Clinical Proteomics

Clinical Proteomics

Doc. RNDr. Jiří Petrák, Ph.D.

Doc. RNDr. Jiří Petrák, Ph.D. — Project head

1st Faculty of Medicine of the Charles University

About us

Proteome is defined as the complete set o proteins present at a given time in organism, tissue or cell. Proteomics aim at quantitative and qualitative description of proteomes and their dynamic changes

 Using the most advanced proteomic methods based on effective separation methods and high-resolution mass spectrometry, identification and quantification of up to 10.000 proteins can be accomplished in a single experiment. This opens a new way toward understanding of physiological and pathological processes on molecular level.  Employing proteomic approaches (based on effective protein and peptide separation methods and mass spectrometry) our team attempts to describe molecular mechanisms of human diseases and identify novel diagnostic or prognostic biomarkers.

Our team employs modern proteomic analyses to study global changes of cellular proteomes in order to describe the molecular mechanisms and proteins involved in human physiology and pathology. Using high-resolution separation methods such as peptide IEF-IPG combined with nano-LC in combination with high-resolution mass spectrometry, we can monitor the quantitative and qualitative changes of thousands of proteins. We use proteomic approaches to study diverse processes, such as the molecular mechanisms of drug resistance in cancer cells or the events responsible for heart failure development and progression. Proteomic methods also enable us to specifically alter proteins present in a patient's blood or other body fluids - i.e. potential disease biomarkers. We are specialized in proteomic analyses (2-DE, LC-MS, iTRAQ, SILAC, analysis of protein complexes and membrane proteins), however, our expertise covers wide fields of molecular and cell biology, including cell cultures and animal models.


Current projects:

  • Molecular mechanism of acquired drug resistance in lymphomas
  • Molecular processes associated with heart failure
  • Development of new methods for proteomic analysis of transmembrane proteins


Group Profile (Home Institution):





Vit O, Talacko P, Musil Z, Hartmann I, Pacak K, Petrak J. Identification of potential molecular targets for the treatment of cluster 1 human pheochromocytoma and paraganglioma via comprehensive proteomic characterization. Clin Proteom 20, 39 (2023).

Benes J, Kroupova K, Kotrc M, Petrak J, Jarolim P, Novosadova V, Kautzner J, Melenovsky V. FGF-23 is a biomarker of RV dysfunction and congestion in patients with HFrEF. Sci Rep. 2023 Sep 25;13(1):16004. doi: 10.1038/s41598-023-42558-4. (IF 18.2)


Soukup J, Kostelanská M, Kereïche S, Hujacová A, Pavelcová M, Petrák J, Kubala Havrdová E, Holada K. Flow Cytometry Analysis of Blood Large Extracellular Vesicles in Patients with Multiple Sclerosis Experiencing Relapse of the Disease. Journal of Clinical Medicine. 2022; 11(10):2832.

Jankovska E, Lipcseyova D, Svrdlikova M, Pavelcova M, Kubala Havrdova E, Holada K, Petrak J. Quantitative proteomic analysis of cerebrospinal fluid of women newly diagnosed with multiple sclerosis. Int J Neurosci. 2022 Jul;132(7):724-734. doi: 10.1080/00207454.2020.1837801. (IF 2.590)


Hrdinova T, Toman O, Dresler J, Klimentova J, Salovska B, Pajer P, Bartos O, Polivkova V, Linhartova J, Machova Polakova K, Kabickova H, Brodska B, Krijt M, Zivny J, Vyoral D, Petrak J. Exosomes released by imatinib‑resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib‑sensitive cells in the presence of imatinib. Int J Oncol. 2021 Feb;58(2):238-250. doi: 10.3892/ijo.2020.5163

Havlenova T, Skaroupkova P, Miklovic M, Behounek M, Chmel M, Jarkovska D, Sviglerova J, Stengl M, Kolar M, Novotny J, Benes J, Cervenka L, Petrak J, Melenovsky V. Right versus left ventricular remodeling in heart failure due to chronic volume overload. Sci Rep. 2021 Aug 24;11(1):17136. doi: 10.1038/s41598-021-96618-8.

Vit O, Patel M, Musil Z, Hartmann I, Frysak Z, Miettinen M, Pacak K and Petrak J. Deep Membrane Proteome Profiling Reveals Overexpression of Prostate-Specific Membrane Antigen (PSMA) in High-Risk Human Paraganglioma and Pheochromocytoma, Suggesting New Theranostic Opportunity. Molecules 2021, 26, 6567.


Petrak J, Havlenova T, Krijt M, Behounek M, Franekova J, Cervenka L, Pluhacek T, Vyoral D, Melenovsky V. Myocardial iron homeostasis and hepcidin expression in a rat model of heart failure at different levels of dietary iron intake. Biochim Biophys Acta Gen Subj. 2019 Apr;1863(4):703-713. doi: 10.1016/j.bbagen.2019.01.010.

Jankovska E, Svitek M, Holada K, Petrak J. Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteom (2019) 16:9


Melenovsky V, Hlavata K, Sedivy P, Dezortova M, Borlaug BA, Petrak J, Kautzner J, Hajek M. Skeletal Muscle Abnormalities and Iron Deficiency in Chronic Heart Failure. Circ Heart Fail. 2018; 11e004800. doi: 10.1161/CIRCHEARTFAILURE.117.004800.

Krijt M, Jirkovska A, Kabickova T, Melenovsky V, Petrak J, Vyoral D. Detection and quantitation of iron in ferritin, transferrin and labile iron pool (LIP) in cardiomyocytes using 55Fe and storage phosphorimaging. BBA-GEN SUBJECTS 1862 (2018) 2895-2901.

Melenovsky V, Cervenka L, Viklicky O, Franekova J, Havlenova T, Behounek M, Chmel M, Petrak J. Kidney Response to Heart Failure: Proteomic Analysis of Cardiorenal Syndrome. Kidney Blood Press Res. 2018 Sep 20;43(5):1437-1450. doi: 10.1159/000493657.


Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics. 2017 Feb 5;153:8-20  

Melenovsky V, Petrak J, Mracek T, Benes J, Borlaug BA, Nuskova H, Pluhacek T, Spatenka J, Kovalcikova J, Drahota Z, Kautzner J, Pirk J, Houstek J. Myocardial iron content and mitochondrial function in human heart failure: a direct tissueanalysis. Eur J Heart Fail. 2017 Apr;19(4):522-530

Vyoral D, Petrak J. Therapeutic potential of hepcidin - the master regulator of iron metabolism. Pharmacol Res. 2017 Jan; 115:242-254.

Zimmermannova O, Doktorova E, Stuchly J, Kanderova V, Kuzilkova D, Strnad H, Starkova J, Alberich-Jorda M, Falkenburg JHF, Trka J, Petrak J, Zuna J, Zaliova
M. An activating mutation of GNB1 is associated with resistance to tyrosine kinase inhibitors in ETV6-ABL1-positive leukemia. Oncogene. 2017 Oct 26;36(43):5985-5994.


Vit O, Man P, Kadek A, Hausner J, Sklenar J, Harant K, Novak P, Scigelova M,Woffendin G, Petrak J. Large-scale identification of membrane proteins based onanalysis of trypsin-protected transmembrane segments. J Proteomics. 2016 Oct 21;149:15-22

Toman O, Kabickova T, Vit O, Fiser R, Polakova KM, Zach J, Linhartova J,Vyoral D, Petrak J. Proteomic analysis of imatinib-resistant CML-T1 cells reveals calcium homeostasis as a potential therapeutic target. Oncol Rep. 2016 Sep;36(3):1258-68.

Sedmera D, Neckar J, Benes J Jr, Pospisilova J, Petrak J, Sedlacek K,Melenovsky V. Changes in Myocardial Composition and Conduction Properties in Rat Heart Failure Model Induced by Chronic Volume Overload. Front Physiol. 2016 Aug 25;7:367.


Lorkova L, Scigelova M, Arrey TN, Vit O, Pospisilova J, Doktorova E, Klanova M, Alam M, Vockova P, Maswabi B, Klener P Jr, Petrak J. Detailed Functional and Proteomic Characterization of Fludarabine Resistance in Mantle Cell Lymphoma Cells.. PLoS One. 2015 Aug 18;10(8):e0135314.


Klanova M, Lorkova L, Vit O, Maswabi B, Molinsky J, Pospisilova J, Vockova P, Mavis C, Lateckova L, Kulvait V, Vejmelkova D, Jaksa R, Hernandez F, Trneny M,Vokurka M, Petrak J, Klener P Jr. Downregulation of deoxycytidine kinase in cytarabine-resistant mantle cell lymphoma cells confers cross-resistance to nucleoside analogs gemcitabine, fludarabine and cladribine, but not to other classes of anti-lymphoma agents.. Mol Cancer. 2014 Jun 27;13:159.