Structural Mass Spectrometry

Structural mass spectrometry (MS3D) core facility provides services for characterization of protein structure using cutting-edge technologies such as high-resolution mass spectrometry, UPLC system, H/D system, chemical cross-linking and native electrospray. The service provided includes data processing and reporting ready for publication. Besides, the platform also offers identification and quantification of proteins, precise determination of protein molecular mass and characterization of various posttranslational modifications.

Key Equipment

  • 15T solariX XR FT-ICR mass spectrometer, with electrospray and MALDI ion sources (Bruker Daltonics)
  • Autoflex Speed MALDI-TOF mass spectrometer (Bruker Daltonics)
  • 1290 UPLC system (Agilent Technologies)
  • Excimer laser (Coherent)
  • UV ExciStar laser (Coherent)
  • timsTOF Pro mass spectrometer (Bruker Daltonics)


  • The utilization of high resolution mass spectrometry (15T FT-ICR MS) to determine the composition of molecules (metabolites, nucleic acid, proteins, and carbohydrates) based on accurate mass measurements and fragment pattern. FT-ICR MS is equipped with atmospheric pressure ionization technique including electrospray/native electrospray and vacuum ionization technique (matrix-assisted laser desorption).
  • FT-ICR MS is able to perform several fragmentation techniques such as sustained off-resonance irradiation (SORI), collision-induced dissociation (CID), electron transfer dissociation (ETD), electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD).
  • Mass spectrometric cutting-edge analysis of post-translational modifications, and of structural states of proteins and complexes in solution
  • Combination of covalent surface labelling, hydrogen/deuterium exchange (HDX), chemical cross-linking
  • Native mass spectrometry measurements
  • Fast Photochemical Oxidation of Proteins (FPOP) - a type of hydroxyl-radical-based protein footprinting
  • Hotgun proteomics, hydrogen-deuterium exchange and covalent labelling experiments, and native mass spectrometry with ion mobility separation (timsTOF Pro)


  • Separation of protein mixtures
  • Intact protein analysis
  • Native mass spectrometry
  • Peptide/protein/metabolite profiling
  • Protein identification
  • Characterization of protein modifications
  • Protein/metabolite quantification
  • Protein surface covalent labelling
  • Chemical cross-linking
  • Hydrogen/deuterium exchange (HDX)
  • Data processing and interpretation of mass spectrometric data

Core Facility contact

Petr Pompach -

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More information about Structural mass spectrometry and related services you can find in document Equipement and services of CIISB (page 17).

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