MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description



Nanosciences and Nanotechnologies, third-level study programme


prof. dr. Marko Fonović


Students will obtain a basic understanding of proteomics methodology, instrumentation and its applications in biomedical research.


Protein separation techniques: sample preparation, PAGE, 2D-PAGE, DIGE, HPLC, MudPIT, affinity chromatography.
Mass spectrometry: basic principles of mass spectrometry, types and components of mass spectrometers, MALDI, ESI, SELDI, CID, ETD, ECD.
Quantitative proteomics: ICAT, SILAC, iTRAQ, absolute quantification
Bioinformatics: statistical data evaluation, protein and genomic databases, identification of MS/MS spectra, “de novo” sequencing
Proteomics and biology: “top down” and “bottom up” approach, protein posttranslational modifications, protein complexes, biomarkers.
Protein microarrays: preparation and application of protein microarrays.

Course literature:

Principles of Proteomics (Advanced Text Series) R. M. Twyman, BIOS Scientific Publ, 2004.

Proteomics in Practice: A Guide to Successful Experimental Design, R. Westermeier, T. Naven, H. R. Höpker, Wiley-VCH, 2008.

Mass Spectrometry Data Analysis in Proteomics (Methods in Molecular Biology), R. Matthiesen (Editor), Humana Press, 2006.

Computational Methods for Mass Spectrometry Proteomics, I. Eidhammer, K. Flikka, L. Martens, S. O. Mikalsen, Wiley-Interscience, 2008.

Significant publications and references:

FONOVIC, Marko, VERHELST, Steven H. L., SORUM, M. T., BOGYO, Matthew. Proteomics evaluation of chemically cleavable activity-based probes. Molecular & cellular proteomics, 2007, vol. 6, no. 10, str. 1761-1770.

VERHELST, Steven H. L., FONOVIC, Marko, BOGYO, Matthew. A mild chemically cleavable linker system for funtional proteomic applications. Angew. Chem. (Int. ed., Print), 2007, vol. 46, str. 1284-1286.

FONOVIC, Marko, BOGYO, Matthew. Activity based probes for proteases: applications to biomarker discovery, molecular imaging and drug screening. Curr. pharm. des., 2007, vol. 13, no. 3, str. 253-261.

FONOVIC, Marko, BOGYO, Matthew. Activity-based probes as a tool for functional proteomic analysis of proteases. Expert review of proteomics, 2008, vol. 5, no. 5, str. 721-730.

ZHANG, Jun, FONOVIC, Marko, SUYAMA, Kaye, BOGYO, Matthew, SCOTT, Matthew P. Rab35 controls actin bundling by recruiting fascin as an effector protein. Science (Wash. D.C.), 2009, vol. 325, no. 5945, str. 1250-1254.


• seminar and oral exam

Students obligations:

• seminar and oral exam