Pracownie badawcze

Prof. dr hab. Michał Dadlez

Pracownia Spektrometrii Mas

Zakres badań

Our laboratory is interested in applying mass spectrometry techniques to solve biomedically oriented problems, with a focus on structural studies of protein assemblies, structural consequences of posttranslational modifications, and targeted proteomic analyses of protein panels with potential use in medicine. Our long-term goal is to popularize new mass spectrometry-based methods to solve problems that are difficult or impossible to tackle using other approaches.


Najważniejsze osiągnięcia badawcze

  • We uncovered a new scheme for tetramer-tetramer contact regions in vimentin for their lateral association into unit-length filaments, leading to a new model of an intermediate filament assembly pathway that is possibly canonical for the entire class of this fundamental cellular scaffold and protein signaling assemblies.
  • We discovered new interactions within participating proteins of the histone pre-mRNA processing complex, eEF1B translation elongation complex, RAGE, and centriolar and kinetochore complexes, providing a basis for a new assembly scheme.

Opis badań

The protein structurome is only partially tractable using classic methods of structure analysis (X-ray, nuclear magnetic resonance [NMR], and cryo-electron microscopy) because of the high content of high dynamics (intrinsic disorder [ID]) and structural heterogeneity. An estimated 70% of signaling proteins contain large ID regions. This is one reason for the increasing gap between the number of protein sequences and their structures. Mass spectrometry (MS) methods help close this gap because they (1) provide access to dynamic properties of proteins and their assemblies by monitoring the kinetics of hydrogen-deuterium exchange (HDX), (2) can characterize coexisting structural variants (ion mobility), and (3) provide structural constraints for modeling even the largest molecular complexes (native MS, X-linking, and HDX). In recent years, we provided unique insights into structural properties of several protein systems, including centrioles, kinetochores, the histone pre-mRNA processing complex, the eEF1B translation elongation complex, intermediate filament proteins (IFs), receptor for advanced glycation endproducts (RAGE), and Alzheimer’s disease amyloid b (Ab) peptide oligomers. We are continuing several research lines and engage in new projects that lead to new experiment-based structural models of challenging protein targets.

One of the fundamental cellular regulation/signaling mechanisms is the tuning of proteins through oxidation-reduction (redox)-based post translational modifications (PTM). We examine structural and functional aspects of PTMs of proteins, particularly two redox modifications of protein cysteines (S-nitrosylation and S-glutathionylation). We seek to provide insights into the molecular aspects of cellular control mechanisms that are performed by multiple protein proteoforms in an interplay between selective modifications of cysteines and protein oligomerization, metal cations, ligands, and target protein binding. Our research subjects are vital human proteins that are related to innate immune response processes and cancer, including the S100 family and IFs. Our long-term goals are to create foundations for the development of new diagnostic methods using various protein proteoforms as biomarkers of inflammation and cancer processes. Our group’s research became the basis of protein/protein interaction-based electrochemical biosensors to detect RAGE ligands, which are biomarkers of many human diseases, including diabetes, rheumatoid arthritis, Alzheimer’s disease, and cancer.

Targeted Proteomics and Medical Applications

The field of MS-based targeted proteomics is on the cusp of entering clinical use and is undeniably the future of clinical protein-biomarker diagnostics1,2. Mass spectrometry is already routinely used clinically for small-molecule quantification. Analyses of peptides/proteins are recently replacing and complementing aging antibody-based tests3. Clinicians are aware of the current diagnostic limitations and are keen to develop new technologies with proteomics researchers to improve patient care. We seek to advance the technology and produce applications to help expedite the process by which proteomics enter the clinic. This has been increasingly happening in our laboratory since 2012 with the arrival of Dr. Dominik Domanski, a specialist in targeted proteomics and its application in translational research. This has occurred through direct financing from institutional grants and national and international collaborations that support the development of targeted proteomics tools and technologies to advance the measurement of biomarkers in medicine with potential clinical application toward cancer diagnostics and personalized medicine. Dr. Domanski has contributed to the field in the standardization of liquid chromatography-MS quantification and sample procurement, improvements in analytical robustness and sensitivity, the development of bioinformatics tools, and novel methods for quantifying the phosphorylation of cancer signaling proteins. Highlights of this work in our laboratory include the development of a panel of cytokeratin cancer markers to improve pleural effusion (PE) diagnosis in patients4,5. The plan for the next 2 years is to move the panel for PE classification toward a validated diagnostic test and develop other technologies for personalized medicine for breast cancer that involves CDK4/6 inhibitors in collaboration with Dr. Basik from McGill.

  • Bibliography
  1. Annesley et al. Clin. Chem. 2015.
  2. Duarte et al. Proteomes
  3. Annesley et al. Chem. 2016.
  4. Domanski et al. Neoplasia
  5. Perzanowska et al. Proteomics – Clin. Appl.
  6. García-Bailo et al. J. Clin. Nutr. 2012.
  7. Parker et al. Curr. Chem. 2014.
  8. Domanski et al. Lab. Med. 2011.
  9. Gillette et al. Methods 2013.


For the structural MS of various proteoforms, such as those that are caused by PTMs, we use MS-based methods (HDX, X-linking, native MS, ion mobility), accompanied by a set of more classic approaches: size-exclusion chromatography coupled with multiangle light scattering mass analysis, analytical ultracentrifugation, electron microscopy, atomic force microscopy, calorimetry, dynamic light scattering, circular dichroism, nuclear magnetic resonance, etc. Using these methods, we study the consequences of PTMs on the conformation, oligomerization properties, metal ions, ligands, and protein binding to the studied proteoforms. HDX maps protein chain dynamics in different protein regions and its changes that accompany structural transformations that are induced by ligand binding. X-linking maps the contact region between protein domains in protein complexes. Native MS characterizes complex stoichiometries. Ion mobility characterizes structural heterogeneity of the protein assemblies. We use classic proteomic methods to identify targets of redox-based modification of protein cysteine thiols. We utilize semi-synthetic strategies to obtain highly homogeneous full-length recombinant proteins, also those that are observed in vivo, that bear site-specific modifications of cysteine thiols.

Mass spectrometry-based targeted proteomics approaches (multiple/parallel reaction monitoring [MRM/PRM]) can overcome the many issues (e.g., cross-reactivity, patient auto-antibodies, low multiplexing, expensive development, etc.) of immunological assays that have been the gold-standard for protein quantification. Our developed MRM/PRM panels, combined with isotope-labeled peptide standards, provide greater detail and specific biological information. They are also less expensive and quicker to develop. Moreover, they are characterized by higher analytical specificity and precision, a wider dynamic range, and the possibility of measuring numerous proteins within a single rapid analysis6-9. Our laboratory houses unique MS systems that are required for these methods.

Wybrane publikacje

  • Structural Dynamics of the Vimentin Coiled-coil Contact Regions Involved in Filament Assembly as Revealed by Hydrogen-Deuterium Exchange. Premchandar A, Mücke N, Poznański J, Wedig T, Kaus-Drobek M, Herrmann H, Dadlez M. J Biol Chem. 2016 Nov 25; 291(48): 24931-24950. doi: 10.1074/jbc.M116.748145.
  • Protein Composition of Catalytically Active U7-Dependent Processing Complexes Assembled on Histone Pre-MRNA Containing Biotin and a Photo-Cleavable Linker. Skrajna, A.; Yang, X.; Dadlez, M.; Marzluff, W. F.; Dominski, Z. Nucleic Acids Research 2018, 46 (9), 4752–4770.
  • Global analysis of S-nitrosylation sites in the wild type (APP) transgenic mouse brain-clues for synaptic pathology. Zaręba-Kozioł M, Szwajda A, Dadlez M, Wysłouch-Cieszyńska A, Lalowski M. Mol Cell Proteomics. 2014 Sep;13(9):2288-305. doi: 10.1074/mcp.M113.036079.
  • Molecular basis for inner kinetochore configuration through RWD-domain interactions. Florian Schmitzberger, Magdalena M. Richter, Yuliya Gordiyenko, Carol V. Robinson, Michał Dadlez, and Stefan Westermann (2017) EMBO J. 2017 Dec 1; 36(23): 3458-3482. doi: 10.15252/embj.201796636.


  • Harald Herrmann, German Cancer Research Center (DKFZ), Universitätsklinikum Erlangen, Institute of Neuropathology.
  • David Glover, California Institute of Technology,
  • Zbigniew Domiński, William Marzluff, North Carolina University.
  • Michał Hetman, Louisville University.
  • Marcin Przewłoka, Southhampton University.
  • Frank Sobott, Leeds University.
  • Aleksander Edelman, Necker Institute.
  • Boris Negrutskii, Institute of Molecular Biology and Genetics, NAS of Ukraine.
  • Paolo d’Avino, University of Cambridge.
  • Zoltan Lipinszki, Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Szeged, web:
  • Sasa Kazazic, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb.
  • Andrzej Ożyhar, Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology.
  • Marc Baumann, Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki.
  • Matthias Bochtler, International Institute of Molecular and Cell Biology, Warsaw.
  • Sylwia Rodziewicz-Motowidło, University of Gdańsk
  • Kasper Rand, Department of Pharmacy, University of Copenhagen.
  • Artur Krężel, Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław.
  • Florian Schmitzberger, Research Institute of Molecular Pathology (IMP), Vienna, Ichnos Sciences.
  • Chris Borchers, Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal.
  • Ruth Chicquet-Ehrisman, University of Basel.
  • Anna Niedźwiecka, Institute of Physics, Polish Academy of Sciences.
  • Katarzyna Koziak, Centre for Preclinical Research and Technology, Department of Immunology, Biochemistry and Nutrition, Medical University of Warsaw
  • prof Hanna i Jerzy Radeccy, Institute of Animal Reproduction and Food Research Polish Academy of Science, Tuwima 10, 10-748 Olsztyn, Poland.
  • Tomasz Bednarczuk, Department of Internal Medicine and Endocrinology, Medical University of Warsaw, Poland.
  • Dr Maciej Lalowski, Biomedicum Helsinki, Institute of Biomedicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Unit, University of Helsinki, Finland
  • Magdalena Kowalewska – Maria Sklodowska-Curie Institute Oncology Center,
  • Grzegorz Wojtas (MD) – Mazovian Center of Pulmonary Disease and Tuberculosis Treatment,
  • Katarzyna Wertheim-Tysarowska (MD) – Institute of Mother and Child,
  • Mark Basik (MD) – Jewish General Hospital, McGill, Canada.
  • Katarzyna Pawlak

Nagrody i wyróżnienia

  • Michał Dadlez – awards for a publication as a co-author: Parnas award 2001, Ministry of Health award 2007, 2008, Polish Internal Medicine Society award 2014, 2015, Warsaw University Rector, 2017


RANGONE H., WEGEL E., GATT M.K., YEUNG E., FLOWERS A., DĘBSKI J., DADLEZ M., JANSSENS V., CARPENTER A.T.C., GLOVER D.M., Suppression of scant identifies endos as a substrate of greatwall kinase and a negative regulator of protein phosphatase 2A in mitosis. PLoS Genetics (2011) 7(8): e1002225 IF 9.543
WINIARSKA B., DVORNYK A., DĘBSKI J., GRZELAK K., BYSTRANOWSKA D., ZALEWSKA M., DADLEZ M., OŻYHAR A., KOCHMAN M., N-linked glycosylation of G. mellonella juvenile hormone binding protein — comparison of recombinant mutants expressed in P. pastoris cells with native protein. Biochimica et Biophysica Acta - Proteins & Proteomics (2011) 1814(5): 610-621 IF 2.773
MIKUŁA M., RUBEL T., KACZMARSKI J., GORYCA K., DADLEZ M., OSTROWSKI J., Integrating proteomic and transcriptomic high-throughput surveys for search of new biomarkers of colon tumors. Functional & Integrative Genomics (2011) 11: 215-224 IF 3.397
PRZEWŁOKA M.R., VENKEI Z., BOLANOS-GARCIA V.M., DĘBSKI J., DADLEZ M., GLOVER D.M., CENP-C is a structural platform for kinetochore assembly. Current Biology (2011) 21: 399-405 IF 10.025
KŁONIECKI M., JABŁONOWSKA A.M., POZNAŃSKI J., LANGRIDGE J., ,HUGHES CH., CAMPUZANO I., GILES K., DADLEZ M., Ion mobility separation coupled with MS detects two structural states of Alzheimer's disease Aβ1–40 peptide oligomers. Journal of Molecular Biology (2011) 407: 110-124 IF 4.008
MIKUŁA M., GAJ P., DZWONEK K., RUBEL T., KARCZMARSKI J., PAZIEWSKA A., DZWONEK A., BRAGOSZEWSKI P., DADLEZ M., OSTROWSKI J., Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. DNA Research (2010) 17: 245-260 IF 4,917
KĘDRACKA-KROK S., FIC E., JANKOWSKA U., JACIUK M., GRUCA P., PAPP M., KUSMIDER M., SOLICH J., DĘBSKI J., DADLEZ M., DZIEDZICKA-WASYLEWSKA M., Effect of chronic mild stress and imipramine on the proteome of the rat dentate gyrus. Journal of Neurochemistry (2010) 113: 848-859 IF 3,999
WAWER I., BUCHOLC M., ASTIER J., ANIELSKA-MAZUR A., DAHAN J., KULIK A., WYSŁOUCH-CIESZYŃSKA A., ZARĘBA-KOZIOŁ M., KRZYWIŃSKA E., DADLEZ M., DOBROWOLSKA G., WENDEHENNE D., Regulation of Nicotiana tabacum osmotic stress-activated protein kinase and its cellular partner GAPDH by nitric oxide in response to salinity. Biochemical Journal (2010) 429(1): 73-83 IF 5,155
KUPNIEWSKA-KOZAK A., GOSPODARSKA E., DADLEZ M., Interwined structured and unstructured regions of exRAGE identified by monitoring hydrogen-deuterium exchange. Journal of Molecular Biology (2010) 403(1): 52-65 IF 3,871
BROOKS M.A., GEWARTOWSKI K., MITSIKI E., LÉTOQUART J., PACHE R.A., BILLIER Y., BERTERO M., CORRÉA M., CZARNOCKI-CIECIURA M., DADLEZ M., HENRIOT V., LAZAR N., DELBOS L., LEBERT D., PIWOWARSKI J., ROCHAIX P., BŐTTCHER B., SERRANO L., SÉRAPHIN B., TILBEURGH van H., ALOY P., PERRAKIS A., DZIEMBOWSKI A., Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations. Structure (2010) 18: 1075-1082 IF 5,904
RÓZGA M., KŁONIECKI M., DADLEZ M., BAL W., A direct determination of the dissociation constant for the Cu(II) complex of amyloid β 1-40 peptide. Chemical Research in Toxicology (2010) 23: 336-340 IF 3,740
JAGUSZTYN-KRYNICKA E.K., DADLEZ M., GRABOWSKA A., ROSZCZENKO P., Proteomic technology in the design of new effective antibacterial vaccines. Expert Review of Proteomics (2009) 6(3) 315-330 IF 3,848
GAMBIN A., SZCZUREK E., DUTKOWSKI J., BAKUN M., DADLEZ M., Classification of peptide mass fingerprint data by novel no-regret boosting method. Computers in Biology and Medicine (2009) 39(5): 460-473 IF 1,272
TRUDEL S., KELLY M., FRITSCH J., NGUYEN-KHOA T., THEROND P., COUTURIER M., DADLEZ M., DĘBSKI J., TOUQUI L., VALLEE B., OLLERO M., EDELMAN A., BROUILLARD F., Peroxiredoxin 6 fails to limit phospholipid peroxidation in lung from Cftr-knockout mice subjected to oxidative challenge. PLoS ONE (2009) 4(6): e6075 (13 p./electronic only) IF 4,351
BAKUN M., KARCZMARSKI J., POZNAŃSKI J., RUBEL T., RÓZGA M., MALINOWSKA A., SANDS D., HENNIG E., OLĘDZKI J., OSTROWSKI J., DADLEZ M., An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study. Proteomics Clinical Applications (2009) 3(8): 932-946 IF 1,514
PETRAKIS S., MALINOWSKA A., DADLEZ M., SKLAVIADIS T., Identification of proteins co-purifying with scrapie infectivity. Journal of Proteomics (2009) 72(4): 690-694 IF 1,994
ARNAIZ O., MALINOWSKA A., KLOTZ C., SPERLING L., DADLEZ M., KOLL F., COHEN J., Cildb: a knowledgebase for centrosomes and cilia. Database (2009) 2009: bap022 (14 p./electronic only)
SIKORA J., TOWPIK J., GRACZYK D., KISTOWSKI M., RUBEL T., POZNAŃSKI J., LANGRIDGE J., ,HUGHES CH., DADLEZ M., BOGUTA M., Yeast prion [PSI+] lowers the levels of mitochondrial prohibitins. Biochimica et Biophysica Acta - Molecular Cell Research (2009) 1793: 1703-1709 IF 4,893
RÓZGA M., PROTAS A.M., JABŁONOWSKA A.M., DADLEZ M., BAL W., The Cu(II) complex of Aβ40 peptide in ammonium acetate solutions. Evidence for ternary species formation. Chemical Communications (2009): 1374-1376 IF 5,340
RUTKOWSKA-WŁODARCZYK I., STĘPIŃSKI J., DADLEZ M., DARZYNKIEWICZ E., STOLARSKI R., NIEDŹWIECKA A., Structural changes of eIF4E upon binding to the mRNA 5' monomethylguanosine and trimethylguanosine cap. Biochemistry (2008) 47: 2710-2720 IF 3,368


  • An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung Cancer Pleural Effusions. Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D. Proteomics Clin Appl. 2018 Mar;12(2). doi: 10.1002/prca.201700084. Multiplexed cytokeratin panel, method for preparing multiplexed cytokeratin panel and method for classification of lung cancer patient (Multipleksowy panel cytokeratynowy, sposób wytwarzania multipleksowego panelu cytokeratynowego i sposób klasyfikowania pacjentów z nowotworem płuc). Perzanowska A, Domanski D, Kistowski M, Michalak A, Wojtas G, Dadlez M. 2015. Patent nr P.414159 (UPRP).