Annotation: Proteomics used to mean identifying proteins. Today, mass spectrometry can do much more: quantify thousands of proteins, map interaction networks, probe conformational dynamics, define molecular architecture, and even help make sense of complex cryo-EM samples. This seminar will explore three distinct but highly complementary “flavors” of modern proteomics.

Marek Vrbacký (Proteomics service laboratory, IPHYS) will start at the systems level, showing how quantitative proteomics can reveal how cells, pathways, and organelles respond to physiological and pathological changes.

Petr Pompach (Structural Mass Spectrometry Core Facility, IBT) will take us closer to molecular structure. Using hydrogen–deuterium exchange mass spectrometry (HDX-MS) and chemical cross-linking mass spectrometry (XL-MS), structural proteomics can uncover interaction interfaces, conformational changes, protein dynamics, and spatial organization, including systems that are too flexible, heterogeneous, or transient for many classical structural methods.

Alan Kadek (Laboratory of Structural Biology and Cell Signaling, IMIC) will then push mass spectrometry to the level of intact proteins and macromolecular assemblies. Native mass spectrometry and ion mobility provide direct information on stoichiometry, oligomerization, ligand binding, heterogeneity, and conformational states. These measurements are becoming particularly valuable alongside cryo-electron microscopy, where they can help define what is actually present in the sample, resolve alternative assemblies, and guide interpretation of structurally heterogeneous complexes.

Three speakers. Three scales. One message: proteomics is no longer just about asking “what proteins are there?” It is increasingly about asking how they interact, how they move, and how they assemble into functional molecular machines.

Contact at IPHYS: Olga Zimmermannova; olga.zimmermannova@fgu.cas.cz

Contact at IMIC: Petr Novák; petr.novak@mbu.cas.cz