Research
Focus
Structural mass spectrometry
method development
- novel covalent labeling and cross-linking chemistry of proteins /nucleic acids
- enzymatic columns as a tool for protein digestion, deglycosylation, etc.
- automation of HDX-MS and CX-MS workflow including software development
- native top-down MS
and application to selected biological problems (medicinally or biotechnologically important proteins), membrane proteins, dynamic and heavily modified proteins and their complexes
Functionalized surfaces for mass spectrometry and clinical diagnostics
- ambient ion landing protein immobilization
- surface Immuno-affinity substrates for clinical diagnostics
- biochemically active plates for desorption mass spectrometry
Current projects
- PHOTOMACHINES – Reorganization of photosynthetic cells for the purpose of high production of therapeutic peptides
- INTER-MICRO - Talking with microbes – understanding microbial interactions within One Health framework
- MULTIOMICS_CZ - Multi-omics platform for the search for biological correlates of diseases and the development of new diagnostic, preventive and therapeutic procedures
- 2D TOP-MASS
- SPIDoc's - The next generation MS SPIDoc's
- Mapping Accessible Surface Area of Soluble and Membrane Proteins by Employing Reactive Probes
- Ions and Surfaces: Methods for manipulation and utilization of biomolecular ions (Ionsurf)
- ODEEP-EU - The Open Data Exchange Ecosystem in Proteomics: Evolving its Utility
- MICRO-BIOTECH - Microorganisms in ecological restoration – bacteria as cell factories for controlled bioremediation of ecosystems
- DIAMOND - National centre for new methods of diagnosis, monitoring, treatment and prevention of genetic diseases
- Novel diagnostic approaches for rapid detection and epidemiological analysis of serious bacterial and viral infections
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PHOTOMACHINES – Reorganization of photosynthetic cells for the purpose of high production of therapeutic peptides
The goal of the project is to eliminate obstacles hindering the broader commercial utilization of phototrophic microorganisms (microalgae) for the production of valuable substances. Using methods of metabolic engineering and synthetic biology, a conceptually new type of photosynthetic cellular factories (PHOTOMACHINES) will be developed, sufficiently productive and robust for industrial biotechnology. The primary goal is the production of therapeutic peptides, but metabolic pathways for the production of other metabolites will be identified and subsequently transferred to the production system.
Funded by: MEYS - OP JAK (CZ.02.01.01/00/22_008/0004624)
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INTER-MICRO - Talking with microbes – understanding microbial interactions within One Health framework
The most important player in the field of microbiology in the Czech Republic, together with two domestic partners, will join forces with the world’s leading research institutions in order to decipher the processes behind the establishment and development of microbiomes in various hosts (plants, fungi and animals, including humans), behind the mechanisms of information exchange between microbes and their hosts, and between microbes themselves, which define their role in host health and ecosystem health. The output will be innovative applications in medicine and ecology.
Funded by: MEYS - OP JAK (CZ.02.01.01/00/22_008/0004597)
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MULTIOMICS_CZ - Multi-omics platform for the search for biological correlates of diseases and the development of new diagnostic, preventive and therapeutic procedures
The aim of this research project is the collaboration between three research institutions and two partners from the commercial sector to create a functional complementary platform of multi-omics technologies at BIOCEV in Vestec, which will enable to increase the quality of research on genetic and biological correlates of a wide range of rare and population-common diseases, targeted research and development of new methodological, diagnostic and therapeutic procedures, and ensure the transfer of research results into clinical and laboratory practice. Furthermore, collaboration with other entities will be developed in order to systematically develop and implement innovative methodological approaches in the areas of bioinformatics and multi-omics analysis of nucleic acids, proteins and metabolites in biological material.
Funded by: MEYS - OP JAK (CZ.02.01.01/00/23_020/0008540)
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2D TOP-MASS
Native mass spectrometry is a powerful structural biology tool to study protein complexes, their dynamics and composition. In its so-called top-down approach, it aims to link specific forms of proteins to higher assemblies, in which they function naturally and/or in a disease. The 2D-TOPMASS project leverages the power and versatility offered by state-of-the-art Fourier transform ion cyclotron resonance mass spectrometry custom-coupled to powerful ultraviolet and infrared laser ion activation techniques in combination with advanced two-dimensional acquisition schemes in order to push the boundaries of native top-down MS of protein complexes.
Funded by: EC - ERA fellowship (101090276)
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SPIDoc's - The next generation MS SPIDoc's
A part of the European Marie Sklodowska-Curie Doctoral Network "SPIDoc's", which through an international and interdisciplinary training educates PhD candidates in a combination of structural mass spectrometry, virology and gas phase experiments at advanced light sources such as synchrotrons and free electron lasers (FELs). The project carried out in BIOCEV aims to develop advanced multimodal experimental schemes for top-down analysis of non-covalent protein complexes as well as to study the conservation of protein structure in the gas phase during native MS and FEL imaging experiments.
Funded by: EC - MSC-DN (101120312)
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Mapping Accessible Surface Area of Soluble and Membrane Proteins by Employing Reactive Probes
Structural proteomics is an emerging direction in structural biology. It covers very broad range of analytical methods from hydrogen/deuterium exchange (HDX) over covalent labeling to chemical cross-linking. In contrast to the HDX, covalent labeling targets amino acid side chains in the protein sequence so it provides complementary structural information. The original labeling approach relies on modification of selected amino acids whereas the fast photochemical oxidation of proteins (FPOP) targets almost any side chains. Recently, a fluoroalkyl radical footprinting has been successfully adopted. It allows haracterization of the solvent-accessible surface area of the proteins by targeting aromatic amino acids. Another footprinting technique that is currently tested for structural studies is based on oxidation by singlet oxygen. Because both fluoralkyl radical and singlet oxygen are relatively non-polar chemical probes, it is worth investigating their potential to label soluble and membrane proteins and thus studying their structural rearrangement in combination with FPOP.
Funded by: Czech Science Foundation (25-18181S)
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Ions and Surfaces: Methods for manipulation and utilization of biomolecular ions (Ionsurf)
This project will investigate manipulation of ions in an atmospheric pressure environment and their utilization for unique surface modifications. These findings will be transformed into implements applicable in bioanalytical chemistry. The focus will be on surface modifications by intact ions (ion soft and reactive landing) and bioanalytical mass spectrometry. One practical output that should originate from the successful execution of the planned research is development of surface modification methods that cannot be achieved by regular wet chemistry in solution. We plan to use unique reactivity and properties of desolvated gas-phase biomolecular ions to prepare modified electrodes for electrochemical analytical devices, and for MALDI substrates usable in novel MALDI-MS affinity assays. Other areas of interest will be investigation of ion soft landing as a technique for preparation of cryo electron microscopy specimen and for modification of inorganic nanomaterials to give them biomolecular functionalities that will convert them into sensors and sensor arrays.
Funded by: Czech Science Foundation (25-16715J)
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ODEEP-EU - The Open Data Exchange Ecosystem in Proteomics: Evolving its Utility
ODEEP-EU will engender a critical breakthrough in the open data exchange ecosystem in proteomics, by ensuring that public data in mass spectrometry-based proteomics can be maximally re-used far into the future, and this both within the field of proteomics, as well as across the life sciences in general. This overall objective will be achieved in five goals, with two goals focused on critical efforts to enable effective internal reanalysis and reuse, and three goals focused on kick-starting widespread external reuse. Internal reuse critically requires two key things right now, tackled in the first two goals: (i) the provision of comprehensive and reliable metadata for publicly available data sets; and (ii) the availability of a variety of very well-annotated and carefully characterized reference data sets to serve as key benchmarking, tutorial, and template materials, amongst others. On the other hand, widespread external re-use across the life sciences will be jump-started by three coordinated and directly complementary efforts, which are captured in the next three goals: (iii) by creating an automated flow of information from proteomics data, over sophisticated reprocessing pipelines, to the UniProt Knowledgebase for protein sequence and context information, and to the Protein Data Bank for protein structural information, thus ensuring that all researchers across the life sciences can easily come across and access this information in the broadest possible context; (iv) by providing a cutting-edge, discovery-driven research showcase for proteomics data re- use, centered on elucidating biological meaning for proteome-wide PTM discovery results; and (v) strongly driven outreach and dissemination efforts that are firmly rooted in open science, and that include standard academic channels, comprehensive and wide-ranging interactions with industry, and even outreach to the general public at a global scale. Taken together, in ODEEP-EU, we can utilize two decades of effort in open science infrastructure establishment in proteomics as the launchpad from which to propel the field into a key role as sheer limitless treasure trove of important novel knowledge and insights for the life sciences at large.
Funded by: TACR - CHIST-ERA (TH86010001)
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MICRO-BIOTECH - Microorganisms in ecological restoration – bacteria as cell factories for controlled bioremediation of ecosystems
The goal of this research project is the cooperation of two research institutions and two application partners on the use of microbial systems with unique enzyme properties for the degradation of a wide spectrum of pharmacologically active environmental micropollutants. As part of this project, a commercially usable whole-cell catalyst will be developed, which will ensure effective and environmentally friendly bioremediation. This catalyst will be implemented in the standard technological processes of wastewater treatment plants, including municipal treatment plants and local treatment plants of hospitals and clinics. In addition, the project will focus on the development of a unique tool for easy detection of monitored micropollutants, which will enable effective monitoring and analysis of the spread of antibiotic resistance in a given environment.
Funded by: MEYS - OP JAK (CZ.02.01.01/00/23_020/0008502)
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DIAMOND - National centre for new methods of diagnosis, monitoring, treatment and prevention of genetic diseases
The DIAMOD project aims to improve diagnostic quality beyond the identification of mutations in the genome and to create a base for monitoring of disease progression and therapy effectiveness as well as for testing and development of cell and gene therapies. We intend to develop new analytic, monitoring and therapy tools products as follows: i) development of new analytic tools and technologies to accelerate diagnosis and facilitate diagnostic monitoring of rare diseases development and treatment; development of AI approaches, ii) development and marketing of digital platform for better patient care, iii) development of humanized preclinical models to test cell/gene therapy, and iv) development of cell therapy based on NK cells.
Funded by: TACR (TN02000132)
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Novel diagnostic approaches for rapid detection and epidemiological analysis of serious bacterial and viral infections
Almost a hundred years after their discovery, antibiotics are still the best weapon in the fight against bacterial infection. Unfortunately, their improper use, whether intentional or out of ignorance, leads to a phenomenon known as antibiotic resistance. In Europe alone, 33.000 people die each year from an infection caused by antibiotic-resistant bacteria. Some studies even estimate that if this trend continues at the same pace, it will cause 10 million deaths a year in 2050, more than cancer. Diagnostics in microbiology is constantly improving. Especially thanks to the introduction of MALDI-TOF mass spectrometry into microbiological practice in the field of taxonomic identification of bacteria, and its further extension into other applications - including into the field of antibiotic resistance detection and epidemiological typing. Despite that, there is still need for improved analytical techniques. Current mass spectrometric approaches suffer limitations due to the limited number of proteins that can be identified from whole microbial cells. Abundant proteins, such as ribosomal proteins, are predominant. This limitation is currently solved by various data analysis approaches, such as machine learning. But still, number of important epidemiological markers remains unidentified at present due to their low representation in the analyzed sample. Therefore, further development of diagnostic methods in the field of clinical microbiology requires new approaches to sample processing and analysis. One of the possibilities is the utilization of mass spectrometry methods coupled with liquid chromatography (LCMS) that are available at number of diagnostic sites. The aim of the project will be development and validation mass spectrometry methods, which allow early detection of the infection severity. With the assistance of the high-capacity proteomics methods, important epidemiological markers for the selected bacteria (agents of serious bloodstream infections and meningitis) will be searched for, especially in connection with virulence and antibiotic resistance. The methods will be further optimized for commonly available triple quadrupole mass spectrometers coupled with liquid chromatography. The result of the project will be the development of completely new methods for routine microbiological laboratories, which will expand their diagnostic capabilities and subsequently increase the effectiveness of treatment and reduce the risks associated with the antibiotic resistance.
Funded by: Ministry of Health / AZV (NW24-09-00464)
Past projects
- Czech Science Foundation (22-27695S) Expanding the analytical toolbox for structural mass spectrometry (2022-2024)
- EU - E-Rare (ERA-LEARN) ReCognitiON - Recognition and Validation of Druggable Targets from the Response to Cognitive Behaviour Therapy in Myotonic Dystrophy type 1 patients from Integrated -Omics Networks (2018-2020)
- Horizon 2020 (82383): EPIC-XS-European Proteomics Infrastructure Consortium providing access (2019-2023)
- MSCA-IF (101003406): HIPPOSTRUCT-Structural insights into binding signatures of transcription factors regulated by HIPPO signalling (2020-2022) Synopsis canbe accessed here
- Czech Ministry of Health (NV19-05-00541): Functional Assays for Rapid Microbiological Diagnostics of Selected Health-Care Associated Infections (2019-2022)
- Horizon 2020 (731077): FT-ICR MS-European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers (2018-2022)
- Czech Science Foundation (19-16084S) Mapping the protein surface accessible area utilizing Top Down mass spectrometry and reactive radical footprinting (2019-2021)
- Czech Science Foundation (16-24309S) Mass Spectrometric 3D Structure Analysis of DNA Response Elements / Transcription Factor Association and Modeling (2016-2018)
- Czech Science Foundation (16-20860S) Structural and functional analysis of Hsp70/Hsp90 chaperone complexes (2016-2018)
- Ministry of Education, Youth, and Sports (COST CZ LD15089) A new tool for structure biology: Combination of high resolution mass spectrometry, chemical cross-linking and H/D exchange (2015-2017)
- Ministry of Education, Youth, and Sports (Kontakt II LH15010) Structural mass spectrometry analysis for complexes of transcription factors with DNA response elements (2015-2017)
- Czech Science Foundation and FWF (Austria) (16-34818L / I 2385-N28) Electron Transfer in Cellulose Degrading Enzymes (2016-2018)