Johannes Schmidt, M.Sc.

Contact

Johannes Schmidt, M.Sc.
Scientist

Department for Molecular Systems Biology (MOLSYB)
Helmholtz Centre
for Environmental Research - UFZ
Permoserstr. 15
04318 Leipzig, Germany

Tel: 0341 235 1078 
johannes.schmidt@ufz.de

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Curriculum Vitae

Since 01-2017

Scientist at the Department for Molecular Systems Biology at the Helmholtz Centre for Environmental Research - UFZ, Leipzig

10-2013 - 12-2016

PhD student at the Department for Molecular Systems Biology (formely known as Department of Proteomics) at the Helmholtz Centre for Environmental Research - UFZ, Leipzig

09-2013

Graduate assistant at the Department of Proteomics at the Helmholtz Centre for Environmental Research - UFZ, Leipzig

03-2013 – 09-2013

Master thesis with the title "Methods for protein extraction from muscle tissue for the 2D-gel and LC-MS based proteome analysis" at the Proteome Center Rostock

10-2011 – 09-2013

Master's program "Microbiology and Biochemistry" at the University of Rostock

08-2011

Presentation of the Bachelor thesis at the "5th European Summer School – Proteomics Basics“ in Brixen, Italy

03-2011 – 09-2011

Bachelor thesis with the title "Development of protein analytical methods for the titer determination of therapeutical antibodies using the example of Rituximab" at the Proteome Center Rostock

10-2008 – 09-2011

Bachelor's program "Biosciences" at the University of Rostock

10-2007 – 09-2008

Millitary service at the German Airforce

07-2007

Abitur at the John-Brinckman-School in Güstrow, Germany


Focus of Research

My PhD project is integrated to the Transregio 67 research program of the German Research Foundation (DFG). This program aims for the development of novel biomaterials that support the healing capacities in skin and bone defects. Glycosaminoglycans (GAG) are in the focus of this research, since they are known to be natural components of the extracellular matrix (ECM) and affect the sorrounding cells by binding to surface proteins and storing growth factors.
The molecular adaptions of cells to different GAG-surfaces is part of my PhD project. My focus is on fibroblasts and osteoblasts as well as osteoclasts in different cell culture systems in presence or absence of GAGs. By using quantitative proteomics and phosphoproteomics based on mass spectrometry, adaptions of cells in terms of an altered protein expression or activity of specific signaling pathways can by studied.
Moreover, I participate in the development of a method based on microdialysis that aims for the extraction and analysis of proteins and metabolites directly from the wound site.


Used methods and expertises

  • Expericences with various mass spectrometers, e.g. QExactive HF, LTQ-Orbitrap Velos, LTQ-Orbitrap XL ETD (all Thermo Scientific), Synapt G2-S , Xevo-G2-S (both Waters) as well as different MALDI-ToF systems
  • Protein extraction from various biological systems, e.g. 2D and 3D cell culture systems, tissues and body fluids
  • Sample processing and fractionation of proteins and peptides, e.g. 1D SDS-PAGE, gel-free protein fractionation, ion exchange chromatography and reversed phase chromatography
  • Enrichment of phosphorylated peptides by using immobilized metal ion affinity chromatography (IMAC) and titan dioxide.
  • Handling of -OMICS data sets including statistical analyses (e.g. R, SigmaPlot, GraphPad Prism), functional cluster enrichment (e.g. DAVID) and pathway analyses (e.g. KEGG, Inginuity Pathway Analysis)

Collaborations

AG Dr. Ute Hempel
Institut of Physiological Chemistry, Faculty of Medicine
University of Technology Dresden
Fiedlerstraße 42, 01307 Dresden, Germany

AG PD Dr. Ulf Anderegg
Department of Dermatology, Venerology and Allergology, Faculty of Medicine
University of Leipzig
Philipp-Rosenthal-Straße 23, 04103 Leipzig, Germany

AG Prof. Dr. Tilo Pompe
Institut of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology
University of Leipzig
Johannisallee 21-23, 04103 Leipzig, Germany

AG Prof. Dr. Stefan Rammelt
University Center of Orthopedics and Trauma Surgery and Center for Translational Bone, Joint and Soft Tissue Research, University Hospital “Carl Gustav Carus”
University of Technology Dresden
Fetscher Straße 74, 01307 Dresden, Germany

AG Prof. Dr. Lorenz Hofbauer
Division of Endocrinology, Diabetes, and Metabolic Bone Diseases, University Hospital “Carl Gustav Carus”
University of Technology Dresden
Fetscher Straße 74, 01307 Dresden, Germany


Publications

2016 (2)

  • Förster, Y., Schmidt, J.R., Wissenbach, D.K., Pfeiffer, S.E.M., Baumann, S., Hofbauer, L.C., von Bergen, M., Kalkhof, S., Rammelt, S., (2016):
    Microdialysis sampling from wound fluids enables quantitative assessment of cytokines, proteins, and metabolites reveals bone defect-specific molecular profiles
    PLOS One 11 (7), e0159580
    full text (url)
  • Schmidt, J.R., Kliemt, S., Preissler, C., Moeller, S., von Bergen, M., Hempel, U., Kalkhof, S., (2016):
    Osteoblast-released matrix vesicles, regulation of activity and composition by sulfated and non-sulfated glycosaminoglycans
    Mol. Cell. Proteomics 15 , 558 - 572
    full text (url)

2014 (1)

  • Kalkhof, S., Förster, Y., Schmidt, J., Schulz, M.C., Baumann, S., Weißflog, A., Gao, W., Hempel, U., Eckelt, U., Rammelt, S., von Bergen, M., (2014):
    Proteomics and metabolomics for in situ monitoring of wound healing
    Biomed Res. Int. 2014 , art. 934848
    full text (url)