Laboratory of Mass Spectrometry

Dr. Łukasz Marczak

Head of Laboratory

lukasmar@ibch.poznan.pl
ext. 1176

Research Projects

Keywords

mass spectrometry,
liquid chromatography,
gas chromatography,
proteomics,
metabolomics,
lipidomics,
qualitative analysis,
targeted analysis,
atherosclerosis,
cancer diseases,
hyperhomocysteinemia,
protein N-homocysteinylation,
small extracellular vesicles,
exosomes,
biomarkers,
biomarker validation.

Offer

The Mass Spectrometry Laboratory of the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IChB PAN) in Poznań provides comprehensive research support in the identification, structural characterization, and quantitative analysis of proteins and low-molecular-weight compounds using advanced mass spectrometry techniques. In the field of proteomics, we conduct, among others, de novo sequencing of peptides and proteins, analyses of post-translational modifications (PTMs), quantitative protein measurements, and validation of protein panels. In metabolomics and analytical chemistry, we perform accurate monoisotopic mass determination of low-molecular-weight compounds using HR-MS, structural elucidation based on tandem mass spectrometry (MS/MS), and quantitative analysis of small molecules. In addition, we analyze volatile compounds using GC-MSn, enabling detailed profiling and comparative studies in both basic and applied research.Przykładowy tekst. Lorem ipsum dolor sit amet, consectetur adipiscing elit nullam nunc justo sagittis suscipit ultrices.

De novo sequencing of peptides and proteins (MALDI, ISD-MALDI)
Mass spectrometry–based analysis of protein post-translational modifications.
Validation analysis of proteomic panels.
Quantitative protein analysis using electrophoretic methods and MS.
Determination of monoisotopic masses of low-molecular-weight compounds by HR-MS.
Structural analysis of low-molecular-weight compounds using tandem mass spectrometry.
Quantitative analysis of low-molecular-weight compounds using MS.
Analysis of volatile compounds by GC-MSn.

Equipment

Nano/micro LC–MS system — Dionex RSLC nano 3000 + Bruker timsTOF Pro (+ Dionex 3000 UPLC).
Nano/micro LC–MS system (Orbitrap) — Dionex RSLC nano 3000 + Thermo Exploris 480 (+ Thermo Vanquish UPLC).
NanoLC–MS system (ion trap) — Waters nanoAcquity + Bruker amaZon SL.
GC–MS system (Triple Quad) — Thermo Trace 1310 + TSQ 8000.

Research activity

OMNIPLANT — National research infrastructure for imaging and multi-omic analysis at the single plant cell level for modern agriculture and forestry. Project co-funded under the European Funds for a Modern Economy 2021–2027 (FENG) program, Action 2.4 Research Infrastructure for a Modern Economy. Implementation period: 2026–2029.
Species identification of animal skeletal remains from archaeological sites using mass spectrometry (PI: Dr Eng. Aleksander Strugała) — NCN MINIATURA 8.
Proteomic predictors of metastasis in colorectal cancer — validation studies (PI: Dr hab. Anna Wojakowska) — NCN OPUS 27.
Exosomes as a potential biomarker for monitoring and predicting kidney transplant rejection (consortium PI: Dr hab. Anna Wojakowska; leader: Medical University of Gdańsk; consortium member: Maria Skłodowska-Curie National Research Institute of Oncology (NIO-PIB), Gliwice branch) — NCN OPUS 22.
Why do cells become smaller to survive? Analysis of tobacco BY-2 cells adapted to osmotic and salt stress to identify key factors regulating energy management, molecular homeostasis, and cell size (consortium PI: Dr Łukasz Marczak; leader: Institute of Dendrology, PAS) — NCN OPUS LAP 20.
Identification of biomolecules released by colorectal cancer cells and detected in blood serum and/or exosomes (PI: Dr Anna Wojakowska) — NCN SONATA 13.

Selected publications

Kania D, Fochtman D, Skoczylas Ł, Gawin M, Marczak Ł, Kurczyk A, Fidyk K, Perkowska-Ptasińska A, Chmielik E, Dębska-Ślizień A, Gołębiewska J, Wojakowska A, Pietrowska M. Biopsy proteome-based classification of T cell-mediated kidney allograft rejection. J Transl Med. 2025 Oct 21;23(1):1139. doi: 10.1186/s12967-025-07116-8.
D. Fochtman, L. Marczak, M. Pietrowska, A. Wojakowska, Challenges of MS-based small extracellular vesicles proteomics. J Extracell Vesicles. 2024 Dec;13(12):e70020. doi: 10.1002/jev2.70020.
A. Wojakowska, L. Marczak, M. Zeman, M. Chekan, E. Zembala-Nożyńska, K. Polanski, A. Strugała, P. Widlak, M. Pietrowska, Proteomic and metabolomic signatures of rectal tumor discriminate patients with different responses to preoperative radiotherapy. Front Oncol. 2024 Feb 12;14:1323961. doi: 10.3389/fonc.2024.1323961.
U. Strybel, L. Marczak, M. Zeman, K. Polanski, Ł. Mielańczyk, O. Klymenko, A. Samelak-Czajka, P. Jackowiak, M. Smolarz, M. Chekan, E. Zembala-Nożyńska, P. Widlak, M. Pietrowska, A. Wojakowska, Molecular composition of serum exosomes could discriminate rectal cancer patients with different responses to neoadjuvant radiotherapy. Cancers. 2022;14(4):99. DOI: 10.3390/cancers14040993.
M. Pietrowska, A. Zebrowska, M. Gawin, L. Marczak, P. Sharma, S. Mondal, J. Mika, J. Polanska, S. Ferrone, J. M. Kirkwood, P. Widlak, T. L. Whiteside, Proteomic profile of melanoma cell-derived small extracellular vesicles in patients’ plasma: a potential correlate of melanoma progression. J. Extracell. VESICLES. 10 (2021), doi:10.1002/jev2.12063.
L. Marczak, J. Idkowiak, J. Tracz, M. Stobiecki, B. Perek, K. Kostka-Jeziorny, A. Tykarski, M. Wanic-Kossowska, M. Borowski, M. Osuch, D. Formanowicz, M. Luczak, Mass spectrometry-based lipidomics reveals differential changes in the accumulated lipid classes in chronic kidney disease. Metabolites. 11 (2021), doi:10.3390/metabo11050275.
A. Liskiewicz, M. Przybyla, A. Wojakowska, L. Marczak, K. Bogus, M. Nowacka-Chmielewska, D. Liskiewicz, A. Malecki, J. Barski, J. Lewin-Kowalik, M. Toborek, Physical activity reduces anxiety and regulates brain fatty acid synthesis. Mol. Brain. 13 (2020), doi:10.1186/s13041-020-00592-7.
A. Szuba, L. Marczak, I. Ratajczak, Metabolome adjustments in ectomycorrhizal Populus x canescens associated with strong promotion of plant growth by Paxillus involutus despite a very low root colonization rate. TREE Physiol. 40, 1726–1743 (2020).
A. Wojakowska, A. Zebrowska, A. Skowronek, T. Rutkowski, K. Polanski, P. Widlak, L. Marczak, M. Pietrowska, Metabolic profiles of whole serum and serum-derived exosomes are different in head and neck cancer patients treated by radiotherapy. J. Pers. Med. 10, 1–14 (2020).
M. Sikora, Ł. Marczak, J. Perła-Kajan, H. Jakubowski, Sex affects N-homocysteinylation at lysine residue 212 of albumin in mice. Sci. Rep. 9 (2019), doi:10.1038/s41598-019-38784-4.
A. Zebrowska, A. Skowronek, A. Wojakowska, P. Widlak, M. Pietrowska, Metabolome of exosomes: Focus on vesicles released by cancer cells and present in human body fluids. Int. J. Mol. Sci. 20 (2019), doi:10.3390/ijms20143461.
K. Kimakova, A. Kimakova, J. Idkowiak, M. Stobiecki, P. Rodziewicz, L. Marczak, E. Cellarova, Phenotyping the genus Hypericum by secondary metabolite profiling: emodin vs. skyrin, two possible key intermediates in hypericin biosynthesis. Anal. Bioanal. Chem. 410, 7689–7699 (2018).
M. Pietrowska, S. Funk, M. Gawin, Ł. Marczak, A. Abramowicz, P. Widłak, T. Whiteside, Isolation of exosomes for the purpose of protein cargo analysis with the use of mass spectrometry (2017), vol. 1654.
P. Kachlicki, A. Piasecka, M. Stobiecki, Ł. Marczak, Structural characterization of flavonoid glycoconjugates and their derivatives with mass spectrometric techniques. Molecules. 21 (2016), doi:10.3390/molecules21111494.
S. J. Gadher, Ł. Marczak, M. Łuczak, M. Stobiecki, P. Widlak, H. Kovarova, Proteomic landscape in central and Eastern Europe: The 9th Central and Eastern European Proteomic conference, Poznan, Poland. Expert Rev. Proteomics. 13 (2016), doi:10.1586/14789450.2016.1116391.
Ł. Marczak, P. Znajdek-Awizeń, W. Bylka, The use of mass spectrometric techniques to differentiate isobaric and isomeric flavonoid conjugates from Axyris amaranthoides. Molecules. 21 (2016), doi:10.3390/molecules21091229.

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