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Research areas
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Separation of complex protein mixtures
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Characterization of proteins and their modifications by mass spectrometry
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Mass spectrometric techniques for the quantification of protein mixtures
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MS-based proteomics in general
Main objectives
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The development of novel techniques for the separation and characterization of proteins using mass spectrometry.
Content of research
Our research interests focus on the field of MS-based proteomics including protein isolation from various matrices, fractionation and separation of complex protein mixtures by chromatographic and electrophoretic techniques, namely on applications of mass spectrometric techniques for qualitative and quantitative characterization of proteins and modifications of them.
At present, we participate in several research projects with diverse topics in areas of molecular biology, biomedicine and agriculture. Our roles within these projects include activities in the development and aplication of MALDI-MS profiling for taxonomic studies of selected bacterial genera and funghi, characterization of differentially expressed proteins (e.g. plant proteins after hormonal treatment), characterization of protein complexes, characterization of histone acetylations and assessments of the influences of selected histone deacetylase inhibitors on histone acetylation states, characterization of phosphorylation states of selected proteins, characterization of groups of patatin proteins in different potato cultivars, and the search for potentional disease biomarkers in blood plasma.
CURRENT RESEARCH INFRASTRUCTURE
The current infrastructure includes instrumentation for protein isolation, protein separation and mass spectrometry.
Key instruments: OrbitrapElite hybrid mass spectrometer
1. Proteomics of the lysine acetylome in cancer cells
Supervisor: doc. RNDr. Zbyněk Zdráhal, Dr.
Consultants: Mgr. Gabriela Lochmanová, Ph.D.
Annotation:
Lysine acetylation represents a dynamic post-translational modification (PTM) which in context of other PTMs increases the functional diversity of proteome. While acetylation has been extensively studied in core histones, cytoplasmic proteins have been reported to be acetylated, too; indicating that acetylation plays key role in a variety of signalling and regulatory pathways. Targeting protein acetylation represents a potentially promising strategy for disease treatment, such as cancer. The aim of the doctoral study is to characterize global protein acetylation in cancer cells by mass spectrometry-based methods. As analysis of acetylome is challenging due to overall low abundance of acetylated proteins, the suggested PhD topic will address development of the methodology consisting of acetylated proteins / peptides enrichment, separation of enriched peptides, and introducing an approach for determining levels of individual acetylated peptides based either on isotopic labelling or label-free quantification. Experimental part of study will be performed in CEITEC proteomics facility. Candidates who are interested in the topic are requested to contact supervisor of the project in advance –Zbyněk Zdráhal (zdrahal@sci.muni.cz).
