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Proteomics Center Erasmus MC

Contact Details

Erasmus MC

Proteomics Center, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands

Dr. Jeroen Demmers

+31 10 7038124

Hotel Description

The Proteomics Center at Erasmus MC develops mass spectrometry based proteomics methodologies for the qualitative and quantitative analysis of (sub)proteomes and provides proteomics services for the Erasmus MC scientific community and for external researchers. Research projects in our laboratory focus on the elucidation of protein complex composition, the analysis of protein posttranslational modifications and on the analysis of proteomes and their dynamic behavior, both in cell cultures and tissue. For quantitation purposes we use SILAC, post-digestion (isobaric) labeling protocols and label free quantitation. The ultimate goal of our research is to develop analytical tools to better understand how cellular processes are controlled at the molecular level.

  • Biomedical & health
  • Protein and peptide fractionation
  • PTM enrichment
  • Bioinformatics
  • Protein ubiquitination
  • Cancer proteomics
  • Tissue proteomics
  • Stem cells

Expertise and Track Record

Customers are always welcome to discuss ideas and possibilities. If necessary, customers will be guided starting from the experimental design phase through the interpretation of data. For identification or your proteins and PTMs, we provide a vast array of different mass spectrometry analyses, including:

** Proteolytic digestion with a variety of proteases: in-gel, ‘in-tube-gel’, in-solution, whole cell lysate in high molar urea or MS compatible detergents, etc.

** Sample clean-up and pre-fractionation by hydrophilic interaction liquid chromatography (HILIC), isoelectric focusing (IEF), strong cation exchange (SCX), strong anion exchange (SAX), etc.

** Phosphopeptide enrichment by TiO2; diGly, methylated, acetylated, etc. peptide enrichment by antibodies

** Multidimensional nanoflow LC-MS/MS(/MS) (mass spectrometers: Orbitrap Fusion Tribrid, Q Exactive Plus, 2 x LTQ-Orbitrap XL (ETD), LTQ (all Thermo), Xevo Q-ToF, Xevo TQ (Waters))

** Intact protein mass spectrometry / native mass spectrometry

** Database searching (software: Mascot, MaxQuant, TheGPM, Scaffold, PEAKS, …)

** Data analysis, reporting and interpretation. Additional informatics services and use of in-house developed software are optional.


A comparison between transcriptomics and proteomics data was performed in a Drosophila cell system, which was stimulated with an insect hormone:

Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster. Sap KA, Bezstarosti K, Dekkers DH, van den Hout M, van Ijcken W, Rijkers E, Demmers JAA. Proteomics 2015 15(4):725-38.

–> doi: 10.1002/pmic.201400308.

  • Raj VS, Mou H, Smits SL, Dekkers DH#, Müller MA, Dijkman R, Muth D, Demmers JA#, Zaki A, Fouchier RA, Thiel V, Drosten C, Rottier PJ, Osterhaus AD, Bosch BJ, Haagmans BL (2013) Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature 495(7440):251-4. doi: 10.1038/nature12005.
  • Adone Mohd-Sarip, Anna Lagarou, Ulku Aslan, Jan van der Knaap, Cecile Doyen, Karel Bezstarosti, Yasmin Yassin, Hugh W Brock, Jeroen AA Demmers & C. Peter Verrijzer (2012) Transcription-independent function of the Polycomb group protein PSC in cell cycle control. Science, doi:10.1126/science.1215927.
  • Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JA, van IJcken WF, Grosveld FG, Medema RH, Hoeijmakers JH, Mullenders LH, Vermeulen W, Marteijn JA (2015) The core spliceosome as target and effector of non-canonical ATM signalling. Nature 523(7558):53-8. doi: 10.1038/nature14512.
  • Gontan C, Achame EM, Demmers J, Barakat TS, Rentmeester E, van IJcken W, Grootegoed JA, Gribnau J (2012) RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Nature 485(7398):386-90. doi: 10.1038/nature11070.
  • Yuri M Moshkin, Tsung Wai Kan, Henry Goodfellow, Karel Bezstarosti, Robert K Maeda, Maxim Pilyugin, Francois Karch, Sarah Bray, Jeroen A. A Demmers & Peter Verrijzer (2009) Histone Chaperone ASF1 Cooperates with a LID/KDM5 Histone H3K4me2/3 Demethylase Complex to Mediate Gene-Selective Silencing. Mol Cell, 35(6):782-93.
  • van den Berg DL, Snoek T, Mullin NP, Yates A, Bezstarosti K, Demmers J, Chambers I, Poot RA (2010) An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6(4):369-81.
  • Sap KA#, Bezstarosti K#, Dekkers DH#, van den Hout M, van Ijcken W, Rijkers E#, Demmers JAA# (2015) Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster. Proteomics (Epub ahead of print: 2014 Nov 18) | doi: doi: 10.1002/pmic.201400308.
  • Karel Bezstarosti*, Alireza Ghamari*, Frank G. Grosveld, Jeroen A. A. Demmers (2010) Differential proteomics based on 18O labeling to determine the Cyclin Dependent Kinase 9 interactome. J Proteome Res 9(9):4464-75.
  • Schwertman, P., Lagarou, A., Dekkers, D. H. W., Raams, A., van der Hoek, A. C., Laffeber, C., Hoeijmakers, J. H. J., Demmers, J. A. A., Fousteri, M., Vermeulen, W. & Marteijn, J. A. (2012) UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nature Genetics, doi:10.1038/ng.2230.
  • Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, Bezstarosti K, Taylor S, Ura H, Koide H, Wutz A, Vidal M, Elderkin S, Brockdorff N (2012) RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell 148(4):664-78. 2012 Jun 22;149(7):1647-8.

Netherlands Peroteomics Centre II | Research Hotel manager
Proteins@Work | Facility manager

Hotel Characteristics

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30% for external partners

  • Orbitrap Tribid Fusion, Q Exactive Plus, LTQ Orbitrap ETD, LTQ Orbitrap Classic, LTQ (all Thermo), Xevo Q-ToF, Xevo TQ (Waters), several LC systems (nano Acquity, Agilent 1100, EASY nLC, etc.)


Part of published data is stored in the PRIDE-EBI archive