News:

  • 2019/10/10:

    Joint paper with Volf's lab showing identification of blood sources of hematophagous arthropods is now in PLOS Neglected Tropical Diseases..

  • 2019/10/04:

    Our new publication combining ambient ion landing of proteases with structural biology is now in Catalyst.

  • 2019/09/27:

    The EPIC-XS proposal submission system is now online. Proposal can be submitted here.

  • 2019/09/26:

    Our paper describing characterization of transcription factor/DNA interaction by structural mass spectrometry has just been accepted!

  • 2019/09/25:

    Collaboration between IMIC, IOCB and CF Plus Chemicals resulted in a publication which is now available in Chemistry journal.

  • 2019/08/05:

    5th Short Course on FT-ICR-MS aimed at "Basics of FT-ICR: dynamic harmonization and computer simulation" will be held in early October in Moscow. Apply now, no participation fee, accommodation and meals covered!

Important:

  • 2019/10/09:

    We are looking for post-doc and PhD to join our team and work on structural mass spectrometry! Send inquiries to Petr Novak.

  • 2019/03/27:

    We are part of another Horizon 2020 project EPIC-XS (reg. no 823839) focused on the cutting edge proteomic techniques. This project provides Trans-National Access and also focuses on the development of the techniques.

  • 2018/01/03:

    Our lab is a part of Horizon 2020 project EU FT-ICR MS (reg. no 731077). Through this project you can access our expertise as well as other participating FT-ICR labs. Check Trans-National Acess web section for more details. Also, various FT-ICR focused courses and schools are organized by the labs participating in the project.

  • 2017/12/20:

    Bachelor and master theses are available in the lab. Areas of structrual biology, cutting edge mass spectrometry and cell signalling are awaiting new students. Check the tab Teaching.

Research

Focus

Structural mass spectrometry

method development

  • novel covalent labeling and cross-linking chemistry of proteins /nucleic acids
  • new acid proteases as a tool for protein digestion
  • automation of HDX-MS and CX-MS workflow including software design
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

  • ambient ion landing protein immobilization
  • surface Immuno-affinity substrates for clinical diagnostics
  • biochemically active plates for desorption mass spectrometry

Projects


  • European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers

    The European Proteomics Infrastructure Consortium providing access (EPIC-XS) consists of a unified network of experienced access providers and research groups who share a common goal; to facilitate the development and sustainability of proteomics exploration to all life science researchers within the European Union. The initiative is coordinated by Albert Heck, professor of Biomolecular Mass Spectrometry and Proteomics at Utrecht University. EPIC-XS will provide scientists transnational access to high end proteomics technologies and resources. The project will strengthen and expand the European proteomics community through its expertise in proteomics. It’s excellent training courses and programs, available to both novices and experts, will attract new research communities who will be schooled in advanced proteomics technologies. The initiative brings together some of the most world renowned proteomics laboratories and researchers. The community has expertise in accommodating and guiding researchers within the life sciences, as many of the members also participated in the pan- European PRIME-XS initiative, which ended in 2015.

    Funded by EU H2020 (EPIC-XS)

  • European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers

    EU_FT-ICR_MS proposal aims to establish a European network of FT-ICR (Fourier Transform Ion Cyclotron Resonance) mass spectrometry (MS) centers in association with a manufacturer and a SME software company. Mass spectrometry (MS) has become the most ubiquitous analytical techniques in use today, providing more information on the composition and the structure of a substance from a smaller amount of sample than any other techniques. Unlike other analytical techniques, such as NMR, which mainly rely on a unique technology, MS is characterized by the existence of a large range of mass analyzers. FT-ICR MS is the most powerful MS technique. It offers up to 100 fold higher mass resolving power and mass accuracy than any other MS technique. On the contrary to NMR community with which the FT-ICR MS shares several features, FT-ICR MS has never been involved in a European INFRA network and so will be a legitimate candidate to the Integrating Activities for Starting Communities call. The EU_FT-ICR_MS network includes 10 FT-ICR MS centers from 8 different European countries (Belgium, Czech Republic, Finland, France, Germany, Italy, Portugal, and United Kingdom) and 1 third country (Russia), a European FT-ICR MS manufacturer and 2 SMEs. It includes centers equipped with up-to-date FT-ICR MS and expertise which will cover most of the field in which FT-ICR mass spectrometry is involved: BioOrganic & BioInorganic, Cultural heritage, Glycomics, Environment, Imaging, InfraRed Spectroscopy of Ions in the Gas Phase, Lipidomics, Medicine, Petroleum & Coal Oil, Nanoparticles, Organic chemistry, Physical chemistry, Proteomics, Structural biology. The EU_FT-ICR_MS proposal contains six work-packages which cover all the aspects of the INFRAIA-02-2017 (RIA) Integrating Activities for Starting Communities (WP1 Transnational access; WP2 Training and Education; WP3 Open Data and e-Infrastructure; WP 4 Joint Research Action; WP 5 Dissemination; WP6 Consortium management).

    Funded by EU H2020 (EU_FT-ICR_MS)

  • Mapping the protein surface accessible area utilizing Top Down mass spectrometry and reactive radical footprinting.

    Structural proteomics has become an emerging technique of current structural biology. It covers very broad range of analytical methods from hydrogen/deuterium exchange to chemical crosslinking. Although, the limitations and potentials of both techniques are well studied, foundations of covalent labelling are still poorly described. While H/D exchange offers information about backbone accessibility, covalent labelling targets amino acid side chains and thus provides complementary structural information. In this proposal we will develop chemical reagents with novel reactivity that will allow targeting of more amino acid side chains and expand the spatial resolution of the method. We will also pursue hydroxyradical footprinting where we aim mainly at the development of top-down mass spectrometric approaches allowing to assign not only the site of the modification but also to assess the reactivity scale of individual modified residues. Such advancements will greatly facilitate protein structure characterization and will provide valuable information for protein structure modelling.

    Funded by Czech Science Foundation (19-16084S)