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Department of Natural Sciences

Medical Proteomics (MSc)

fb05_bio_proteomics.jpg (DE)


Compulsory Course

  • in MSc Biomedical Sciences, 3rd Semester 
  • 6h/week (2L/2E/2P)
  • Credits: 8 ECTS


Learning outcomes:

Successful students can

  • find suitable research articles in the literature and select the necessary information in publications for state of the art sample preparation for electrophoretic, chromatographic and mass spectrometric analyses
  • write detailed lab scripts for sample preparation based on published procedures in the literature
  • design reasonable proteomics work-flows for selected introductionary applications in the field of mining and differential proteomics
  • decide on reasonable methods for protein purification
  • explain typical current proteomics strategies and applications to a novice in the field


  • Sample preparation: sampling, sample handling, cell lysis methods, laser microdissection, diverse prefractionation techniques (like i.e. affinity and gel filtration chromatography, protein depletion, ultracentrifugation), protein digestion, protein quantification, clinical requirements
  • Separation techniques: 1- and 2D gel electrophoresis, DIGE, preparative IEF, capillary electrophoresis, HPLC and UPLC (employing Reversed Phase and Ion Exchange), multidimensional LC
  • Mass spectrometry: general principles, MALDI and ESI ionization, TOF, quadrupole, FT-ICR/ orbitrap, ion trap, tandem and hybrid instrumentation, CID, ECD/ETD, LC-ESI, SELDI, MALDI imaging
  • Proteomics strategies: bottom up, middle down, top down, discovery vs. hypothesis based, identification based on PMF and peptide sequencing, label and label free quantification approaches like SRM/MRM, SILAC, iTRAQ, ICAT, database analysis, search algorithm
  • Applications: mining, differential like biomarker discovery, protein-protein interactions, posttranslational modifications


Lab Class


  • Isolation and purification of Benzoylformate decarboxylase from P. putida, overexpressed in E. coli. Determination of the purity, activity and overall yield.
  • 2D-gel electrophoresis analysis of E. coli cell lysates, analyzing differences of the bacterial proteome in response to overexpression induction in cell culture




  • Basic Organic Chemistry
  • Instrumental Analysis
  • Clinical Chemistry
  • Biochemistry


  • The grade of the final exam determines the overall grade of the course

  • A pass of six on-line tests and a lab report is required

  • Attendance of lab class is mandatory


  • Lovric, J. (2011): Introducing Proteomics from Concepts to Sample Preparation, Mass Spectrometry and Data Analysis, Wiley-Blackwell
  • Westermeier, R. (2016): Electrophoresis in Practice: A guide to Methods and Applications of DNA and Protein Separations, Wiley-VCH
  • Greaves, J., Roboz, J. (2014): Mass Spectrometry for the Novice, CRC Press