Specialized Proteomic and Mass Spectrometry Laboratory

About us

The laboratory is focused on interdisciplinary studies that require the state-of-art mass spectrometry technology for identification, relative quantification, and structure/function characterization of biologically active macromolecules, particularly those that can be associated with stress response or disease (infection/tumor) development. Results of these studies may provide unique insight into host-pathogen interrelationship and reveal previously unknown virulence strategies of the microorganisms. The noticeable impact can be also achieved by investigations of the role of molecules involved in disease development or altered in response to abiotic stress factors.

The specialists of the laboratory continuously develop and improve methods for:

  • sample preparation (protein extraction, enzymatic digestion, biofunctionalized nanoparticles)
  • electrophoretic and chromatographic (multidimensional) separations of proteins and peptides
  • mass spectrometric detection and quantification
  • statistical and bioinformatical characterization, and
  • determination of posttranslational modification and their localization.

At the same time, the laboratory provides scientific services for research groups at the BMC SAS as well as contractual work for other academic, governmental or industrial partners. (Please address your request to head of the laboratory Ľudovít Škultéty, DrSc. at viruludo@savba.sk)


The Proteomic and Mass Spectrometry Facility (PMSF) provides:

  • Accurate molecular mass determination of biomolecules
  • Identification of proteins
  • Sequence characterization of peptides
  • In-gel, in-solution and on-filter digestion of proteins
  • Separation and purification of proteins and peptides by various scale liquid chromatography
  • Protein 1-D and 2-D gel electrophoresis
  • Robotic excision of gel spots and bands
  • Localization of protein post-translational modification sites (phosphorylation)
  • Bioinformatic interpretation of the proteomic datasets
  • Other analytic services for biomedical research projects (negotiable upon inquiry)

Note: In order to discuss important issues of sample preparation and to clarify the open questions, the investigators are encouraged to meet the members of the laboratory. Please address your requests to viruludo@savba.sk.


Samples can be delivered to the laboratory in person or sent by an appropriate carrier for outside users. Subsequently, the samples are registered and generally processed on a “first-come” basis unless prior arrangements have been made. Final report of the achieved result is prepared by the staff under the guidance of the laboratory head and sent to the applicant by e-mail.

Sample charges:

Fees are generally charged on a per-sample basis to cover operating expenses of the laboratory. For some multi-faceted complex investigations, a project charge can be negotiated.

Unique equipment

  • Tandem mass spectrometers: ESI-Q-TOF Premier (Waters), MALDI Ultraflextreme (Bruker), ESI QTRAP 4500 (Sciex)
  • Electron impact and chemical ionization mass spectrometer
  • Various scale liquid chromatography: fast-flow Bio-Logic (Bio-Rad), two-dimensional Acquity M-class (Waters), nano UHPLC nanoAcquity (Waters), two-dimensional capillary/nano UHPLC Ultimate 3000 (Thermo Scientific), capillary UHPLC Exigent expert 100 (Sciex)
  • Gas chromatography (Agilent Technologies)
  • Protean XL Cell and Multi-Cell vertical electrophoresis units (Bio-Rad)
  • Multiphor isoelectric focusing unit (GE Healthcare)
  • Universal imaging system Pharos FX molecular imager (Bio-Rad) with EXQuest spot cutter (Bio-Rad)
  • 2D gel analysis software Image Master 2D Platinum (GE Healthcare) and PDQuest Advanced (Bio-Rad)

Mass spectrometry data analysis software:

  • ProteinLynx Global Server (Waters) for peak peaking, protein database queries, and denovo sequencing;
  • Progenesis QI for proteomics (Waters) capable of label-free quantification with advanced alignment, filtering, and statistic features;
  • BioTools (Bruker) for manual spectra interpretation;
  • ProteinScape (Bruker) for proteomic data management;
  • Mascot (Matrix Science) for protein identification;
  • Analyst (Sciex) for method development, peak peaking, and structural analysis;
  • MassQuant (Sciex) for targeted quantitation and statistical evaluation.