Facilities

Michał Dadlez, PhD, DSc, Prof.

Mass Spectrometry Facility

Homepage: http://mslab-ibb.pl

Service and research scope

Our facility performs biologically and medically oriented mass-spectrometry analyses. Our main services include quantitative and qualitative proteomic approaches, PTM analysis, and the targeted quantification of protein panels. The metabolomic division of our facility allows small-molecule quantification, with a special focus on drugs and their metabolites. Mass spectrometric approaches to protein structure characterization are offered, including hydrogen-deuterium exchange, X-linking, native mass spectrometry, and ion mobility.

Contact persons

Agnieszka Fabijańska (MSc), email: agafab@ibb.waw.pl, Tel.: +48 22 592 34 71 – proteomics
Emilia Samborowska (MSc), email: emi.sambor@gmail.com, Tel.: +48 592 34 73 – metabolomics

Service

Service Description

The Mass Spectrometry Facility is engaged in a wide array of proteomic, metabolomic, and structural studies. In addition to conducting our own research, the mission of the facility is to provide access to advanced mass spectrometry platforms for biomedical laboratories at both the national and international levels. Many years of experience allow us to actively support scientific collaborators at every stage of their projects, from designing experiments and method development to data analysis and publishing.

Global and targeted proteomics. Proteomic services include protein mass determination, protein identification from gel or solution, qualitative and semi-quantitative characteristics of the protein interactome, and the characterization and mapping of a wide spectrum of posttranslational modifications. Our facility also offers several proteomic relative quantification strategies, including label-free analysis and stable isotope labeling, both in vivo and in vitro, using a variety of labeling tags. Recently, the data-independent acquisition (DIA) analysis has been added to the spectrum of our offered methods, which enables protein quantification in complex samples in a more accurate manner than the aforementioned data-dependent techniques. To confirm differential proteins that are revealed by the above techniques and develop protein diagnostic panels, targeted proteomics methods based on multiple reaction monitoring/parallel reaction monitoring  (MRM/PRM) data acquisition protocols are applied.

We use a wide range of sample preparation protocols, which are adapted to the requirements of analytical methods, sample composition, and planned volume of the project. The laboratory has a comprehensive informatic infrastructure that allows the effective analytical and bioinformatic processing of a large number of samples in a short time. In-house LIMS software on the Mass Spectrometry Facility website secures sample information flow and clients’ access for placing orders, discussions with laboratory personnel, and results transfer. This solution ensures equal access to laboratory services. Currently, the proteomic facility operates nanoAcquity UPLC Waters liquid chromatographs connected to Waters Q-TOF Premier, Thermo Orbitrap Elite, three Thermo Orbitrap Velos, Waters Xevo TQ, and two Thermo QExactive spectrometers. The facility is equipped with other peripheral devices that allow the homogenization and sonication of samples and lyophilization and fractionation of peptides before liquid chromatography-mass spectrometry separations. Depending on the type of analysis, proteomic data are processed using commercial software (Mascot, Scaffold, Spectronaut, Ingenuity Pathway Analysis), non-commercial software (MaxQuant, Perseus, Skyline), and in-house software (MScan, MSparky, Diffprot). In December 2020, the latest-generation Thermo Exploris 480 spectrometer with equipped with ion mobility module and an Evosep One sample separation system will be installed in the laboratory. This purchase will increase the throughput of analyses and further extend the range of our proteomics services.

Metabolomics. Metabolomic and pharmacokinetic studies are performed by the Laboratory of Quantitative Analysis of Drugs and Metabolites (registration no. 3089, National Chamber of Laboratory Diagnosticians), which is part of the Mass Spectrometry Facility.

As a diagnostic laboratory, we provide drug monitoring services for medications with a narrow therapeutic index. The mass spectrometry-based methods of therapeutic drug monitoring generally have better quantitative precision than immunoassays at a comparable cost. Both types of analytical systems (Waters Xevo TQ-S and Waters Xevo TQ-MS) are paired. Therefore, the facility is always ready for analysis and can ensure the continuity of services that are required in day-to-day clinical practice.

As a contract pharmacokinetic laboratory, we offer the development of analytical procedures for newly synthesized compounds. The laboratory offers quantitative measurements for a broad range of molecules and optimized protocols for sample preparation and liquid chromatography-mass spectrometry analysis. The wide range of additional equipment allows us to work with various types of analytical matrices. We offer flexible experiment designs and short development times.

Structural proteomics. The laboratory, as one of the few in Europe, offers mass spectrometry-based methods for providing structural information on biomolecules, mainly proteins. Mass spectrometry-based methods in recent years became an important companion to classic methods, such as X-ray, nuclear magnetic resonance, and cryo-electron microscopy, in the case of molecular assemblies that are intractable using classic approaches. For protein structure analysis, several mass spectrometry-based methods are used, including the monitoring of hydrogen-deuterium exchange, cross-linking, mass measurements of non-covalent complexes, and ion mobility measurements. We have two systems that are solely dedicated to structural analyses: Waters Synapt MS spectrometer coupled with Waters nanoAcquity or Acquity UPLC with an HDX module and Waters Synapt HDMS spectrometer with optional ETD fragmentation, additionally equipped with an ion mobility adapter that allows the separation of isobaric particles. Structural data analysis is conducted using HDexaminer and DynamX, supported by in-house HaDex exchange data handling software. Because of the complex nature of the research, the structural facility mostly focuses on long-term cooperation with other laboratories.

Equipment

  • Thermo Orbitrap Elite coupled with Waters nanoAcquity UPLC.
  • 2 ´ Thermo Q Exactive coupled with Waters nanoAcquity UPLC.
  • 3 ´ Thermo Orbitrap Velos coupled with Waters nanoAcquity UPLC.
  • Waters SYNAPT HDMS coupled with Waters HDX/LC module.
  • Waters SYNAPT MS coupled with Waters HDX/LC module.
  • Waters nanoAcquity UPLC with TRIZAIC technology.
  • WatersXevo TQ-MS coupled with Waters nanoAcquity UPLC.
  • Waters Xevo TQ-S coupled with Waters Acquity UPLC equipped with high-volume automated sample organizer.
  • Waters Xevo TQ-S coupled with Waters Acquity UPLC I-Class 2D in-house modified to work as a multiplexing liquid chromatograph.
  • Bruker ultrafleXtreme MALDI-TOF/TOF.
  • Waters Q-TOF Premier.
  • High-performance computing. This is a computing part of the Lumos cluster. It provides 96 physical dual-processor server nodes. Some of the nodes are a farm of GPU accelerators based on 24 NVidia Tesla cards and 24 Intel MIC cards. The virtualization environment is a part of the Lumos cluster. It Contains a pool of Citrix XEN, KVM Linux, and VMware servers. It comprises 100 powerful servers, mostly quad processors, hosting more than 50 virtual machines. The total theoretical performance of these servers is significantly above 100 gigaflops.
  • Mascot suite for protein identification and quantification. The Mascot Server (version 2.4.1, licensed for 300 CPU units), Mascot Daemon (version 2.4), and Mascot Distiller (version 2.6) have the following functionalities: library core functionality, library peptide mass fingerprint processing, library dual mass spectrometry processing, GUI core functionality, Mascot search toolbox, De novo toolbox, Quantitation toolbox, Mascot Daemon toolbox, and Developer toolbox.
  • Spectronaut software for DIA-type analysis. Scaffold software is used to visualize and validate complex dual mass spectrometry proteomics experiments. Skyline software is used for targeted proteomics. Whenever necessary, the Andromeda/MaxQuant suite is used for analyses of SILAC experiments and other mass spectrometry data.
  • An original software suite that was developed in collaboration with the Warsaw University of Technology (http://proteom.ibb.waw.pl/) is dedicated to mass spectrometry data analysis (MScan), label-free quantification (MSparky), and the statistical analysis of quantitative data (Diffprot).
  • HDexaminer Sierra Analytics – HDXMS analysis software. DynamX 3.0 data analysis software and ProteinLynx Global SERVER (PLGS) 2.5 software are used to analyze data from HDX structural experiments, supported by in-house HaDex exchange data handling software.
  • Precellys Evolution tissue homogenizer with a Precellys Cryolys cooling unit, produced by Bertin Instruments.
  • Thermo Exploris 480 mass spectrometer equipped with the FAIMS Pro module and Evosep One liquid chromatograph.

Collaborations

Customers

  • Domestic scientific institutions:

    • Centrum Medyczne Kształcenia Podyplomowego
    • Centrum Onkologii-Instytut im. Marii Skłodowskiej-Curie
    • Instytut Biologii Doświadczalnej PAN im. M. Nenckiego
    • Instytut Biologii Medycznej Polskiej Akademii Nauk
    • Instytut Biologii Molekularnej i Biotechnologii
    • Instytut Chemii i Techniki Jądrowej
    • Instytut Dendrologii Polskiej Akademii Nauk
    • Instytut Fizyki Polskiej Akademii Nauk
    • Instytut Genetyki Roślin Polskiej Akademii Nauk
    • Instytut Hematologii i Transfuzjologii
    • Instytut Immunologii i Terapii Doświadczalnej Polskiej Akademii Nauk
    • Instytut Medycyny Doświadczalnej i Klinicznej Polskiej Akademii Nauk
    • Instytut Parazytologii Polskiej Akademii Nauk
    • Instytut Rozrodu Zwierząt i Badań Żywności Polskiej Akademii Nauk
    • Międzynarodowy Instytut Biologii Molekularnej i Komórkowej
    • Państwowy Instytut Badawczy, Instytut Hodowli i Aklimatyzacji Roślin
    • Państwowy Instytut Badawczy, Instytut Ochrony Roślin
    • Państwowy Instytut Weterynaryjny – Państwowy Instytut Badawczy
    • Politechnika Gdańska
    • Politechnika Łódzka
    • Politechnika Warszawska
    • Politechnika Wrocławska
    • Szkoła Główna Gospodarstwa Wiejskiego w Warszawie WRiB, KFR
    • Uniwersytet Adama Mickiewicza w Poznaniu
    • Uniwersytet Gdański
    • Uniwersytet Jagielloński
    • Uniwersytet Łódzki
    • Uniwersytet Marii Curie-Skłodowskiej w Lublinie
    • Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu
    • Uniwersytet Medyczny w Gdańsku
    • Uniwersytet Medyczny we Wrocławiu
    • Uniwersytet Mikołaja Kopernika
    • Uniwersytet Przyrodniczy w Lublinie
    • Uniwersytet Przyrodniczy w Poznaniu
    • Uniwersytet Rolniczy w Krakowie
    • Uniwersytet Rzeszowski
    • Uniwersytet w Białymstoku
    • Uniwersytet Warmińsko-Mazurski w Olsztynie
    • Uniwersytet Warszawski
    • Uniwersytet Wrocławski
    • Warszawski Uniwersytet Medyczny
    • Wojskowy Instytut Higieny i Epidemiologii im. gen. K. Kaczkowskiego
    • Wojskowy Instytut Medyczny

  •  

  • Foreign scientific institutions:

    • Instituto Gulbenkian de Ciência
    • Centre CEA de Saclay
    • Charité Universitätsmedizin Berlin
    • University of Cambridge
    • Fatih University
    • Imperial College London
    • Institut Européen de Chimie et Biologie IECB
    • Instituto de Tecnologia Química e Biológica
    • JSC Biocentras
    • The University of Cardiff
    • University of Agriculture Faisalabad
    • University of Exeter
    • University of Helsinki
    • University of Oxford
    • University of Palermo
    • Vilnius University

  •  

  • Companies:

    • Novartis Poland
    • Sandoz
    • OncoArendi Therapeutics
    • Alcresta
    • Laboratoria Medyczne Synevo
    • DUO-MED Marzena Dominiak (Wrocław)
    • Uniwersytecki Szpital Kliniczny we Wrocławiu
    • Szpital Dzieciątka Jezus w Warszawie
    • Instytut Kardiologii im. Prymasa Tysiąclecia Stefana Kardynała Wyszyńskiego (Warszawa)

Research

Research Description

Mass spectrometry-based methods potentially find applications in a very large variety of biomedically oriented research projects because questions about proteome or metabolome levels can be asked in virtually all areas of biological research. The facility is enrolled in a multitude of interdisciplinary projects, mainly of a biomedical nature. A short list of our current research projects and projects with the laboratory partnerships exemplifies the wide range of research topics for which mass spectrometry-based analyses can be applied:

  • Proteomic analysis of the interaction of Zika virus proteins with nucleolar host cell proteins.
    NCN OPUS 15. PI: Michał Dadlez.
  • Application of novel diagnostic and therapeutical methods in epilepsy and neurodevelopmental abnormalities in children, based on the clinical and cellular model of mTOR dependent epilepsy. NCBiR STRATEGMED III. PI: Sergiusz Jóźwiak (the Mass Spectrometry Facility is part of the consortium).
  • Next-generation cancer diagnostics and therapy guidance of lung and breast cancer patients using mass spectrometry-based proteomics. FNP FIRST TEAM. PI: Dominik Domański.
  • Role of TBC1D5 phosphorylation in neurodevelopment and TSC-related cell pathology. NCN OPUS 14. PI: Jacek Jaworski (a Mass Spectrometry Facility member is one of the investigators).
  • Mass spectrometry of biopharmaceuticals: improved methodologies for qualitative, quantitative and structural characterization of drugs, proteinaceous drug targets and diagnostic molecules. TEAM TECH CORE FACILITY. PI: Michał Dadlez.

As a result of previous projects and in cooperation with other scientific and commercial laboratories, the facility has numerous publications (159 in 2015-2020) and six patent applications. Several experimental procedures and data analysis programs have been developed that are also available to external users. For metabolome studies, the laboratory offers the absolute quantification of molecules of interest using isotopically labeled standards and an MRM approach in various matrices, tissues homogenates, and biological fluids, from method design and optimization to large-series analyses, such as pharmacodynamic tests of new drug candidates. Procedures for clinically valid measurements of drugs and their metabolites have been developed and implemented and are currently performed for Polish healthcare units.

Selected Publications

    • Inhibition of Proteasome Rescues a Pathogenic Variant of Respiratory Chain Assembly Factor COA7. Mohanraj, K.; Wasilewski, M.; Benincá, C.; Cysewski, D.; Poznanski, J.; Sakowska, P.; Bugajska, Z.; Deckers, M.; Dennerlein, S.; Fernandez‐Vizarra, E.; Rehling, P.; Dadlez, M.; Zeviani, M.; Chacinska, A. EMBO Molecular Medicine 2019, 11 (5). https://doi.org/10.15252/emmm.201809561.
    • Dedicated Surveillance Mechanism Controls G-Quadruplex Forming Non-Coding RNAs in Human Mitochondria. Pietras, Z.; Wojcik, M. A.; Borowski, L. S.; Szewczyk, M.; Kulinski, T. M.; Cysewski, D.; Stepien, P. P.; Dziembowski, A.; Szczesny, R. J. Nature Communications 2018, 9 (1). https://doi.org/10.1038/s41467-018-05007-9.
    • 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. https://doi.org/10.1093/nar/gky133.
    • Molecular Basis for Inner Kinetochore Configuration through RWD Domain–Peptide Interactions. (2017) Schmitzberger, F.; Richter, M. M.; Gordiyenko, Y.; Robinson, C. V.; Dadlez, M.; Westermann, S. The EMBO Journal 2017, 36 (23), 3458–3482. https://doi.org/10.15252/embj.201796636.
    • Bobrowicz, M.; Dwojak, M.; Pyrzynska, B.; Stachura, J.; Muchowicz, A.; Berthel, E.; Dalla Venezia, N.; Kozikowski, M.; Siernicka, M.; Miazek, N.; Zapala, P.; Domagala, A.; Bojarczuk, K.; Malenda, A.; Barankiewicz, J.; Graczyk-Jarzynka, A.; Zagozdzon, A.; Gabrysiak, M.; Diaz, J.-J.; Karp, M.; Lech-Maranda, E.; Firczuk, M.; Giannopoulos, K.; Efremov, D. G.; Laurenti, L.; Baatout, D.; Frenzel, L.; Malinowska, A.; Slabicki, M.; Zenz, T.; Zerrouqi, A.; Golab, J.; Winiarska, M. HDAC6 Inhibition Up-Regulates CD20 Levels and Increases the Efficacy of Anti-CD20 Monoclonal Antibodies. Blood 2017, blood-2016-08-736066. https://doi.org/10.1182/blood-2016-08-736066.

Publications (IBB PAS affiliated)

HENNIG E., MIKUŁA M., RUBEL T., DADLEZ M., OSTROWSKI J., Comparative kinome analysis putative colon tumor biomarkers. Journal of Molecular Medicine - JMM (2012) 90 (4): 447-456 IF 4.668
KOWALCZYK J.E., KAWALEC M., BERESEWICZ M., DEBSKI J., DADLEZ M., ZABŁOCKA B., Protein kinase C beta in postischemic brain mitochondria. Mitochondrion (2012)12(2): 138-143 IF 3.615
THOUVEREY C., MALINOWSKA A., BALCERZAK M., STRZELECKA-KILISZEK A., BUCHET R., DADLEZ M., PIKULA S., Proteomic characterization of biogenesis and functions of matrix vesicles released from mineralizing human osteoblast-like cells. Journal of Proteomics (2011) 74(7): 1123-34 IF 5.074
ZAREMBA-CZOGALLA M., GAGAT P., KOZIOŁ K., DUBIŃSKA-MAGIERA M., SIKORA J., DADLEZ M., RZEPECKI R., Identification of new in vivo phosphosites on lamin Dm - the evidence of heterogeneity of phosphorylation sites in different Drosophila tissues. Nucleus (2011) 2(5): 478-488
GOSPODARSKA E., KUPNIEWSKA-KOZAK A., GOCH G., DADLEZ M., Binding studies of truncated variants of the Aβ peptide to the V-domain of the RAGE receptor reveal Aβ residues responsible for binding. Biochimica et Biophysica Acta - Proteins and Proteomics (2011) 1814: 592-609 IF 2.773
RANGONE H., WEGEL E., GATT M.K., YEUNG E., FLOWERS A., DEBSKI 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., DEBSKI J., GRZELAK A., BYSTRANOWSKA D., ZALEWSKA M., DADLEZ M., OZYHAR 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
PRZEWLOKA M.R., VENKEI Z., BOLANOS-GARCIA V.M., DEBSKI J., DADLEZ M., GLOVER D.M., CENP-C is a structural platform for kinetochore assembly. Current Biology (2011) 21: 399-405 IF 10.025
KLONIECKI M., JABLONOWSKA A.M., POZNANSKI 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., DEBSKI 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., WYSLOUCH-CIESZYNSKA 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
ROZGA M., KLONIECKI 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., DEBSKI 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., POZNANSKI J., RUBEL T., ROZGA M., MALINOWSKA A., SANDS D., HENNIG E., OLEDZKI 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

Team