Laboratory of cell biochemistry and proteome analysis

členové laboratoře
  • RNDr Zbyňek Hrkal, DrSc
  • Ing Dana Grebeňová
  • RNDr Kateřina Kuželová, PhD
  • Ing Michaela Pluskalová
  • RNDr Jitka Bartošová, Dr
  • Jana Sedlmaierová (technician)
  • Hana Pilcová (technician)
Zbyňek Hrkal, PhD, DrSc
Department of Cellular Biochemistry (chairman)
Institute of Hematology and Blood Transfusion
U Nemocnice 1
128 20 Prague-2
Czech Republic
Tel.: +420 221977304
Fax.: +420 224918390

The proteomic laboratory studies the ‘global’ protein expression (the proteome) of leukemic cells and their changes due to the variety of experimental treatments (anti-cancer drugs, differentiation agents, the photodynamic therapy). The basic tool employed is the two-dimensional electrophoresis, the method that resolves proteins/peptides according to their isoelectric point (pI) in the first dimension and according to their molecular size/weight (MW) in the direction perpendicular to the first one. In this way the two-dimensional polypeptide maps are obtained each peptide spot being characterized by its pI and MW. By means of computerized image analysis using AIDA Proteomix 2D Version 2.01 software the peptide maps are analyzed and the proteins revealed, which are differentially expressed due to the effects of the particular agent (anti-cancer drug, differentiation agent, photodynamic treatment). Subsequently, the differentially expressed proteins are identified using mass spectrometry (MALDI-MS) in collaboration with the Mass Spectrometry laboratory of the Institute of Microbiology, AS CR, Prague, CR (Dr Havlícek, Ing Halada). From the changes in the expression of individual proteins their roles in the mechanism of the particular treatment are derived.


Institute of Molecular Pathology and Proteome Centre for the Study of Intracellular Parasitism of Bacteria

členové laboratoře
  • Doc. RNDr. Aleš Macela, DrSc.
  • MUDr. Jirí Stulík, CSc.
  • RNDr. Zuzana Krocová, Ph.D.
  • Ing. Lenka Hernychová, Ph.D.
  • Pharm.Dr. Ivona Klimtová, Ph.D.
  • Mgr. Sylva Szkanderová (Ph.D. student)
  • Mgr. Blanka Hartmanová (Ph.D. student)
  • Mgr. Martin Hubálek (Ph.D. student)
  • Mgr. Valeria Sheshko (Ph.D. student)
  • Mgr. Juraj Lenco (Ph.D. student)
  • Mgr. Jana Zechovská
  • Martin Brychta (Student of Pharmaceut. Fac. Charles University, Hradec Králové)
  • Zdenka Petrová (administrative support)
  • Jana Michalicková (technician)
  • Alena Firychová (technician)
  • Jitka Žáková (technician)
  • Marie Šafárová (technician)
  • Lenka Lukšíková (technician)
Ing. Lenka Hernychová, Ph.D.
Purkyne Military Medical Academy Hradec Králové
Trebešská 1575
500 01 Hradec Králové
Czech Republic
Tel.: +420 973 251 537
Fax.: +420 495 513 018

The major program for the scientific work at the Institute still covers three main topics: biomolecular signatures of biological agents, the immunoreactive components of bacteria expressed mainly under the artificial in vitro conditions mimicking the conditions existing in intracellular compartments, and finally the host gene expression under the influence of infection. The favorite microbial model is live vaccine strain of Francisella tularensis, a gram-negative facultative intracellular bacterial pathogen from the gamma subdivision of Proteobacteriae. In the frame of proteome studies realized in the collaboration with University of Umea, Umea, Sweden, Institute of Virology, Slovak Academy of Science, Bratislava, Slovak Republic, and Institute of Parasitology, Czech Academy of Science, Ceske Budejovice, Czech Republic, the materials prepared from virulent strains of Francisella tularensis, three members of Borrelia burgdorferi sensu lato complex, and Coxiella burnetii are currently analyzed.

Quadrupole Time-of-Flight Laboratories of the Institute are currently equipped for realization of proteomic analyses using both 2DE technology for separation of complex protein mixtures and identification of proteins by mass spectrometry (MALDI-TOF, Q-TOF) and bioinformatics. The materials for analyses are prepared in the Institute’s tissue culture and microbiological labs. In parallel, the basic search for gene expression can be controlled in the same experimental system in PCR laboratory. The adopted technologies enable researchers, Ph.D. students, and pre-graduate students to realize complex studies oriented to the analyses of the reaction of living systems to external (and internal modulatory) signals as are the chemicals, biologically active bio-molecules, physical influences (temperature, radiation, etc.), and microorganisms.

The Proteome centre for the study of intracellular parasitism of bacteria exists from the year 2001, it is fully supported from grant of Ministry of Education, Youth and Sport, Czech Republic. During years of its existence the laboratory basis for proteomic technology was created on the institutional basis of the Institute for Molecular Pathology of Purkyne Military Medical Academy, Hradec Kralove. The molecular approach utilizing proteome technology was applied in microbiological, immunological, radiobiological, and oncological studies. More information about the Proteome centre for the study of intracellular parasitism of bacteria you can find on .


Laboratory of Reproduction Physiology, Proteome Research Group

členové laboratoře
  • RNDr. Hana Kovářová, CSc.
  • Ing. Michal Kubelka, CSc.
  • Ing. Zdenka Ellederová
  • Prof. MVDr. Jan Motlík, Dr Sc.
  • Mgr. Helena Skalníková
  • Bc. Kateřina Opatová
RNDr. Hana Kovářová, CSc.
Academy of Sciences of the Czech Republic
Institute of Animal Physiology and Genetics and Centre of Cell Therapy and Tissue Replacement
Rumburská 89
277 21 Liběchov
Czech Republic
Tel. +420 315639582
Fax: +420 315697186

Main research activities of the Laboratory of Reproduction Physiology are focused on following topics:

  • establishment of cultivation systems enabling enrichment of popupations of mammalian oocytes that are capable to undergo successful fertilization and the initiation of zygotic development
  • biochemical mechanisms regulating initiation of translation and chromatin condensation during oocyte maturation
  • molecular mechanisms of the resumption of the meiosis as a specific model of the G2/M transition of cell cycle
  • expansion of follicular cumulus cells and communication with oocyte
  • culture of fetal or adult stem cells and their diferentiation into specialized populations of tissue cells

Major research interests of Proteome Research Group involve:

  • Analysis of oocyte proteomes during maturation using classical proteomics approach (2-DE and MS). Currently described pig oocyte proteome represents the largest protein pattern in oocyte available so far that may be used as a 2-DE reference map. The proteins that are up-regulated during IVM may present potential biomarkers of oocyte maturation and quality.
  • proteomic analyses of neural stem cells and definition of their differentiated counterparts
  • study of proteomes and state specific protein phosphorylations (phosphoproteomes) induced by inhibition of cellular cyclin-dependent kinases
  • phosphoproteomes of maturing mammalian oocytes as a fine regulatory mechanisms underlying developmental processes

Our papers and presentations are available on our web address

Recently, the Joint Laboratory of Proteome analysis was established between Institute of Animal Physiology and Genetics AS CR, Institute of Microbiology AS CR, Institute of Experimental Medicine AS CR, and Immunotech a.s., a representative of Beckman Coulter Inc. This cooperation allows the expansion of our current proteome analyses from 2-D gel electrophoretic and mass spectrometry techniques to the 2-D chromatographic protein separations performed on ProteomeLab PF 2D.


Laboratory of Bioinformatics

členové laboratoře
  • Ing. Jiří Vohradský, PhD.
  • Jana Novotná, PhD.
  • Tra Thi Vu
  • Cuong Chieu To
Ing. Jiří Vohradský, PhD.
Institute of Microbiology
Academy of Sciences of the Czech Republic
Vídeňská 1083
142 20 Prague
Czech Republic
Tel:(+420) 2 4106 2513
(+420) 2 9644 2513
Fax: (+420) 2 4172 2257

Our main objective is to analyze, model, and simulate regulatory processes in the cell, and provide bioinformatics support for measured data. We develop computerized models of regulation of gene expression and we use statistics and artificial intelligence for analysis of proteomic and other large scale data. In proteomics we have focused on two prokaryotic microorganisms – Streptomyces and Caulobacter.

The computerized model of gene expression is based on the concept of genetic network which is in our case formalized to a principle of neural network. We assume that the rate of protein expression of each individual protein is a result of combinatorial action of all molecules which influence expression of the given gene. The influence of each molecule is expressed in a weight matrix. This principle has been expressed in a set of time dependent differential equations. Their solution allows simulation of behavior of the given system over time. The concept was successfully tested on the simple regulatory network of the phage lambda. Inverse problem - reconstruction of the weight matrix from experimentally measured time series is being solved. The reconstructed weight matrix then allows drawing of mutual interaction maps among member molecules of the system and the design of regulatory pathways.

The image of current state of gene expression can be monitored mainly by transcriptomics and proteomics. We have focused on the proteomic analysis of gene expression during development of two microorganisms – Caulobacter crescentus, which serves as a model for the study of cell cycle, and streptomycetes, which are industrially important producers of antibiotics with complex developmental cycle. We have been analyzing quantitative changes in the proteome during different stages of development in both species, including initial transition from dormant spores to metabolically active vegetative forms in Streptomyces. We use proteomic data together with statistics and artificial intelligence for identification of global trends in gene expression, principles of transition between different developmental phases, and identification of proteins and protein functional groups involved in the process. We are developing tools for data mining of complex proteomic, transcriptomic and metabolic databases.

For the storage of large scale proteomics data, together with Biozentrum, Univ. Basel, we have established a database and proteomics server SWICZ ( The server hosts the databases for the above mentioned species, and is equipped with graphical interface and search engines which allow retrieving relevant information. The databases are linked with other data sources as GeneBank, and KEGG metabolic pathway server.


Department of Biological Chemistry, Group of Proteomics, Institute of Organic Chemistry and Biochemistry, Academy of Science of Czech Republic

členové laboratoře
  • RNDr. Jiří Jiráček, CSc.
  • Mgr. Irena Selicharová, Dr.
  • Mgr. Lucia Sviteková
  • Ing. Petra Kabeleová
  • Jana Mládková
RNDr. Jiří Jiráček, CSc.
Ústav organické chemie a biochemie
Akademie věd České Republiky
Flemingovo nám. 2
166 10 Praha
Czech Republic
Tel. +420 220183441
Fax: +420 2183571

Cílem našeho výzkumu je nalezení nových diagnostických a prognostických markerů nádoru prsu. Projekt je řešen ve spolupráci s Ústavem molekulární genetiky AV ČR a 1. Lékařskou fakultou UK. V naší skupině analyzujeme nádorové buňky pomocí dvourozměrné elektroforézy. K problematice analýzy prsních epiteliálních buněk přistupujeme z těchto hledisek:

  • 2-DE analýza buněčné linie EM-G3, vytvoření referenční proteinové mapy.
  • Analýza dalších buněčných linií využívaných při výzkumu rakoviny prsu (MCF7, MDA-MB231, HCC1937). Určení jejich fenotypu na základě 2-D profilu.
  • 2-DE analýza primárních kultur epiteliálních buněk z nádorů prsu nebo zdravé prsní tkáně. Nalezení rozdílně exprimovaných proteinů a posouzení jejich významu jako potenciálních prognostických markerů nádorů prsu.
  • Prefrakcionace buněčného extraktu s cílem nabohatit proteiny obsažené v buňce v nižší koncentraci s využitím metod izolace buněčných organel a afinitní chromatografie.

Identifikace proteinů je prováděna v laboratoři hmotové spektrometrie ÚOCHB (Ing Josef Cvačka, Ph.D., Mgr. Miloslav Šanda) na přístrojích MALDI-MS (reflex IV BRUKER-DALTONICS) nebo Q-TOF micro (WATERS).


Department of Proteomics, Institute of Analytical Chemistry, Brno

Oddělení proteomiky,
Ústav analytické chemie AV ČR
Veveří 97
602 00 Brno
Tel.: +420-532 290 107
Fax: +420-541 212 113,

Oddělení proteomiky ústavu analytické chemie v Brně je relativně mladé oddělení – a to jak dobou vzniku, tak lidmi, kteří jej tvoří. Vedle převážně analytických úkolů, které jsou podstatnou částí náplně naší práce, se zabýváme hlavně proteomikou ječmene a jejím vztahem k technologickým vlastnostem odrůd ječmene hlavně v pivovarnickém a potravinářském průmyslu. Dalšími úkoly jsou například hmotnostně-spektrometrická charakterizace sacharidů hrajících důležitou roli v živých systémech; dále enzymů řídících chemické procesy v buňkách apod. Mezi naše cíle též patří rozvíjení metod a technik používaných v proteomice, jež pak mohou usnadnit práci a pomoci získávat odpovědi na reálné problémy.


Mass spectrometry at the Institute of biochemistry and microbiology, University of Chemical Technology, Praha

V roce 2001, kdy byl zakoupen hmotnostní spektrometr MALDI-TOF firmy Bruker Daltonics, začala na ústavu biochemie a mikrobiologie vznikat pod vedením prof. Kodíčka skupina zabývající se aplikací hmotnostní spektrometrie v proteomice. V rámci této skupiny byla od té doby řešena celá řada projektů z oblasti základního výzkumu, konkrétních aplikací metody hmotnostní spektrometrie a v neposlední řadě i z oblasti bioinformatiky a vývoje nových softwarů.

Jeden z hlavních projektů je zaměřen na studium prostorového uspořádání bílkovin. Zabýváme se podrobnou analysou možnosti mapování povrchových aminokyselin proteinů pomocí specifických kovalentních modifikací s následnou detekcí pomocí hmotnostní spektrometrie. Jako součást tohoto projektu byl vyvinut i komplexní nástroj pro precizní analýzu hmotnostních spekter, dostupný zdarma na adrese

V rámci spoluprací s dalšími pracovišti se dále zabýváme metodikou identifikace proteinů ve vzorcích malby z obrazů, pro určení pravosti obrazu či pro volbu vhodných restaurátorských postupů; určováním primární struktury cyklických peptidů spojených azo-vazbou; studiem struktury peptidů vážících kovové ionty; studiem fibrinogenu u pacientů trpících poruchami hemokoagulace a v neposlední řadě studiem struktury lipoproteinových komplexů rostlin.


Laboratory of Molecular Structure Characterization, Institute of Microbiology , Academy of Sciences of the Czech Republic

členové laboratoře
  • Doc. Ing. Vladimír HAVLÍČEK, Dr.
  • Ing. Petr SEDMERA, CSc.
  • Ing. Petr HALADA, PhD
  • RNDr. Petr NOVÁK, PhD
  • RNDr. Petr MAN, PhD
  • RNDr. Miroslav ŠULC, PhD
  • Mgr. Petr POMPACH, PhD
  • Mgr. Jan SKLENÁŘ, PhD
  • Mgr. Martin ŽABKA, PhD
  • Ing. Helena PELANTOVÁ
  • Ing. Marek KUZMA
  • Mgr. Jan NEDVĚD
Doc. Ing. Vladimír Havlíček, Dr.
Mikrobiologický ústav
Akademie věd České Republiky
Vídeňská 1083
142 20 Praha
Tel: +420-241 062 786
Fax: +420-241 062 749, +420-241 062 156

Characterization and molecular structure determination of natural compounds, their semisynthetic derivatives or biotransformation products as well as of some biologically important compounds is performed by nuclear magnetic resonance and mass spectrometry.

Mass spectrometric applications to:
Proteomics - protein identification, peptide sequencing, analysis of post-translational modifications.
Structure Biology – chemical crosslinking and protein surface labeling.
Biomarkers – tissue imaging.


  • Bruker APEX-Q FTMS (9.4 T, Combi I ion source, µ-capillary LC, DESI)
  • Finnigan LCQ-DECA (ESI, nano-ESI, µ-capillary LC)
  • Bruker BIFLEX II mass spectrometer (MALDI-TOF)
  • Finnigan MAT 95 (ESI, µ-ESI, APCI, FAB, EI, CI, DCI, FD, FI)
  • Varian Unity Inova 400MHz

For further information and scope of the lab visit


Centre of molecular interactions and biotransformations, interacademic laboratory of Charles University Faculty of Science and Institute of Microbiology Academy of Sciences of Czech Republic

členové laboratoře
  • Doc. RNDr. Karel Bezouška CSc.
  • Doc. RNDr. Marie Stiborová DrSc.
  • Mgr. Kateřina Hofbauerová PhD.
  • Mgr. Petr Pompach PhD.
  • Mgr. Daniel Kavan
  • Mgr. Markéta Vančurová
  • Mgr. Ondřej Vaněk
  • Mgr. Zuzana Kubínková
Mikrobiologický ústav
Akademie věd České Republiky
Laboratoř architektury proteinů
Vídeňská 1083
142 20 Praha
Czech Republic
Tel: +420-241 062 142
Fax: +420-241 062 383

Katedra biochemie PřFUK
Hlavova 8
12840 Praha 2

Centrum molekulárních interakcí a biotransformací léčiv řeší vědecko-výzkumné projekty v oblasti výzkumu struktury receptorů a jejich ligandových vazebných domén, vývoje a syntézy ligandových mimetik, chemoenzymatických syntéz a modelování proteinů. Projekty v proteomice a glykomice se týkají zejména identifikace proteinů v receptorových komplexech lymfocytů a přirozených zabíječských buněk (1,2), výzkumu biologického významu glykosylace (3,4), změn v povrchové nádorové glykosylaci, identifikace přirozených sacharidových ligandů rozpoznávaných specifickými lymfocytárními receptory, a konstrukce ligandových mimetik (5,6). Aktivní výzkum probíhá v poslední době v oblasti strukturní proteomiky (7,8).

(1) Pompach P. et al.(2004) Biochem. Soc. Trans. 32, 777.
(2) Man P. et al. (2005) Proteomics 5, 113.
(3) Plíhal O. et al. (2004) Biochem. Soc. Trans. 32, 764.
(4) Martínek V. et al. (2005) FEBS J. 272, Suppl.1, 422.
(5) Bezouška K. (2002) J. Biotechnol. 90, 269.
(6) Vepřek P. et al. (2006) J. Med. Chem. v tisku.
(7) Pavlíček J. et al. (2003) Biochemistry 42, 9295.
(8) Pavlíček J. et al. (2004) Biochem. Soc. Trans. 32, 1124.

Další informace můžete najít na stránkách


Centrální laboratoř (CL)

Členové laboratoře
  • RNDr. Zbyněk Zdráhal, Dr.
  • RNDr. Ondrej Šedo, PhD.
  • RNDr. Hana Konečná
  • Mgr. Eva Paděrová
  • Ing. Renata Bendová
  • Mgr. Irena Kasalová
  • Danuše Fridrichová
  • Lenka Vorbisová
RNDr. Zbyněk Zdráhal, Dr.
Oddělení funkční genomiky a proteomiky
Přírodovědecká fakulta
Masarykova univerzita
Kamenice 5, Pavilon A2-ILBIT
625 00 Brno
Tel. +420 549491466
Fax: +420 549492640

Centrální laboratoř Masarykovy univerzity (CL) vznikla na podporu výzkumu na kampusu i mimo něj. CL umožňuje akademické komunitě přístup k finančně náročným technologiím. Genomické techniky zahrnují DNA sekvenování, fragmentační analýzu a syntézu oligonukleotidů (včetně Real-Time PCR sond). Proteomické techniky pokrývají spektrum od izolace proteinů až po jejich charakterizaci a bioinformatické zpracování dat. Provádíme solubilizaci vzorku, depleci abundantních proteinů, prefrakcionaci, isoelektrickou fokusaci na imobilizovaných gradientech pH, separaci polyakrylamidovou gelovou elektroforézou (1-DE, 2-DE), barvení po separaci v gelu, image analýzu, dále pak frakcionaci a separaci kapalinovou chromatografií a MS analýzu (MALDI-TOF MS a LC-MS/MS). CL se podílí na výuce a nabízí praktické kurzy. CL je aktivním členem Association of Biomolecular Resource Facilities (ABRF).


Laboratory of Microbial proteomics

členové laboratoře
  • Mgr. Karolína Buriánková PhD.
  • RNDr. Jiří Janeček PhD.
  • Mgr. Denisa Petráčková
  • MVDr. Silvia Bezoušková
  • RNDr. Zuzana Dobrová
  • Mgr. Ladislava Kalachová
RNDr. Jaroslav Weiser, PhD.
Mikrobiologický ústav
Akademie věd České Republiky
Vídeňská 1083
142 20 Praha
Tel:(+420) 241 062 378
Fax: (+420) 241 722 257

The research in the laboratory is oriented towards the complex studies of gene expression on protein level in populations of bacteria growing under conditions resembling their natural living environment. The methodology used involves both classical bacterial physiology practices and progressive proteomics techniques.

The projects of the laboratory cover two important areas of microbiology, the first represents mechanisms governing differentiation of soil bacteria from the order Actinomycetales, where namely Streptomycetes undergo complex morphological changes and are known to produce many diverse secondary metabolites including antibiotics. There was developed in the laboratory two-phase cultivation system resembling the soil epitope. The system enables studies of Streptomycetes differentiation by molecular biological and global techniques such as transcriptomics and proteomics. Using the system the regulatory mechanisms and cell signalling in both primary and secondary metabolism are being exploited by the analysis of Streptomyces developmental proteomes.

The second field which is studied is connected with the widely spread antibiotic resistance among bacterial pathogens. It was observed quite often that when the antibiotic is removed from the environment the resistant population does not tend to revert back to sensitivity and thus better fitness. But, instead, after growth for many generations it starts to accumulate secondary adaptive mutations, which improve the fitness of the organisms and sometimes also restores lost virulence, and the most important, the antibiotic resistance stays. This phenomenon was studied on the model of entero-bacteria in erythromycin resistant Escherichia coli grown in continuous culture, which corresponds to its natural environment in intestinal tract. The 2D protein electrophoresis is used for identification and quantitative analysis of adaptive mutations in several antibiotic resistant mutants grown in the presence or absence of the drug during cultivation in turbidostat.


Department of Biochemistry and Laboratory of Growth Regulators, Faculty of Science, Palacký University

Prof. Mgr. Marek Šebela, Ph.D.
Department of Biochemistry and Laboratory of Growth Regulators
Faculty of Science, Palacký University
Šlechtitelů 11
783 71 Olomouc
Tel: (+420) 585 634 927;

Proteomic laboratory in the Department of Biochemistry, Faculty of Science, Palacký University, is equipped with basic instruments for protein and peptide separation and their analysis. Such devices involve various systems for vertical 1–D gel electrophoresis, a system for 2–D gel electrophoresis in both large gels and minigels, a gel documentation system, a calibrated scanner and software for evaluation plus quantitative and statistical analysis of 2–D gels. Two chromatographic systems are used for gel-free separation of proteins and peptides: a non-metallic HPLC system and an FPLC system for protein purification using conventional chromatographic methods. Protein identification is performed using a MALDI-TOF mass spectrometer (model 2006) equipped with a nitrogen laser (337 nm, repetition rate 10–20 Hz), which is controlled by a PC containing local versions of protein databases and software for database search. There are several thermostated shakers, centrifuges and a vacuum concentrator available for in-gel digestion and further processing of protein digests. A Q–TOF mass spectrometer (model 2005), which is equipped by electrospray ionization and connected to a nanoLC system, is accessible in the neighboring Laboratory of Growth Regulators. The research team is involved in the study of protein digestion focused mainly on chemical modification and immobilization of proteolytic enzymes. Other research topics involve isolation of microbial proteolytic enzymes, expression and differential proteomics of urine, serum, plant tissues and cell cultures. The proteomic laboratory also provides frequent service analyses for colleagues from the Faculty of Science, Faculty of Medicine and Faculty Hospital. The staff comprises two researchers and several Ph.D. and undegraduate students.

  • Havliš J. et al. (2003) Anal. Chem. 75 (6), 1300-1306.
  • Lenobel R. et al. (2005) Folia Microbiol. 50 (5), 401-408.
  • Šebela M. et al. (2006) Proteomics 6 (10), 2959-2963.
  • Stránská J. et al. (2007) Biochimie 89 (1), 135-144.
  • Štosová T. et al. (2008) Anal. Biochem. 376 (1), 94-102.