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Mass Spectrometry Laboratory (MS)

The Mass Spectrometry Laboratory ensures rich infrastructure and know-how indispensable for performance of analyses in the field of proteomics, metabolomics, lipidomics, glycomics and tissue imaging using the mass spectrometry.

We specialize in development, optimizing and validation of organic compounds analysis methods on the basis of the mass spectrometry technique using the majority of the available mass analysers types (low and high resolution) and the analysis of compound mixes in complex matrixes thanks to interfacing with the liquid chromatography technique (nano-, micro- and ultra-LC).

We perform research for our scientific and industrial partners and participate in research projects in cooperation with the scientific institutions and industrial partners. We also cooperate with a number of laboratories in the area of our campus for complex execution of our research services.

The Laboratory features the implemented management system in compliance with standard PN-EN ISO/IEC 17025:2018-02 (AB 1661).


The Laboratory performs the qualitative and quantitative analysis with determining the structure of chemical compounds in the scope of:

  • Proteomics: peptide analysis with the “bottom up” method and fragmentation type CID, HCD and ETD in order to identify proteins, post translation modification analysis (phosphorylation and glycosylation), peptide quantitative analysis (SRM/MRM), de novo proteins identification, “top down” method protein analysis
  • Metabolomics: profiling and identification of metabolites in clinical samples (serum, urine) and tissue material, analysis of low molecular weight substances
  • Lipidomics: separation and identification of lipids and derived compounds, profiling of cell and membrane lipids of plant, animal and human origin, quantitative analysis
  • Pharmacokinetics: DMPK analysis of medicines and their derivates in physiological liquids (serum, urine), test of medicines and cosmetics components, identification and structure determination of medicines and dietary supplements
  • MALDI Imaging: identification and analysis of protein and metabolites distribution in tissues
  • MALDI Biotyper: an innovative method of identification of microorganisms in biological materials (bacteria, yeasts, fungi)

PORT Polish Center for Technology Development


The accredited methods at the Mass Spectrometry Laboratory (AB 1661)

Subject of testing:

  • Chemicals: organic substances in solid and liquid form

Identity confirmation except isomers in the range of 150 – 3000 m/z. The mass spectrometry method with ionization in the ESI ion source and CID (ESI-MS/MS) fragmentation on the basis of testing procedure PB-MS-01.

  • Chemicals: organic substances in solid and liquid form

Identification of chemical compounds. The mass spectrometry method with ESI ionization and CID fragmentation (ESI-MS/MS) in the range of 150 – 3000 m/z (except isomers) and/or the magnetic resonance spectroscopy method on the basis of PB-MS-01 and/or PB-NMR-01 research pocedures. The obtained results are given with method limitations.

  • Pharmaceutical products: water for pharmaceutical products, infusion fluids

The content of antibacterial drugs in the range of 0,005-600000 mg/l (penicillin G, amphotericin B) and 0,01-500000 mg/l (streptomycin) by high-performance liquid chromatography with mass spectrometry detection (LC-ESI-MS/MS) according to the research procedure PB-MS-02.

  • Biological materials: bacteria, yeasts, and fungi

The identification of microorganisms with consideration of the limits indicated by the mass spectrum database (Bruker). The MALDI-TOF-MS method using the mass spectrum MBT DB 4613 library on the basis of the procedure PB-MS-03. Preparation of samples executed at the Microbiology Laboratory according to the  PB-MIKRO-01 procedure.

Ultra-high resolution, hybrid mass spectrometer with Fourier’s transformation LTQ Orbitrap Elite (Thermo Scientific)

  • mass analysers: LTQ (linear ion trap), high field Orbitrap
  • exchangeable ion sources: ESI (HESI), APCI and Nano
  • fragmentation CID, PQD, HCD and ETD
  • ion mobility FAIMS module
  • liquid chromatograph Easy nano-LC 1000 and Ultimate 3000

High resolution mass spectrometer QTOF Maxis Impact (Bruker)

  • mass analysers: quadrupole and time of flight analyser
  • exchangeable ion sources: ESI, APCI and nano CaptiveSpray
  • fragmentation: CID
  • ultra high-performance liquid chromatograph Ultimate 3000 (Thermo Fisher Scientific) Ultimate 3000 (Thermo Fisher Scientific)

High resolution mass spectrometer ultrafleXtreme MALDI TOF/TOF (Bruker)

  • Biotyper for microorganism identification (bacteria, fungi)
  • ImagePrep for tissue analysis with the MALDI imaging method
  • fragmentation: CID, LIFT
  • Proteineer fc II automatic robot
  • liquid chromatograph Easy nLC (Bruker)

Mass spectrometer LTQ (Thermo Scientific)

  • mass analyser: LTQ (linear ion trap)
  • ion source: ESI
  • fragmentation CID
  • ultra high-performance liquid chromatograph Ultimate 3000 (Thermo Fisher Scientific) Ultimate 3000 (Thermo Fisher Scientific)

PORT Polish Center for Technology Development – Mass Spectrometry Laboratory


Anna Czajkowska PhD – Laboratory Manager MS

Paweł Pasikowski PhD – Senior Research Engineer MS

Katarzyna Kapczyńska PhD – Research Engineer MS

Piotr Biniarz PhD – Process Engineer MS

Research team of the MS laboratory takes part in preparation of grant applications.

Currently the laboratory is performing the following scientific-research projects:

  • “Development and implementation of an innovative platform for screening analysis of the degron type therapeutic compounds” (acronym: DegScreen, NCBiR)
  • “ANEURYSENS-an innovative micro sensor for diagnostics and monitoring of the abdominal aorta aneurism risk” (acronym: DegScreen, NCBiR)
  • “Green technology of production of succinic acid from renewable and waste materials” (acronym: GreenAmber, NCBiR)
  • “Application of polymer sorbents with molecular imprinting (MIP-SPE) for selective profiling of catecholamines and their metabolites” (acronym: BabyMIP, NCN)
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Posted by abachmatiuk, Posted on 08.10.2015