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Proteomika i Spektrometria Mas

Core Facility

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Pracownia Proteomiki i Spektrometrii Mas

Pracownia Proteomiki i Spektrometrii Mas

Proteomics and Mass Spectrometry Core Facility provides proteomic services to the researchers from the Jagiellonian University and to external users from academia and industry.

Proteomics and Mass Spectrometry Core Facility provides proteomic services to the researchers from the Jagiellonian University and to external users from academia and industry. We apply state-of-the-art methods for analyzing peptides and proteins, including their post-translational modifications (PTMs). We perform complete proteomic workflow that includes sample preparation, mass spectrometry measurement and data analysis.

dr Urszula Jankowska

dr Urszula Jankowska

Core Facility Leader

Personal informations:


więcej o dr Urszula Jankowska

Dr Bożena Skupień-Rabian



Dr Olga Mucha

Part-time Technician


Q Exactive (Thermo Scientific)

Q Exactive (Thermo Scientific)

It is a hybrid mass spectrometer, which  combines high-performance quadrupole precursor selection with high-resolution, accurate-mass Orbitrap™ detection. Principally used for protein identification and quantification in complex samples (e.g. cell lysates), as well as identification of post-translational modifications.


micrOTOF-Q II (Bruker Daltonics)

micrOTOF-Q II (Bruker Daltonics)
It is used to measure molecular weight of intact proteins, peptides or nucleic acid fragments.


Proteomics and Mass Spectrometry Core Facility provides proteomic services to the researchers from the Jagiellonian University and to external users from academia and industry. We apply state-of-the-art methods for analyzing peptides and proteins, including their post-translational modifications (PTMs). We perform complete proteomic workflow that includes sample preparation, mass spectrometry measurement and data analysis. We also offer support in the conceptual design of experiments to apply the best strategy for each research question.

Figure 1. Scheme of the proteomic workflow and methodology available at the Proteomics and Mass Spectrometry CF. Among the variety of options, we recommend an optimal procedure fora given scientific question.




Proteomics is a comprehensive, large-scale analysis of the entire protein complement of a cell line, tissue, or organism. Mass spectrometry (MS) as a robust, sensitive and precise technique, enables the study of proteomes providing information on protein abundances, post-translational modifications  and protein-protein interaction networks. In shotgun proteomics, proteins are first digested with protease, and then the resulting peptides are separated by liquid chromatography and analyzed by MS. As a result, in a large-scale proteomic experiment, thousands of different proteins can be identified and quantified, which can be utilized to i.a. characterize two biological states, elucidate mechanisms of disease, detect diagnostic markers or drug targets.

MS is also a powerful tool to analyze single protein providing mass determination of intact molecule, confirmation of protein identification, characterization of PTMs, detection of potential truncations and mutations.

Services offered by the Proteomics and Mass Spectrometry Core Facility include:

•    Intact protein/peptide mass determination by ESI-MS 
Submission form (file: Form_1_Mass_determination.pdf)   

•    Protein identification from gel bands; characterization of post-translational modifications (PTMs) of single proteins
Submission form (file: Form_ ProteinID_gel.pdf)

•    Global proteome profiling – identification and/or relative quantification of proteins in complex mixtures 
Submission form (file: Form_Global_proteomics.pdf)

•    Protein-protein interaction (PPIs) analysis 
Submission form (file: Form_Interactome.pdf)

•    Targeted proteomic analysis – data acquisition for predefined sets of peptides using parallel reaction monitoring (PRM) method
Please contact us directly.

Terms of use

All users are required to acknowledge the Core Facility if any data obtained in the facility has been used in posters, papers, and all other publications.

Please, use the wording as follows:
We acknowledge Proteomics and Mass Spectrometry Core Facility of the Malopolska Centre of Biotechnology, Jagiellonian University for mass spectrometry analysis.

Apart from routine services, we also apply individual solutions to meet various research needs. Collaborative projects that require nonroutine sample preparation or extensive data analysis justifies a coauthorship on a manuscript that contains data generated in our facility.



Co-authorships :


Poplawski P, Alseekh S, Jankowska U, Skupien-Rabian B, Iwanicka-Nowicka R, Kossowska H, Fogtman A, Rybicka B, Bogusławska J, Adamiok-Ostrowska A, Hanusek K, Hanusek J, Koblowska M, Fernie AR, Piekiełko-Witkowska A. Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell Int. 2023 Jan 5;23(1):2. doi: 10.1186/s12935-022-02845-y. 

Surman M, Jankowska U, Wilczak M, Przybyło M. Similarities and Differences in the Protein Composition of Cutaneous Melanoma Cells and Their Exosomes Identified by Mass Spectrometry. Cancers (Basel). 2023 Feb 8;15(4):1097. doi: 10.3390/cancers15041097


Ravichandran KE, Kaduhr L, Skupien-Rabian B, Shvetsova E, Sokołowski M, Krutyhołowa RC, Kwasna D, Brachmann C, Lin S, Guzman Perez S, Wilk P, Kösters M, Grudnik P, Jankowska U, Leidel SA, Schaffrath R, Glatt S. E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to cysteine persulfidation. EMBO J. 2022 Oct 17;41(20):e111318. doi: 10.15252/embj.2022111318
Rząca C, Jankowska U, Stępień EŁ. Proteomic profiling of exosomes derived from pancreatic beta-cells cultured under hyperglycemia. Bio-Algorithms and Med-Systems 2022  Dec  19; 18(1):151-157. doi: 10.2478/bioal-2022-0085
Kubiak-Szymendera M, Skupien-Rabian B, Jankowska U, Celińska E. Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica-molecular background revealed by quantitative proteomics. Appl Microbiol Biotechnol. 2022 Jan;106(1):349-367. doi: 10.1007/s00253-021-11731-y
Ibáñez A, Skupien-Rabian B, Jankowska U, Kędracka-Krok S, Zając B, Pabijan M. Functional Protein Composition in Femoral Glands of Sand Lizards (Lacerta agilis). Molecules. 2022 Apr 6;27(7):2371. doi: 10.3390/molecules2707237
Surman M, Kędracka-Krok S, Wilczak M, Rybczyński P, Jankowska U, Przybyło M. Comparative Proteomic Profiling of Ectosomes Derived from Thyroid Carcinoma and Normal Thyroid Cells Uncovers Multiple Proteins with Functional Implications in Cancer. Cells. 2022 Mar 31;11(7):1184. doi: 10.3390/cells11071184


Pinski A, Betekhtin A, Skupien-Rabian B, Jankowska U, Jamet E, Hasterok R. Changes in the Cell Wall Proteome of Leaves in Response to High Temperature Stress in Brachypodium distachyon. Int J Mol Sci. 2021 Jun 23;22(13):6750. doi: 10.3390/ijms22136750
Smejda M, Kądziołka D, Radczuk N, Krutyhołowa R, Chramiec-Głąbik A, Kędracka-Krok S, Jankowska U, Biela A, Glatt S. Same but different - Molecular comparison of human KTI12 and PSTK. Biochim Biophys Acta Mol Cell Res. 2021 Apr;1868(4):118945. doi: 10.1016/j.bbamcr.2020.118945
Zacchini F, Heber MF, Arena R, Radczuk N, Jankowska U, Ptak GE. Perturbations of the hepatic proteome behind the onset of metabolic disorders in mouse offspring developed following embryo manipulation. Theriogenology. 2021 Sep 1;171:119-129. doi: 10.1016/j.theriogenology.2021.05.022
Surman M, Kędracka-Krok S, Jankowska U, Drożdż A, Stępień E, Przybyło M. Proteomic Profiling of Ectosomes Derived from Paired Urothelial Bladder Cancer and Normal Cells Reveals the Presence of Biologically-Relevant Molecules. Int J Mol Sci. 2021 Jun 24;22(13):6816. doi: 10.3390/ijms22136816
Jankowska U, Skupien-Rabian B, Swiderska B, Prus G, Dziedzicka-Wasylewska M, Kedracka-Krok S. Proteome Analysis of PC12 Cells Reveals Alterations in Translation Regulation and Actin Signaling Induced by Clozapine. Neurochem Res. 2021 Aug;46(8):2097-2111. doi: 10.1007/s11064-021-03348-4


Pabis M, Termathe M, Ravichandran KE, Kienast SD, Krutyhołowa R, Sokołowski M, Jankowska U, Grudnik P, Leidel SA, Glatt S. Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation. EMBO J. 2020 Oct 1;39(19):e105087. doi: 10.15252/embj.2020105087


Publications with Core Facility support:


Kulig K, Kowalik K, Surowiec M, Karnas E, Barczyk-Woznicka O, Zuba-Surma E, Pyza E, Kozik A, Rapala-Kozik M, Karkowska-Kuleta J. Isolation and Characteristics of Extracellular Vesicles Produced by Probiotics: Yeast Saccharomyces boulardii CNCM I-745 and Bacterium Streptococcus salivarius K12. Probiotics Antimicrob Proteins. 2023 May 20. doi: 10.1007/s12602-023-10085-3
Grygier P, Pustelny K, Nowak J, Golik P, Popowicz GM, Plettenburg O, Dubin G, Menezes F, Czarna A. Silmitasertib (CX-4945), a Clinically Used CK2-Kinase Inhibitor with Additional Effects on GSK3β and DYRK1A Kinases: A Structural Perspective. J Med Chem. 2023 Mar 23;66(6):4009-4024. doi: 10.1021/acs.jmedchem.2c01887
Sarewicz M, Szwalec M, Pintscher S, Indyka P, Rawski M, Pietras R, Mielecki B, Koziej Ł, Jaciuk M, Glatt S, Osyczka A. High-resolution cryo-EM structures of plant cytochrome b6f at work. Sci Adv. 2023 Jan 13;9(2):eadd9688. doi: 10.1126/sciadv.add9688
Fic E, Cieślik A, Figiel M, Dziedzicka-Wasylewska M. Identification of mitogen-activated protein kinase phosphatase-1 (MKP-1) protein partners using tandem affinity purification and mass spectrometry. Pharmacol Rep. 2023 Apr;75(2):474-481. doi: 10.1007/s43440-023-00471-7
Śmiałek-Bartyzel J, Bzowska M, Mężyk-Kopeć R, Kwissa M, Mak P. BacSp222 bacteriocin as a novel ligand for TLR2/TLR6 heterodimer. Inflamm Res. 2023 Mar 25. doi: 10.1007/s00011-023-01721-3
Mazur P, Dumnicka P, Tisończyk J, Ząbek-Adamska A, Drożdż R. SDS Electrophoresis on Gradient Polyacrylamide Gels as a Semiquantitative Tool for the Evaluation of Proteinuria. Diagnostics (Basel). 2023 Apr 23;13(9):1513. doi: 10.3390/diagnostics13091513


Lin TY, Smigiel R, Kuzniewska B, Chmielewska JJ, Kosińska J, Biela M, Biela A, Kościelniak A, Dobosz D, Laczmanska I, Chramiec-Głąbik A, Jeżowski J, Nowak J, Gos M, Rzonca-Niewczas S, Dziembowska M, Ploski R, Glatt S. Destabilization of mutated human PUS3 protein causes intellectual disability. Hum Mutat. 2022 Dec;43(12):2063-2078. doi: 10.1002/humu.24471
Kulig K, Karnas E, Woznicka O, Kuleta P, Zuba-Surma E, Pyza E, Osyczka A, Kozik A, Rapala-Kozik M, Karkowska-Kuleta J. Insight Into the Properties and Immunoregulatory Effect of Extracellular Vesicles Produced by Candida glabrata, Candida parapsilosis, and Candida tropicalis Biofilms. Front Cell Infect Microbiol. 2022 Jun 6;12:879237. doi: 10.3389/fcimb.2022.879237
Śmiałek J, Bzowska M, Hinz A, Mężyk-Kopeć R, Sołtys K, Mak P. Bacteriocin BacSp222 and Its Succinylated Forms Exhibit Proinflammatory Activities Toward Innate Immune Cells . J Inflamm Res. 2022 Aug 12;15:4601-4621. doi: 10.2147/JIR.S362066
(PREPRINT) Matsuda A, Plewka J, Chykunova Y, Jones AN, Pachota M, Rawski M,  Mourão A, Karim A, Kresik L, Lis K, Minia I, Hartman K, Sonani R, Schlauderer F, Dubin G, Sattler M, Suder P, Popowicz G, Pyrć K, Czarna A; Despite the odds: formation of the SARS-CoV-2 methylation complex; bioRxiv 2022.01.25.477673;


Kumar M , Markiewicz-Mizera J , Janna Olmos JD , Wilk P , Grudnik P , Biela AP , Jemioła-Rzemińska M , Górecki A , Chakraborti S , Heddle JG . A single residue can modulate nanocage assembly in salt dependent ferritin. Nanoscale. 2021 Jul 15;13(27):11932-11942. doi: 10.1039/d1nr01632f

We currently have no vacancies.

Proteomics and Mass Spectrometry Core Facility
Malopolska Centre of Biotechnology
Room: MCB 1/40
Phone: +48 12 664 6096
Gronostajowa 7A
30-387 Kraków