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Characterization of Biomolecules by Mass Spectrometry

English title Characterization of Biomolecules by Mass Spectrometry
Applicant Dengjel Jörn
Number 177088
Funding scheme R'EQUIP
Research institution Département de Biologie Faculté des Sciences Université de Fribourg
Institution of higher education University of Fribourg - FR
Main discipline Biochemistry
Start/End 01.01.2018 - 31.12.2018
Approved amount 442'287.00
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Keywords (4)

proteomics; mass spectrometry; metabolomics; liquid chromatography

Lay Summary (German)

Lead
Januar 2017 wurde die Metabolomics/Proteomics Platform (MAPP) des Departments für Biologie, Universität Fribourg ins Leben gerufen (https://www.unifr.ch/go/mapp), um dem Campus Fribourg lokalen Zugang zu erstklassischer Metabolit/Protein Analytik zu ermöglichen. MAPP offeriert massenspektrometrische Analysen, um die quantitative Zusammensetzung des Proteoms zu untersuchen, Proteininteraktionen und Modifikationen zu charakterisieren, und Lipide und lipophile Metaboliten zu studieren. Der R`Equip Antrag unterstützt MAPP bei der Anschaffung eines high-end Flüssigkeitschromatographie-Massenspektromters, das für den Forschungsstandort Fribourg von essentieller Bedeutung ist.
Lay summary

Januar 2017 wurde die Metabolomics/Proteomics Platform (MAPP) des Departments für Biologie, Universität Fribourg ins Leben gerufen (https://www.unifr.ch/go/mapp), um dem Campus Fribourg lokalen Zugang zu erstklassischer Metabolit/Protein Analytik zu ermöglichen. MAPP offeriert massenspektrometrische Analysen, um die quantitative Zusammensetzung des Proteoms zu untersuchen, Proteininteraktionen und Modifikationen zu charakterisieren, und Lipide und lipophile Metaboliten zu studieren. Der R`Equip Antrag unterstützt MAPP bei der Anschaffung eines high-end Flüssigkeitschromatographie-Massenspektromters, das für den Forschungsstandort Fribourg von essentieller Bedeutung ist.

Direct link to Lay Summary Last update: 21.11.2017

Responsible applicant and co-applicants

Publications

Publication
Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control
Dokládal Ladislav, Stumpe Michael, Pillet Benjamin, Hu Zehan, Garcia Osuna Guillermo Miguel, Kressler Dieter, Dengjel Jörn, De Virgilio Claudio (2021), Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control, in Molecular Cell, 81(9), 1879-1889.e6.
The APMAP interactome reveals new modulators of APP processing and beta-amyloid production that are altered in Alzheimer’s disease
Gerber Hermeto, Mosser Sebastien, Boury-Jamot Benjamin, Stumpe Michael, Piersigilli Alessandra, Goepfert Christine, Dengjel Joern, Albrecht Urs, Magara Fulvio, Fraering Patrick C. (2019), The APMAP interactome reveals new modulators of APP processing and beta-amyloid production that are altered in Alzheimer’s disease, in Acta Neuropathologica Communications, 7(1), 13-13.
Ciliary neurotrophic factor stimulates cardioprotection and the proliferative activity in the adult zebrafish heart
Bise Thomas, de Preux Charles Anne-Sophie, Jaźwińska Anna (2019), Ciliary neurotrophic factor stimulates cardioprotection and the proliferative activity in the adult zebrafish heart, in npj Regenerative Medicine, 4(1), 2-2.
Cyclin-dependent kinase 5 (CDK5) regulates the circadian clock
Brenna Andrea, Olejniczak Iwona, Chavan Rohit, Ripperger Jürgen A, Langmesser Sonja, Cameroni Elisabetta, Hu Zehan, De Virgilio Claudio, Dengjel Jörn, Albrecht Urs (2019), Cyclin-dependent kinase 5 (CDK5) regulates the circadian clock, in eLife, 8, e50925.
Phosphorylation of mitochondrial matrix proteins regulates their selective mitophagic degradation
Kolitsida Panagiota, Zhou Jianwen, Rackiewicz Michal, Nolic Vladimir, Dengjel Jörn, Abeliovich Hagai (2019), Phosphorylation of mitochondrial matrix proteins regulates their selective mitophagic degradation, in Proceedings of the National Academy of Sciences, 116(41), 20517-20527.
Retromer and TBC1D5 maintain late endosomal RAB7 domains to enable amino acid–induced mTORC1 signaling
Kvainickas Arunas, Nägele Heike, Qi Wenjing, Dokládal Ladislav, Jimenez-Orgaz Ana, Stehl Luca, Gangurde Dipak, Zhao Qian, Hu Zehan, Dengjel Jörn, De Virgilio Claudio, Baumeister Ralf, Steinberg Florian (2019), Retromer and TBC1D5 maintain late endosomal RAB7 domains to enable amino acid–induced mTORC1 signaling, in Journal of Cell Biology, 218(9), 3019-3038.
Alternate Day Fasting Improves Physiological and Molecular Markers of Aging in Healthy, Non-obese Humans
Stekovic Slaven, Hofer Sebastian J., Tripolt Norbert, Aon Miguel A., Royer Philipp, Pein Lukas, Stadler Julia T., Pendl Tobias, Prietl Barbara, Url Jasmin, Schroeder Sabrina, Tadic Jelena, Eisenberg Tobias, Magnes Christoph, Stumpe Michael, Zuegner Elmar, Bordag Natalie, Riedl Regina, Schmidt Albrecht, Kolesnik Ewald, Verheyen Nicolas, Springer Anna, Madl Tobias, Sinner Frank, et al. (2019), Alternate Day Fasting Improves Physiological and Molecular Markers of Aging in Healthy, Non-obese Humans, in Cell Metabolism, 30(3), 462-476.e6.
Multilayered Control of Protein Turnover by TORC1 and Atg1
Hu Zehan, Raucci Serena, Jaquenoud Malika, Hatakeyama Riko, Stumpe Michael, Rohr Rudolf, Reggiori Fulvio, De Virgilio Claudio, Dengjel Jörn (2019), Multilayered Control of Protein Turnover by TORC1 and Atg1, in Cell Reports, 28(13), 3486-3496.e6.
AutophagyMethods and Protocols
Kaeser-Pebernard Stéphanie, Diedrich Britta, Dengjel Jörn (2019), AutophagyMethods and Protocols, Springer New York, New York, NY.
Spatially Distinct Pools of TORC1 Balance Protein Homeostasis
Hatakeyama Riko, Péli-Gulli Marie-Pierre, Hu Zehan, Jaquenoud Malika, Garcia Osuna Guillermo Miguel, Sardu Alessandro, Dengjel Jörn, De Virgilio Claudio (2018), Spatially Distinct Pools of TORC1 Balance Protein Homeostasis, in Molecular Cell, 325.
Beyond Global Charge: Role of Amine Bulkiness and Protein Fingerprint on Nanoparticle-Cell Interaction
Burnand David, Milosevic Ana, Balog Sandor, Spuch-Calvar Miguel, Rothen-Rutishauser Barbara, Dengjel Jörn, Kinnear Calum, Moore Thomas L., Petri-Fink Alke (2018), Beyond Global Charge: Role of Amine Bulkiness and Protein Fingerprint on Nanoparticle-Cell Interaction, in Small, 14(46), 1802088-1802088.
Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins
Becker Andrea C., Gannagé Monique, Giese Sebastian, Hu Zehan, Abou-Eid Shadi, Roubaty Carole, Paul Petra, Bühler Lea, Gretzmeier Christine, Dumit Veronica I., Kaeser-Pebernard Stéphanie, Schwemmle Martin, Münz Christian, Dengjel Jörn (2018), Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins, in Molecular & Cellular Proteomics, 17(10), 1909-1921.
Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome
Hiebert Paul, Wietecha Mateusz S., Cangkrama Michael, Haertel Eric, Mavrogonatou Eleni, Stumpe Michael, Steenbock Heiko, Grossi Serena, Beer Hans-Dietmar, Angel Peter, Brinckmann Jürgen, Kletsas Dimitris, Dengjel Jörn, Werner Sabine (2018), Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome, in Developmental Cell, 46(2), 145-161.e10.

Datasets

Influenza A virus induced proteome changes

Author Dengjel, Jörn
Publication date 12.07.2018
Persistent Identifier (PID) Project PXD009924
Repository PRIDE DB


Multilayered control of protein turnover by TORC1 and ATG1

Author Dengjel, Joern
Persistent Identifier (PID) PXD013271
Repository PRIDE DB


Cyclin dependent kinase 5 (CDK5) regulates the circadian clock

Author Dengjel, Joern
Persistent Identifier (PID) PXD012068
Repository PRIDE DB


NRF2-dependent ECM

Author Dengjel, Joern
Persistent Identifier (PID) PXD007999
Repository PRIDE DB


Influenza A virus induces autophagosomal targeting of ribosomal proteins

Author Dengjel, Joern
Persistent Identifier (PID) PXD007809
Repository PRIDE DB


Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
REPP-SO Winter Meeting Talk given at a conference Phosphoproteomics Update 14.01.2021 Lausanne - online, Switzerland Dengjel Jörn;


Self-organised

Title Date Place
REPP-SO Winter Meeting 23.01.2020 Fribourg, Switzerland
REPP-SO Winter Meeting 17.01.2019 Fribourg, Switzerland

Associated projects

Number Title Start Funding scheme
169732 Establishment and functioning of arbuscular mycorrhizal symbiosis 01.10.2016 Project funding (Div. I-III)
173003 Lipid Storage, Binding, and Export 01.12.2017 Project funding (Div. I-III)
184781 Stimulus- and time-dependent protein dynamics in autophagy analyzed by quantitative mass spectrometry 01.04.2019 Project funding (Div. I-III)
156346 Translational neuropeptidomics of major depressive disorder 01.12.2015 China
152777 Coordination Compounds: From Basics towards Applications in Materials and Medicine 01.04.2014 Project funding (Div. I-III)
166474 Amino acid signaling and growth control in yeast 01.08.2016 Project funding (Div. I-III)
184433 Functional characterisation of dynamic BRAF signalling complexes and their modulation by tumour specific mutations and clinically relevant kinase inhibitors 01.06.2019 Project funding (Div. I-III)
166482 Stimulus and time-dependent protein dynamics in autophagy analyzed by quantitative mass spectrometry 01.04.2016 Project funding (Div. I-III)

Abstract

January 2017 the joined Metabolomics/Proteomics Platform (MAPP) of the Department of Biology, University of Fribourg was officially launched (https://www.unifr.ch/go/mapp). The aim of MAPP is to provide all research groups of the University of Fribourg and the associated NCCR Bio-Inspired Materials with mass spectrometry (MS) expertise. So far, the offered services include quantitative expression proteomics analyses, analyses of protein-protein interactions by affinity-purification (AP)-MS, characterization of posttranslational modifications (PTMs) including phosphorylation and ubiquitination, and the analysis of lipids and lipophilic metabolites. Currently MAPP is equipped with two liquid chromatography (LC)-MS/MS systems, of which one, a 12 year old LTQ-Orbitap Classic, is outdated and only used for method development. Thus, almost the entire workload is handled by one Q-Exactive Plus system, which creates a serious bottleneck in sample throughput and causes increasingly long waiting times. We apply for a new generation Thermo Scientific Q-Exactive HF system offering enhanced resolution and sequencing speed. We exemplify with eight diverse research projects that this state-of-the-art system is essential for the future functioning of MAPP and for the entire natural science community in Fribourg:Project 1 characterizes ubiquitination-dependent signaling events in stress-induced autophagy employing human cell culture systems. Autophagy is an essential cellular turnover path-way often deregulated in human diseases such as cancer and neurodegeneration. Project 2 studies phosphorylation-dependent signaling events regulating cell growth. Using yeast Saccharomyces cerevisiae as model the TORC1 signaling network is analyzed mechanistically. In Project 3 we employ crosslinking MS to study the topology of membrane proteins and how it changes upon movement from the lipid bilayer of the endoplasmic reticulum onto the putative monolayer membrane of lipid droplets. Project 4 deals with the role of the transcription factor Creb (cAMP-response-element binding protein) in long-term memory formation using Drosophila melanogaster as model system. In Project 5 top-down MS is applied to study the regulation of small molecular neurotransmitters, neuropeptides and proteins in animal models of major depression disorder. Project 6 characterizes organelles and protein-protein interactions important in arbuscular mycorrhizal symbiosis in the model plant Petunia hybrid. In Project 7 we investigate the antimicrobial effects of silver ions and silver nanoparticles and how the gram-negative bacterium Geobacter sulfurreducens copes with it. Project 8 aims at characterizing the cellular uptake of newly developed nanoparticles and their interaction with serum and cellular proteins. Thus, with these projects we cover the major research areas in Fribourg having need for a state-of-the-art LC-MS/MS system and highlight the importance of MAPP for the research location Fribourg.
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