

Presenter: Karl Mechtler (Head of Protein Chemistry Facility bei Research Institute of Molecular Pathology (IMP), Vienna Biocore Facilities, Austria)

Main Research Areas

• Major topics: Proteomics, Mass Spectrometry, Bioinformatics
• Specialized in: Analysis of post-translational modifications, cross-linking mass spectrometry, single cell proteomics
• Development of new mass spectrometry methods to increase sensitivity, accuracy and precision of protein identification and quantification.
• Development of novel algorithms to increase the number of identified peptides, determine the localization of post-translational modifications and for label-free quantification.

Main Research Achievements

• Establishment of the first Proteomics Core Facility in Austria in 2000, which is embedded in the Campus Vienna Biocenter and available to scientists from the Research Institute of Molecular Pathology (IMP), the Institute of Molecular Biotechnology (IMBA) and the Gregor Mendel Institute (GMI) today.
• Development of methods for the analysis of post-translational modifications (phosphorylated arginine, glycoproteomics)
• Development of different algorithms for qualitative and quantitative MS data analysis (available at http://ms.imp.ac.at), that are increasingly used by proteomics labs world-wide
• (Co-)Author of more than 180 publications including contributions in Nature, Cell and Science.

Presenter: Dr. Julia Mergner (Head of Proteomics, TU - Munich, Germany)

I am a molecular biologist running a newly established proteomic competence center at the hospital campus of the TU Munich. I am applying label-free, tandem-mass-tag and targeted proteomic techniques to study global proteome expression, protein complex compositions and PTM site localizations. The aim of my research is to advance technologies for the detection and quantification of proteins and post-translational modifications using liquid-chromatography-based tandem mass spectrometry.

Career

Professional experience

• 2020 – present Head of Proteomics at the Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), TU Munich, Germany
• 2015 - 2020 Post-Doc at the Chair of Proteomics and Bioanalytics, TU Munich, Germany
• Research project “The Arabidopsis proteome”, Proteomic Z-project coordinator for SFB924 “Molecular mechanisms regulating yield and yield stability in plants”

Education

• 2010 - 2015 PhD in Molecular Biology at the Chair of Plant Systems Biology, TU Munich, Germany
• Project “Characterization of DENEDDYLASE1 function in Arabidopsis”
• 2004 - 2010 Biology training at the Albert-Ludwigs-University Freiburg i. Breisgau, Germany
• Diploma thesis “Ontogenetic changes in biomechanics and functional morphology of weeping plants”

Presenter: Alessandro Cuomo (Coordinator Mass Spectrometry Unit, IEO Research - Milano, Italy)

Alessandro is the Head of Mass Spectrometry Unit (MSU) at European Institute of Oncology (IEO), Department of Experimental Oncology (DEO).

Education and Training

• January 2015: Staff Scientist at European Institute of Oncology (IEO)
• April-October 2012: Visiting Scientist:Max Plank Institute (MPI)-

M. Mann Lab

• October 2008: Post-Doc position: European Institute of Oncology (IEO).
• October 2008: Doctor of Philosophy (PhD) in Molecular Medicine (SEMM program- http://www.semm.it).
• April 2007- Sept. 2008: Visiting Scientist:Utrecht University (The Netherlands) - A. J. Heck Lab
• January 2004-Dec. 2004: Temporary staff: CEINGE Biotechnology Institute, School of medicine Naples.
• Oct. 2002-Dec. 2003: Temporary staff: DSTB School of medicine of Udine.
• June 2002: B. Sc. (Laurea) Chemistry, University of Naples “Federico II”.