News:

  • 2026/05/15:

    The Boss always tells us how to do the experiments correctly. And now, he speaks to you. YES! 👉 ALL OF YOU! Together with many colleagues from the FPOP field. The white paper on hydroxyl radical protein footprinting–mass spectrometry is out in Nature Methods!🍾

  • 2026/04/29:

    Maartje moved to another lab some time ago, but we still have things to finish. Published in JASMS, this work expands phase-corrected absorption mode processing for 2D mass spectrometry. This advancement doubles the signal-to-noise ratio and resolving power, significantly improving proteoform sequencing and small-molecule (ergot alkaloid) analysis.

  • 2026/04/27:

    The OP JAK InterMicro project has been instrumental in strengthening intra-institutional collaboration: functional and biophysical assays together with structural mass spectrometry revealed how calcium loading in the acylated segment acts as a molecular switch, controlling the structural folding and membrane penetration capacity of RTX toxins. Now out in J Biol Chem.

  • 2026/04/20:

    Fast, efficient, and online: This recent ACS Omega paper showcases a PNGaseRc-based deglycosylation column that streamlines analysis for therapeutic proteins and antibodies.

  • 2026/04/14:

    Is it time to move past formic acid? In this collaborative study in Anal. Chem., we contributed to establishing propionic acid as a robust alternative for LC-MS. This simple tweak boosts peptide IDs and offers a true “drop-in” way to increase proteome depth without compromising chromatography.

  • 2026/03/25:

    Wrapping up this final piece of research marks a bittersweet milestone. Initiated by our late colleague Angel Luis Pey and led to completion by Milagros Medina, this work reveals new insights into NQO1 function. To your memory, Angel, thank you for the inspiring collaboration.

  • 2026/01/09:

    Fantastic news! Huge dedication and hard work of Jasmin and Luky led to great data on CLC exchange coupling and this fitted perfectly to cryoEM and MD simulations obtained at Stanford by Maduke, Chiu and Dror labs! Joint paper is now out Nat Commun!

  • 2025/12/25:

    Perfect Xmas present 🎄 🎁 for Tomas - his first contribution to a paper and what's even better - it is in the Nat Commun! Collaboration with Roman Sobotka within the Photomachines project.

  • 2025/12/01:

    Great grant news - joint proposal by Ales Hnizda and Alan has been selected for support by the Czech Science Foundation (GACR)! What a continuation of their collaboration, where structural biology meets the clinic.

  • 2025/11/30:

    New Nat Commun paper with the Haitin&Giladi labs is out! Now, with the great molecular dynamics topping from the Giacomello group. Another step towards understanding the mechanism of cis-prenyltrasferases.

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Important:

Software

You can find thecollection of software tools created in our laboratory:

  • DeutEx

    Application for evaluating of HDX/MS experiments.

    DeutEx is now licensed to Bruker and we will work together on further development.

  • DigDig

    DigDig, a standalone, Java-based software tool for evaluating and comparing proteolytic digestion across diverse experimental conditions.

    To obtain a copy of DigDig visit its dedicated webpage. You can also jump straight to the documentation.

  • LinX

    Software for interpretation of high-resolution MS data obtained after protein chemical cross-linking. The software is free to use. If you are using LinX for your research please cite the related publication.

    Download here

    This software is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 731077P.

  • MSTools

    Web based application for visualization and presentation of HXMS data. Learn more about this set of tools in IJMS.

    To use MSTools, visit its section on our website.

  • HDX tools