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Center for Proteomics and Metabolomics LUMC

Contact Details

LUMC

Albinusdreef 2 2333ZA Leiden

Prof. Dr. Manfred Wuhrer (proteomics) and Dr. Martin Giera (metabolomics)

0031 (0)71 5266989 (Prof. Wuhrer) and 031 (0)71 5266887 (Dr. Giera)

Hotel Description

The Center for Proteomics and Metabolomics (CPM) is a Technology Focus Area of the Leiden University Medical Center. The CPM aims at developing and implementing cutting-edge proteomics and metabolomics methodology and technology for analyzing disease-associated molecular mechanisms and fingerprints within all research focus areas of the LUMC, to promote innovation within biomedical research and public health.

 

The CPM houses MS- and NMR-based technology and expertise, distributed over 5 groups: proteomics, glycomics, metabolomics, MS-imaging, and bioinformatics. The CPM has the ambition to continuously push technology and methodology forward while maintaining reliable and efficient support and collaboration with our research partners. We strive to deepen research collaborations with academic groups, including national research centers and platforms, to develop, implement and apply new analytical tools, biological model systems and informatics methods. In addition, we pursue collaborations with industry to apply and adapt the latest state-of-the-art technology in robotic sample preparation, liquid separation methods, mass spectrometry and NMR, within the scope of biopharmaceutical development and biomarker discovery. We train and educate students and scientists within the LUMC, as well as bachelors and masters from outside.

 

Metabolomics
Public
  • Biomedical & health
  • Agri & Food
  • Industrial biotech
  • Mass spectrometry
  • Advanced liquid and gas-phase separations
  • MS and NMR integration
  • Proteomics
  • Metabolomics
  • Proteomics, particularly clinical proteomics
  • Metabolomics, in particular clinical metabolomics
  • Glycomics and glycoproteomics
  • Lipidomics
  • Bioinformatics

Expertise and Track Record

43500984129 Characterization of glycosphingolipids with an immunosuppressing function with R.M. Spaapen (Sanquin Research). 43500984043 Dehydrocholesterol reductase 24: a novel target for the treatment of nonalcoholic steatohepatitis? with Y. Wang (Leiden University). 43500984024 Targeting the HER2 receptor: finding biomarkers for optimal anti-HER2 treatment with M. Hoogstraat (NKI). 43500984009 Determining the role of lipid mediators in MSC-mediated immunomodulation with A. Wiekmeijer (Leiden University). 4350098204 In-depth mapping of the species-lipidome in the kefir community with prof.dr. B. Teusink (Free University Amsterdam). 435000033 High throughput analysis of ACPA-IgG Fab-glycosylation: clinical application and functional perspectives with dr. Y.J.P.C. Rombouts (LUMC). 435002003 Analysis of omega3 and 6 fatty acid metabolism in cigarette smoke-induced lung inflammation With Hiemstra (LUMC).

The CPM has a range of high-performance workflows established in proteomics, metabolomics, lipidomics, and glycomics analyses to address research questions in biomedicine, biopharma, and nutrition. These lines are complemented by high-end mass spectrometry imaging which allows to analyze the distribution of the different types of biomolecules in tissues. Finally, the CPM has expertise in integrated data analysis and building robust, scalable workflows for data analysis and dissemination based on FAIR principles.

Among our unique infrastructure is a 15 T FTICR solariX XR and a fully automated metabolic profiler with a 600 MHz NMR. This is complemented by the latest Orbitrap instruments for quantiative proteomics and PTM analyses, as well as highly standardized lipidomics platforms that are used in a vast range of clinical research settings. The CPM has a strong background in exploiting a broad range of separation techniques for the different types of biomolecules, including nanoLC and capillary electrophoresis.

 

Recent projects illustrating our broad range of expertise are:

1) Arthritis heal: Establishing the molecular fundamentals of arthritic diseases – a step forward to heal arthritis. A H2020 Marie-Skowdowska-Curie Action – ITN. https://www.arthritisheal.eu/

2) ETH projects: 40-43500-98-5004- Biomarker study to South Asian T2DM patients using alipidomic approach; 40-43500-98-5008- Oxylipids as anti-inflammatory mediators in adipose tissue during krill-oil intervention; 0-43500-98-5048- Mapping metabolic interactions downstream of Alzheimer risk variant APOE4.

3) GlySign: Glycosylation Signatures for Precision Medicine. A H2020 Marie-Skowdowska-Curie Action – ITN. https://www.glysign.eu/

4) ELIXR implementation study “ Comparison, Benchmarking and Dissemination of Proteomics data Analysis pipelines”; ELIXR implementation study “Proteomics Community – Improving Annotation of PRIDE datasets”.

5) Cleaving like a Pro: PPEP (Pro-Proendopeptidase)-regulated processes in Clostridiodes difficile. NWO klein.

 

 

We have significant experience (first publications 2008) in integrating gene and protein expression data in model systems. We have also compared genomics (NGS) and metabolomics, as well as proteomics data. Using mass spectrometry imaging, we are integrating multiple modalities (immunohistochemistry, MALDI-TOF, MALDI-FTICR etc.) using advanced bioinformatics and image analysis software largely developed in-house (http://www.ncbi.nlm.nih.gov/pubmed/25201776, http://www.ncbi.nlm.nih.gov/pubmed/24661141).

 

  • Inhibition of Δ24-dehydrocholesterol reductase activates pro-resolving lipid mediator biosynthesis and inflammation resolution. Körner A, Zhou E, Müller C, Mohammed Y, Herceg S, Bracher F, Rensen PCN, Wang Y, Mirakaj V, Giera M. Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20623-20634
  • Identification of bioactive metabolites using activity metabolomics. Rinschen MM, Ivanisevic J, Giera M, Siuzdak G. Nat Rev Mol Cell Biol. 2019 Jun;20(6):353-367
  • Linkage-specific in-situ sialic acid derivatization for N-glycan mass spectrometry imaging of formalin-fixed paraffin-embedded tissues. Holst S, Heijs B, de Haan N, van Zeijl RJM, Briaire-de Bruijn IH, van Pelt GW, Metha AS, Mesker WE, Tollenaar RA, Drake RR, Bovée JVMG, McDonnell LA, Wuhrer M. Anal Chem 2017; 88(11): 5904-5913. doi:10.1021/acs.analchem.6b00819
  • Cholesterol Metabolism Is a Druggable Axis that Independently Regulates Tau and Amyloid-β in iPSC-Derived Alzheimer's Disease Neurons. van der Kant R, Langness VF, Herrera CM, Williams DA, Fong LK, Leestemaker Y, Steenvoorden E, Rynearson KD, Brouwers JF, Helms JB, Ovaa H, Giera M, Wagner SL, Bang AG, Goldstein LSB. Cell Stem Cell. 2019 Mar 7;24(3):363-375.e9
  • Platelet Acetyl-CoA Carboxylase Phosphorylation: A Risk Stratification Marker That Reveals Platelet-Lipid Interplay in Coronary Artery Disease Patients. Kautbally S, Lepropre S, Onselaer MB, Le Rigoleur A, Ginion A, De Meester de Ravenstein C, Ambroise J, Boudjeltia KZ, Octave M, Wéra O, Hego A, Pincemail J, Cheramy-Bien JP, Huby T, Giera M, Gerber B, Pouleur AC, Guigas B, Vanoverschelde JL, Kefer J, Bertrand L, Oury C, Horman S, Beauloye C. JACC Basic Transl Sci. 2019 Sep 11;4(5):596-610
  • Lowering the increased intracellular pH of human-induced pluripotent stem cell-derived endothelial cells induces formation of mature Weibel-Palade bodies. Tiemeier GL, de Koning R, Wang G, Kostidis S, Rietjens RGJ, Sol WMPJ, Dumas SJ, Giera M, van den Berg CW, Eikenboom JCJ, van den Berg BM, Carmeliet P, Rabelink TJ. Stem Cells Transl Med. 2020 Mar 12. doi: 10.1002/sctm.19-0392
  • Round Robin Study of Formalin-Fixed Paraffin-Embedded Tissues in Mass Spectrometry Imaging. Buck A, Heijs B, Beine B, Schepers J, Cassese A, Heeren R, McDonnell L, Henkel C, Walch A, Balluff B. Anal Bioanal Chem 2018, doi: 10.1007/s00216-018-1216-2.
  • Ultra-high resolution MALDI-FTICR-MSI analysis of intact proteins in mouse and human pancreas tissue. Piga I, Heijs B, Nicolardi S, Giusti L, Marselli L, Marchetti P, Mazzoni MR, Lucacchini A, McDonnell LA, Int J Mass Spectrom, 2017, in press. doi:10.1016/j.ijms.2017.11.001.
  • Automated workflow composition in mass spectrometry-based proteomics. Palmblad M, Lamprecht AL, Ison J, Schwämmle V. Bioinformatics, 35(4):656-664, 01 Feb 2019, DOI: 10.1093/bioinformatics/bty646
  • One Thousand and One Software for Proteomics: Tales of the Toolmakers of Science. Tsiamis V, Ienasescu HI, Gabrielaitis D, Palmblad M, Schwämmle V, Ison J. J Proteome Res, 18(10):3580-3585, 29 Aug 2019, DOI: 10.1021/acs.jproteome.9b00219

 

We have initiated and/or remain highly active and serve on the boards of several national and international technology networks, such as the Netherlands Proteomics Platform (NPP), the Netherlands Mass Spectrometry Society (NVMS), the European Cooperation in Science and Technology (COST) Action for Biomolecular Mass Spectrometry Imaging, and the US-based Association of Biomolecular Resource Facilities, ABRF, (and its Proteome Informatics Research Group, iPRG).

Hotel Characteristics

  • 9 fte post docs
  • 10 fte dedicated technicians
  • 1 fte lab manager
  • 3 fte biostatisticians
  • 3 fte IT-specialists
  • We operate a broad range of:
  • - sample preparation robotics (Hamilton)
  • - gas- and liquid separation systems [Agilent, Dionex (Thermo), Eksigent (SCIEX), Beckman]
  • - mass spectrometers (SCIEX, Bruker, Thermo)

yes, the LUMC works accoring to the GRP norm LUMC (a norm adapted from ISO 9001)

We deposit much of our published data in PRIDE (ProteomeXchange) and GEO, but also make databases and spectral libraries available on our own servers when no suitable repository exists.