MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Joef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

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


Course Description



Ecotechnologies, third-level study programme


prof. dr. Urška Vrhovšek


This course aims to give to the students a knowledge how to perform a metabolomic experiment, from start to finish. It covers study design, sample preparation, the use of mass spectrometry for global profiling and targeted methodologies and data analysis.


The food metabolome - i.e. the entirety of all low molecular weight compounds in a specific food. It can be extremely complex, often comprising several thousand chemical species. Food metabolomics can nowadays be considered as a valuable tool for the assessment of food quality, food safety, food tracability and food-related health effects. Students will meet with different metabolomic approaches in the analysis of diverse classes of food metabolites. They will get a knowledge how to properly design an experiment for metabolomics studies. They will learn about different sample preparation techniques, and quality control for metabolomics studies. In the frame of the course, several analytical technologies applied in the untargeted and targeted metabolomics studies: liquid chromatography, gas chromatography coupled to mass spectrometry and also some basic information about NMR based metabolomics will be introduced. The students will learn the basics about the data mining methodologies of a complex data sets and the knowledge how to extract biologically meaningful information.

Course literature:

1) Saito K, Dixon RA, Willmitzer L. 2006 Plant Metabolomics: 57 (Biotechnology in Agriculture and Forestry) Kindle Edition, Springer, 347 p
2) Villas-Bas SG, Roessner U., Hansen MAE, Smedsgaard J, Nielsen J (2007) Metabolome Analysis: An Introduction, John Wiley & Sons, Inc., 311 p.
3) Weckwerth, W. 2007 Metabolomics: Methods in Molecular Biology 2007, Humana press, 293 p.
4) Robert D. Hall. 2011. Annual Plant Reviews, Volume 43, Biology of Plant Metabolomics, 420 p.
5) Review from Metabolomics Journal

Significant publications and references:

Beckner Whitener, M.E., Stanstrup, J., Panzeri, V., Carlin, S., Divol, B., Du Toit, M., Vrhovsek, U.
Untangling the wine metabolome by combining untargeted SPMEGCxGC-TOF-MS and sensory analysis to profile Sauvignon blanc co-fermented with seven different yeasts
(2016) Metabolomics, 12 (3), art. no. 53, pp. 1-25.

Fontana, A., Copetti, M., Di Gangi, I.M., Mazza, T., Tavano, F., Gioffreda, D., Mattivi, F., Andriulli, A., Vrhovsek, U., Pazienza, V. Development of a metabolites risk score for one-year mortality risk prediction in pancreatic adenocarcinoma patients (2016) Oncotarget, 7 (8), pp. 8968-8978.

Gasperotti, M., Masuero, D., Guella, G., Mattivi, F., Vrhovsek, U. Development of a targeted method for twenty-three metabolites related to polyphenol gut microbial metabolism in biological samples, using SPE and UHPLC-ESI-MS/MS (2014) Talanta, 128, pp. 221-230.

Vrhovsek, U., Lotti, C., Masuero, D., Carlin, S., Weingart, G., Mattivi, F. Quantitative metabolic profiling of grape, apple and raspberry volatile compounds (VOCs) using a GC/MS/MS method
(2014) Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences, 966, pp. 132-139.

Gika, H.G., Theodoridis, G.A., Vrhovsek, U., Mattivi, F. Quantitative profiling of polar primary metabolites using hydrophilic interaction ultrahigh performance liquid chromatography-tandem mass spectrometry (2012) Journal of Chromatography A, 1259, pp. 121-127.

Vrhovsek, U., Masuero, D., Gasperotti, M., Franceschi, P., Caputi, L., Viola, R., Mattivi, F.
A versatile targeted metabolomics method for the rapid quantification of multiple classes of phenolics in fruits and beverages (2012) Journal of Agricultural and Food Chemistry, 60 (36), pp. 8831-8840.

Theodoridis, G., Gika, H., Franceschi, P., Caputi, L., Arapitsas, P., Scholz, M., Masuero, D., Wehrens, R., Vrhovsek, U., Mattivi, F.
LC-MS based global metabolite profiling of grapes: Solvent extraction protocol optimisation
(2012) Metabolomics, 8 (2), pp. 175-185.


Seminar (50%)
Oral defence of seminar work (50%)

Students obligations:

Oral defence of seminar work