News:

  • 2019/06/24: 

    Few years ago, we helped Petrak's lab with the development of transmembrane proteome analysis. We are happy that Jirka's team is pushing it further and even happier we still keep in touch as this resulted in another nice J Proteomics paper.

  • 2019/06/12: 

    Congratulations to our Bc students (Zuzka, Verča, Týna, Kamila and Jana) on successful defense of their Bc theses.

  • 2019/05/31: 

    Congratulations to Lucka Wallenfels (Hernychová) on successful defense of her PhD thesis and other happy life events. All the best in the future Lucka!.

  • 2019/05/06:

    Attempts to fully uderstand and somehow unify chemical cross-linking pushed further through interlaboratory comparion in which we participated. Read more in this community-wide Analytical Chemistry paper.

  • 2019/04/29:

    New publication about oligomerisation of NK cell receptors evaluated using homo-FRET and high resolution mass spectrometry - colaboration with Marek Cebecauer's group - is online in the International Journal of Molecular Sciences.

  • 2019/01/26:

    Joint paper with Ales Hnizda on structural characterization of pyrophosphatase NUDT15 and its thiopurine intolerance causing mutations is now available in Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.

Important:

  • 2019/01/10:

    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.

Downloads

LinX

  • Software for interpretation of high-resolution MS data obtained after protein chemical cross-linking

    The software is free to use, however the download is password protected. For access please contact Zdenek Kukacka. If you are using LinX for your research please consider to cite our work.

    Download here

    Download beta version here

HDX tools

  • DeutEx - Software for interpretation of HDX-MS data will be available here.

    The software is free to use, however is distributed upon signing of Software Transfer Agreement. The download is password protected. For access please contact Petr Man. If you are using these tools for your research please consider to cite our work.

    Other HDX-MS related tools for data processing and visualization are below.

  • Digestion_metrics - Microsoft Excel macro calculating simple digestion metrics (coverage, average peptide length, redundancy, etc.) Modified supplementary file to publication Kadek A et al Anal Chem. 2014, 86(9):4287-94.
  • HDXPeptideSplitter - Python script for preporcesing of HDX-MS results before using them in PyMol. Processed data are then used by data2bfactor Pymol script written by Robert L. Campbell. This version works with Python version 2.x. For version 3.x and higher use this modified data2bfactor script.
  • Kunaverse - 3D printed labware

    • Here you can find various 3D printed things, mostly generated by Dan Kavan. Fell free to use them! We will always provide FreeCAD files together with *.stl and some basic comments.

      Our passion in 3D printing is strongly supported by a collaboration with the TRILAB company.