Photo by Patrick Tomasso on Unsplash

Next Meeting Details

29.5.2024 – 4.30 pm CET

link to the meeting

Meeting ID: 668 1556 0107
Password: 628384

Who?

Speaker: Ter Kubatova (Uni Wien)

Paper: Kovács, I.A., Luck, K., Spirohn, K. et al. Network-based prediction of protein interactions. Nat Commun 10, 1240 (2019). https://doi.org/10.1038/s41467-019-09177-y

Where?

It is hosted through an online meeting system. We will use an recurring Zoom link (see above)

The APMA Journal Club is an official journal club in the Ph.D. program of the Medical University of Vienna, Technical University of Vienna, University of Vienna and University of Innsbruck . If you are there, you can book the course to get credits for it. One paper presentation and attendance for at least 50% of the meetings is required.

All can join the meeting through the link posted at the top of the page.

What?

The APMA Journal Club is a classical journal club where we will discuss one key paper from the fields of mass spectrometry, proteomics, metabolomics, and bioinformatics er week.

This Journal Club is held online. Therefore, everyone is invited to join.

Previous Meetings

22.05.2024

Speaker: Marlene Pühringer (Uni Wien)

Paper: Calabrese, V., Brunet, T.A., Degli-Esposti, D. et al. Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarumAnal Bioanal Chem 416, 2893–2911 (2024). https://doi.org/10.1007/s00216-024-05232-w

15.05.2024

Speaker: Raphael Pfleger (TU Wien)

Paper: Md Shadman Ridwan Abid, Eric C. Bredahl, Ashley D. Clifton, Haowen Qiu, Matthew T. Andrews, and James W. Checco,Proteomic Identification of Seasonally Expressed Proteins Contributing to Heart Function and the Avoidance of Skeletal Muscle Disuse Atrophy in a Hibernating Mammal, Journal of Proteome Research, 2024 23 (1), 215-225, DOI: 10.1021/acs.jproteome.3c00540

08.05.2024

Speaker: Stefanie Brandstetter (Uni Wien)

Paper: Şule Yılmaz, Florian Busch, Nagarjuna Nagaraj, and Jürgen Cox, Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx, Analytical Chemistry 2022 94 (3), 1608-1617, DOI: 10.1021/acs.analchem.1c03688

24.04.2024

Speaker: Martyna Asai (Uni Wien)

Paper: Gentry, E.C., Collins, S.L., Panitchpakdi, M. et al. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626, 419–426 (2024). https://www.nature.com/articles/s41586-023-06906-8

17.04.2024

Speaker: Sara Schlachter (Uni Wien)

Paper: Fröhlich K, Furrer R, Schori C, Handschin C, Schmidt A. Robust,. Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme. J Proteome Res. 2024 Mar 1;23(3):1028-1038. doi: 10.1021/acs.jproteome.3c00736

10.04.2024

Speaker: Maya Petek (University of Maribor, Slowenia)

Paper: Arribas Diez I, Govender I, Naicker P, Stoychev S, Jordaan J, Jensen ON. Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment. J Proteome Res. 2021 Jan 1;20(1):453-462. doi: 10.1021/acs.jproteome.0c00508 .

17.1.2024

Speaker: Anna Lena Mayr (Uni Wien)

Paper: Sundaram, T.S., Addis, M.F., Giromini, C. et al. Comprehensive proteomic analysis reveals omega-3 fatty acids to counteract endotoxin-stimulated metabolic dysregulation in porcine enterocytes. Sci Rep 13, 21595 (2023). https://doi.org/10.1038/s41598-023-48018-3

10.1.2024

Speaker: Christina Brenner (Uni Wien)

Paper: Fanzhou Kong, Uri Keshet, Tong Shen, Elys Rodriguez, and Oliver Fiehn, LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers, Analytical Chemistry 2023 95 (46), 16810-16818 , doi: 10.1021/acs.analchem.3c02263

20.12.2023

Speaker: Lukas Schmidt (MedUni Wien)

Paper: David M. Hollenstein, Margarita Maurer-Granofszky, Wolfgang Reiter, Dorothea Anrather, Thomas Gossenreiter, Riccardo Babic, Natascha Hartl, Claudine Kraft, Markus Hartl, Journal of Proteome Research, 2023 22 (10), 3383-339

https://doi.org/10.1021/acs.jproteome.3c00424

13.12.2023

Speaker: Tobias Kipura (Uni Innsbruck)

Paper: Adam L. Hollerbach, Yehia M. Ibrahim, Vanessa Meras, Randolph V. Norheim, Adam P. Huntley, Gordon A. Anderson, Thomas O. Metz, Robert G. Ewing, and Richard D. Smith, A Dual-Gated Structuresfor Lossless Ion Manipulations-IonMobility Orbitrap Mass Spectrometry Platformfor Combined Ultra-High-Resolution Molecular Analysis, Anal. Chem. 2023, 95, 25, 9531–9538, https://doi.org/10.1021/acs.analchem.3c00881

06.12.2023

Speaker: Beatriz Data Prieto (TU Vienna )

Paper: Bennett, H.M., Stephenson, W., Rose, C.M. et al. Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods20, 363–374 (2023). https://doi.org/10.1038/s41592-023-01791-5

29.11.2023

Speaker: Stefan Plott (University of Vienna )

Paper: Zhi-Fang Gao, Xiu Yang, Yingchang Mei, Jiao Zhang, Qing Chao, Bai-Chen Wang, A dynamic phosphoproteomic analysis provides insight into the C4 plant maize (Zea mays L.) response to natural diurnal changes, The plant journal 2023, 113, 2, 291–307, https://doi.org/10.1111/tpj.16047

22.11.2023

Speaker: Raphael Pfleger (TU Wien)

Paper: Yuka Li, Eisuke Kanao, Tomoyoshi Yamano, Yasushi Ishihama, and Koshi Imami, TurboID-EV: Proteomic Mapping of Recipient Cellular Proteins Proximal to Small Extracellular Vesicles. Anal. Chem. 2023, 95, 38, 14159–14164, https://doi.org/10.1021/acs.analchem.3c01015

15.11.2023

Speaker: Lena Fragner (Uni Vienna)

Paper: Anke P. Willems, Maria van der Ham, Birgit G. M. Schiebergen-Bronkhorst, Mirjam van Aalderen, Martina M. J. de Barse, Fini E. De Gruyter, Ilja N. van Hoek, Mia L. Pras-Raves, Monique G. M. de Sain-van der Velden, Hubertus C. M. T. Prinsen, Nanda M. Verhoeven-Duif and Judith J. M. Jans, A one-year pilot study comparing direct-infusion high resolution mass spectrometry based untargeted metabolomics to targeted diagnostic screening for inherited metabolic diseases. Frontiers in molecular biosciences 2023, 10, https://doi.org/10.3389/fmolb.2023.1283083

08.11.2023

Speaker: Viktoria Enkmann (Uni Vienna)

Paper: Laura S. Bailey, Fanran Huang, Tianqi Gao, Jinying Zhao, Kari B. Basso, and Zhongwu Guo, Characterization of Glycosphingolipids and Their Diverse Lipid Forms through Two-Stage Matching of LC-MS/MS Spectra, Analytical Chemistry 2021 93 (6), 3154-3162, https://doi.org/10.1021/acs.analchem.0c04542

25.10.2023

Speaker: Julian Preiner (Uni Vienna)

Paper: Tiffany R. Sanchez, Xin Hu, Jinying Zhao, ViLinh Tran, Nancy Loiacono, Young-Mi Go, Walter Goessler, Shelley Cole, Jason Umans, Dean P. Jones, Ana Navas-Acien, Karan Uppal, An atlas of metallome and metabolome interactions and associations with incident diabetes in the Strong Heart Family Study, Environment International, 157,  2021, 106810, https://doi.org/10.1016/j.envint.2021.106810

18.10.2023

Speaker: Anna-Sophia Egger (Uni Innsbruck)

Paper: Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, and Ole N. Jensen, Full Separation and Sequencing of Isomeric Proteoforms in the Middle-Down Mass Range Using Cyclic Ion Mobility and Electron Capture Dissociation, Analytical Chemistry 2023 95 (29), 11141-11148, DOI: 10.1021/acs.analchem.3c02120

11.10.2023

Speaker: Maya Petek (University of Maribor, Slowenia)

Paper: Youming Wang, Rui Sun, Weigang Ge, Lei Xue, Qianwen Xu, Hui Xu, Sujun Li, Miaomiao Wu, Tiannan Guo, and Xingbing Wang, Longitudinal Serum Proteomics Characterization of CD19-CAR-T Cell Therapy for B-Cell Malignancies, Journal of Proteome Research, 2023 ,22 (9), 2985-2994, https://pubs.acs.org/doi/full/10.1021/acs.jproteome.3c00322

14.6.2023

Speaker: Tobias Kipura (Uni Innsbruck)

Paper: Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography
Richard Lauman, Hee Jong Kim, Lindsay K. Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio, and Benjamin A. Garcia

https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c04114 me.2c008

7.6.2023

Speaker: Dominik Hofreither (TU Wien)

Paper: Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography. Xinyue Liu, Valentina Rossio, Steven P. Gygi, and Joao A. Paulo J. Proteome Res. 2023, 22, 4, 1270–1279 https://doi.org/10.1021/acs.jproteome.2c00806

Host: Ruth Birner-Gruenberger (TU Wien)

31.05.2023

Speaker: Ramul Samrat (Uni Wien)

Paper: Shen, X., Kellogg, R., Panyard, D.J. et al. Multi-omics microsampling for the profiling of lifestyle-associated changes in health. Nat. Biomed. Eng (2023). https://doi.org/10.1038/s41551-022-00999-8

Host: Sarah Theiner (Uni Vienna)

24.05.2023

Speaker: Maya Petek (Univerza v Mariboru, Slovenia)

Paper: Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing. Journal of Proteome Research, 2023. https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00740

Host: Marcel Kwiatkowski (Uni Innsbruck)

17.5.2023

Speaker: Julia Höhlschen (TU Wien)

Paper: Desai HS, Yan T, Yu F, Sun AW, Villanueva M, Nesvizhskii AI, Backus KM. SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines. Mol Cell Proteomics. 2022 Apr;21(4):100218. https://doi.org/10.1016/j.mcpro.2022.100218

Host: Tamara Tomin (TU Wien)

26.4.2023

Speaker: Pamela Waked (Meduni Graz)

Paper: Chen, Cai-Ling et al. Perturbated glucose metabolism augments epithelial cell proinflammatory function in chronic rhinosinusitis. https://doi.org/10.1016/j.jaci.2022.09.036

Host: Ruth Birner-Gruenberger (TU Wien)

19.4.2023

Speaker: Eva Rauch (Uni Innsbruck)

Paper:

Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation

Cell Rep. 2022 Dec 13;41(11):111809. doi: 10.1016/j.celrep.2022.111809 .

https://www.sciencedirect.com/science/article/pii/S2211124722016977?via%3Dihub

Host: Marcel Kwiatkowski (Uni Innsbruck)

29.3.2023

Speaker: Tobias Kipura (Uni Innsbruck)

Paper: A Workflow to Perform Targeted Metabolomics at the Untargeted Scale on a Triple Quadrupole Mass Spectrometer, Michaela Schwaiger-Haber, Ethan Stancliffe, Valerie Arends, Bharat Thyagarajan, Miriam Sindelar, and Gary J. Patti ACS Measurement Science Au 20211 (1), 35-45 DOI: 10.1021/acsmeasuresciau.1c00007

Speaker: Anna-Sophia Egger (Uni Innsbruck)

Paper: Rapid Multi-Omics Sample Preparation for Mass Spectrometry, Laura K. Muehlbauer, Annie Jen, Yunyun Zhu, Yuchen He, Evgenia Shishkova, Katherine A. Overmyer, and Joshua J. Coon Analytical Chemistry 202395 (2), 659-667 DOI: 10.1021/acs.analchem.2c02042

Host: Marcel Kwiatkowski (Uni Innsbruck)

18.1.2023

Speaker: Julia Höhlschen(TU Wien)

Paper: Jonathan G Van Vranken, Jiaming Li, Dylan C Mitchell, José Navarrete-Perea, Steven P Gygi (2021) Assessing target engagement using proteome-wide solvent shift assays, eLife10:e70784. https://doi.org/10.7554/eLife.70784

Host: Ruth Birner-Gruenberger (TU Wien)

11.1.2023

Speaker: Emma Pelllegrini (TU Wien)

Paper: Sridharan, G. et al., Evaluation of salivary metabolomics in oral leukoplakia and oral squamous cell carcinoma, 2019, J. Oral Pathol. Med. 48:299-306 https://doi.org/10.1111/jop.12835

Host: Ruth Birner-Gruenberger (TU Wien)

21,12.2022

Speaker: Dina Abdel (TU Wien)

Paper: Neinast, Michael D. et al., Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids, Cell Metabolism, Volume 29, Issue 2, 417 – 429.e4, https://doi.org/10.1016/j.cmet.2018.10.013

Host: Matthias Schittmayer (TU Wien)

14.12.2022

Speaker: Gabriel Braun (UniWien)

Paper: Kuett, L., Catena, R., Özcan, A. et al. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nat Cancer 3, 122–133 (2022). https://doi.org/10.1038/s43018-021-00301-w

Host: Sarah Theiner (Uni Vienna)

7.12.2022

Speakers: Kevin Mildau (1), David Loibnegger (2) (UniWien)

Papers:

    1. MetGem Software for the Generation of Molecular Networks Based on the t-SNE AlgorithmFlorent Olivon, Nicolas Elie, Gwendal Grelier, Fanny Roussi, Marc Litaudon, and David TouboulAnalytical Chemistry 2018 90 (23), 13900-13908 DOI: 10.1021/acs.analchem.8b03099

    1. van Maldegem, F., Valand, K., Cole, M. et al. Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry. Nat Commun 12, 5906 (2021). https://doi.org/10.1038/s41467-021-26214-x

Host: Sarah Theiner (Uni Vienna)

30.11.2022

Speaker: Martin Schaier (UniWien)

Paper: Schlecht, A., Boneva, S., Salie, H. et al. Imaging mass cytometry for high-dimensional tissue profiling in the eye. BMC Ophthalmol 21, 338 (2021). https://doi.org/10.1186/s12886-021-02099-8

Host: Sarah Theiner (Uni Vienna)

23.11.2022

Speaker: Alexander Wenger (UniWien)

Paper: Cebo M, Calderón Castro C, Schlotterbeck J, et al. Untargeted UHPLC-ESI-QTOF-MS/MS analysis with targeted feature extraction at precursor and fragment level for profiling of the platelet lipidome with ex vivo thrombin-activation. J Pharm Biomed Anal 205, 114301 (2021). https://doi.org/10.1016/j.jpba.2021.114301

Host: Sarah Theiner (Uni Vienna)

16.11.2022

Speaker: Isabella Burger (TU Wien)

Dührkop, K., Nothias, LF., Fleischauer, M. et al. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nat Biotechnol 39, 462–471 (2021). https://doi.org/10.1038/s41587-020-0740-8

Host: Tamara Tomin (TU Wien)

9.11.2022

Speaker: Elisabeth Föls (Uni Vienna)

Paper: Jackson, H.W., Fischer, J.R., Zanotelli, V.R.T. et al. The single-cell pathology landscape of breast cancer. Nature578, 615–620 (2020). https://doi.org/10.1038/s41586-019-1876-x

Host: Sarah Theiner (Uni Vienna)

19.10.2022

Speaker: Maya Petek (International)

Messner, C.B., Demichev, V., Bloomfield, N. et al. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol 39, 846–854 (2021). https://doi.org/10.1038/s41587-021-00860-4

Host: Marcel Kwiatkowski (Uni Innsbruck)

12.10.2022

Speaker: Christina Wagner (TU Wien)

Victor Yin, Paul W.A. Devine, Janet C. Saunders, Alistair Hines, Sam Shepherd, Marcin Dembek, Claire L. Dobson, Joost Snijder, Nicholas J. Bond, Albert J.R. Heck. Spectral Interferences Impede the High-Resolution Mass Analysis of Recombinant Adeno-Associated Viruses. bioRxiv 2022.08.27.505551; https://www.biorxiv.org/content/10.1101/2022.08.27.505551v1

Host: Ruth Birner-Gruenberger (TU Vienna)

18.5.2022

Speaker : Anna-Sophia Egger (Uni Innsbruck)

Sean M. Colby, Christine H. Chang, Jessica L. Bade, Jamie R. Nunez, Madison R. Blumer, Daniel J. Orton, Kent J. Bloodsworth, Ernesto S. Nakayasu, Richard D. Smith, Yehia M. Ibrahim, Ryan S. Renslow, and Thomas O. Metz, DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data. Analytical Chemistry 202294 (16), 6130-6138 https://doi.org/10.1021/acs.ana

11.5.2022

Speaker 1 : Tobias Pointner (Uni Vienna)

M. Curujo et al. Use of omics analytical methods in the study of genetically modified maize varieties tested in 90 days feeding trials. Food Chemistry 292, 359–371 (2019). https://doi.org/10.1016/j.foodchem.2018.05.109

Speaker 2 : Richard Urban (Uni Vienna)

C. Wang and Y. Wen et al. High-sensitivity quantification of glycosphingolipid glycans by ESI-MS utilizing ozonolysis-based release and isotopic Girard’s reagent labeling. Analytical Biochemistry 582, 113355 (2019). https://doi.org/10.1016/j.ab.2019.113355

Host: Katharina Hohenwallner, Evelyn Rampler (Uni Vienna)

4.5.2022

Speaker : Isabella Burger (TU Vienna)

Nothias, LF., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat Methods 17, 905–908 (2020). https://doi.org/10.1038/s41592-020-0933-6

Host: Ruth Birner-Gruenberger (TU Vienna)

27.4.2022

Speaker 1 : Kevin Mildau (University of Vienna)
Title: Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nat Methods 18, 1524–1531 (2021). https://doi.org/10.1038/s41592-021-01331-z .

Speaker 2 : Tobias Kipura (University of Innsbruck)
Title: Philipp T. Kaulich, Liam Cassidy, Konrad Winkels, and Andreas Tholey, Improved Identification of Proteoforms in Top-Down Proteomics Using FAIMS with Internal CV Stepping, Analytical Chemistry 2022 94 (8), 3600-3607 https://doi.org/10.1021/acs.analchem.1c05123

Host: Evelyn Rampler (Uni Vienna), Marcel Kwiatkowski (Uni Innsbruck)

6.4.2022

Speaker 1 : Katharina Hohenwallner (University of Vienna)
Title: Fanran Huang, Laura S. Bailey, Tianqi Gao, Wenjie Jiang, Lei Yu, David A. Bennett, Jinying Zhao, Kari B. Basso, and Zhongwu Guo, Analysis and Comparison of Mouse and Human Brain Gangliosides via Two-Stage Matching of MS/MS Spectra ACS Omega 2022 7 (7), 6403-6411 https://doi.org/10.1021/acsomega.1c07070 .

Speaker 2 : Magdalena Krausova (University of Vienna)
Title: van der Laan, T., Kloots, T., Beekman, M. et al. Fast LC-ESI-MS/MS analysis and influence of sampling conditions for gut metabolites in plasma and serum. Sci Rep 9, 12370 (2019). https://doi.org/10.1038/s41598-019-48876-w .

Host: Evelyn Rampler (Uni Vienna)

30. 3. 2022

Speaker : Lisa Panzenboeck (University of Vienna)
Title: Goryńska, P.Z.; Chmara, K.; Kupcewicz, B.; Goryński, K.; Jaroch, K.; Paczkowski, D.; Furtak, J.; Harat, M.; Bojko, B. Metabolomic Phenotyping of Gliomas: What Can We Get with Simplified Protocol for Intact Tissue Analysis? Cancers 202214, 312. https://doi.org/10.1016/ j.mcpro.2022.100218 .

Host: Evelyn Rampler (Uni Vienna)

23.3. 2022

Speaker : Maya Petek (Faculty of Medicine, University of Maribor, first international university speaker)
Title: P.S. Hari, Lavanya Balakrishnan, Chaithanya Kotyada, Arivusudar Everad John, Shivani Tiwary, Nameeta Shah, Ravi Sirdeshmukh, Proteogenomic analysis of breast cancer transcriptomic and proteomic data, using de novo transcript assembly: Genome-wide identification of novel peptides and clinical implications, Molecular & Cellular Proteomics (2022), https://doi.org/10.1016/ j.mcpro.2022.100218 .

Host: Marcel Kwiatkowski (Uni Innsbruck)

16.3. 2022

Speaker : Felina Hildebrand (Uni Wien)
Title: Isabel Meister, Pei Zhang, Anirban Sinha, C. Magnus Sköld, Åsa M. Wheelock, Takashi Izumi, Romanas Chaleckis, and Craig E. Wheelock, High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology, Analytical Chemistry 2021 93 (12), 5248-5258

https://pubs.acs.org/doi/10.1021/acs.analchem.1c00203

Host: Evelyn Rampler (Uni Vienna)

9.3. 2022

Speaker : Veronika Fitz (Uni Wien)
Title: Angela K. Boysen, Katherine R. Heal, Laura T. Carlson, and Anitra E. Ingalls, Best-Matched Internal Standard Normalization in Liquid Chromatography–Mass Spectrometry Metabolomics Applied to Environmental Samples, Analytical Chemistry 2018 90 (2), 1363-1369 https://doi.org/ 10.1021/acs.analchem.7b04400

Host: Evelyn Rampler (Uni Vienna)

26.1. 2022

Speaker 1: Katharina Hohenwallner (Uni Wien)
Title 1: Mirela Sarbu, Adrian C. Robu, Roxana M. Ghiulai, Željka Vukelić, David E. Clemmer, and Alina D. Zamfir, Analytical Chemistry 2016, 88 (10), 5166-5178. https://doi.org/10.1021/acs.analchem.6b00155

Host: Evelyn Rampler (Uni Vienna)

Speaker 2: Ilse Hrasdin (TU Wien)
Title 2: Bojkova, Denisa, Rui Costa, Philipp Reus, Marco Bechtel, Mark-Christian Jaboreck, Ruth Olmer, Ulrich Martin, Sandra Ciesek, Martin Michaelis, and Jindrich Cinatl “Targeting the Pentose Phosphate Pathway for SARS-CoV-2 Therapy” Metabolites 11, no. 10: 699, 2021. https://doi.org/10.3390/metabo11100699

Host: Evelyn Rampler (Uni Vienna)

19.1. 2022

Speaker 1: Anna Schöberl (Uni Wien)
Title 1: Kuett, L., Catena, R., Özcan, A. et al. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nat Cancer (2021). https://doi.org/10.1038/s43018-021-00301-w

Host: Evelyn Rampler (Uni Vienna)

12.1. 2022

Speaker 1: Felina Hildebrand (Uni Wien)
Title 1: Chen, L., Lu, W., Wang, L. et al. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods 18, 1377–1385 (2021). https://doi.org/10.1038/s41592-021-01303-3

Speaker 2: Yifan Bao (Uni Wien)
Title 2: Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021 ;29(8):1294-1304.e4. https://doi.org/10.1016/j.chom.2021.06.019

Host: Evelyn Rampler (Uni Vienna)

22.12. 2021

Speaker 1: Nina Troppmair (Uni Wien)
Title 1: K. Horesji et al. Comprehensive Identification of Glycosphingolipids in Human Plasma Using Hydrophilic Interaction Liquid Chromatography—Electrospray Ionization Mass Spectrometry. Metabolites , 11(3), 140 (2021). https://doi.org/10.3390/metabo11030140

Speaker 2: Gabriel Braun(Uni Wien)
Title 2: F. van Maldegem et al. Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry. Nat Commun 12, 5906 (2021). https://doi.org/10.1038/s41467-021-26214-x

Host: Evelyn Rampler (Uni Vienna)

15.12.2021

Title: Y. He et al. Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis. Anal Chem 93, 9, 4217-4222 (2021). https://doi.org/10.1021/acs.analchem.0c04764 .

Host: Marcel Kwiatkowski (Uni Innsbruck)

1.12.2021

Title: Zhang, X., Ning, Z., Mayne, J. et al. Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn’s disease. Nat Commun 11, 4120 (2020). https://doi.org/10.1038/s41467-020-17916-9 .

Host: Marcel Kwiatkowski (Uni Innsbruck)

24.11.2021

Manuscript: Tripathi et al. Chemically informed analyses of metabolomics mass spectrometry data with Qemistree, Nature Chemical Biology , 17, 146–151, 2021. https://doi.org/10.1038/s41589-020-00677-3 .

Host: Evelyn Rampler (Uni Wien)

17.11.2021

Manuscript 1: DMS as an orthogonal separation to LC/ESI/MS/MS for quantifying isomeric cerebrosides in plasma and cerebrospinal fluid, Journal of Lipid Research, 60, 2019 (link)

Manuscript 2: Single-cell lipidomics with high structural specificity by mass spectrometry, Nature Communications, 12, 2869 (2021) (link)

Host: Evelyn Rampler (Uni Wien)

10.11.2021

Manuscript: Pre-analytical monitoring and protection of oxidizable lipids in human plasma (vitamin E and ω−3 and ω−6 fatty acids): An update for redox-lipidomics methods, Free Radical Biology and Medicine, 2021 (link)
Host: Evelyn Rampler (Uni Wien)

03.11.2021

Manuscript: Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV, 2021, Nature (link)
Host: Marcel Kwiatkowski (Uni Innsbruck)

27.10.2021

    • Host: Evelyn Rampler (Uni Wien)

12.05.2021

    • Manuscript: Dugourd et al. Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses. Mol Syst Biol (2021)17:e9730. doi.org/10.15252/msb.20209730

    • Host: Marcel Kwiatkowski (Uni Innsbruck)

05.05.2021

    • Manuscript: Buljan et al. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases (2020) Molecular Cell doi: 10.1016/j.molcel.2020.07.001

    • Host: Marcel Kwiatkowski (Uni Innsbruck)

28.04.2021

    • Manuscript: Banini et al., Identification of a Metabolic, Transcriptomic, and Molecular Signature of Patatin‐Like Phospholipase Domain Containing 3–Mediated Acceleration of Steatohepatitis (2020) Hepatology, doi: 10.1002/hep.31609

    • Host: Ruth Birner-Gruenberger (TUW)

21.04.2021

    • Manuscript: Uliana F. et al. Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen (2021) Nat Comm12, 1693. doi: 10.1038/s41467-021-21754-8

    • Host: Ruth Birner-Gruenberger (TUW)

14.04.2021

24.03.2021

    • Manuscript: Kevin Klann, Georg Tascher, Christian Münch. Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α.  Mol Cell. 2020 Feb 20;77(4):913-925.e4. doi:10.1016/j.molcel.2019.11.010

    • Hosts: Marcel Kwiatkowski (Univ. Innsbruck), Tamara Tomin (TUW)

17.03.2021

    • Manuscript: Malone, B., Simovski, B., Moliné, C. et al. Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs. Sci Rep 10, 22375 (2020). https://doi.org/10.1038/s41598-020-78758-5

    • Host: Johannes Griss (MUW)

10.03.2021

    • Manuscript: Vasilopoulou CG, Sulek K, Brunner AD, Meitei NS, Schweiger-Hufnagel U, Meyer SW, et al. Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts. Nat Commun. 2020;11(1):331. doi: 10.1038/s41467-019-14044-x

    • Hosts: Evelyn Rampler (Uni Wien), Ruth Birner-Gruenberger (TUW)

03.03.2021

    • Manuscript: Atabaki-Pasdar N. et al. (2020) Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts. PLOS MEDICINE https://doi.org/10.1371/journal.pmed.1003149

    • Hosts: Evelyn Rampler (Uni Wien), Ruth Birner-Gruenberger (TUW)

03.02.2021

    • Hosts: Evelyn Rampler (Uni Wien), Ruth Birner-Gruenberger (TUW)

27.01.2021

    • Hosts: Evelyn Rampler (Uni Wien), Martina Marchetti-Deschmann (TU Wien)

20.01.2021

    • Hosts: Evelyn Rampler (Uni Wien), Johannes Griss (MUW)

13.01.2021

    • Manuscript: Santan-Cotina et al. (2020) Defining and Targeting Adaptations to Oncogenic KRASG12C Inhibition Using Quantitative Temporal Proteomics. Cell Reports 30 (13) 4584-4599.e4. doi: 10.1016/j.celrep.2020.03.021

16.12.2020

    • Manuscript: Mikan et al. (2020). Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. ISME 14:39–52, doi: 10.1038/s41396-019-0503-z

    • Hosts: Ruth Birner-Gruenberger (TUW)

09.12.2020

    • Manuscript: Harel et al. (2019) Proteomics of Melanoma Response to Immunotherapy Reveals Mitochondrial Dependence. Cell 179(1):236-250.e18, doi: 10.1016/j.cell.2019.08.012

    • Hosts: Evelyn Rampler (Uni Wien)

02.12.2020

    • Hosts: Ruth Birner-Gruenberger (TUW), Johannes Griss (MUW)

25.11.2020

    • Manuscript: Coman et al. (2016) Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology, MCP 15 (4) 1453-1466; doi: 10.1074/mcp.M115.053702

    • Hosts: Evelyn Rampler (Uni Wien), Klaus Kratochwill (MUW)

18.11.2020

    • Manuscript: Scheubert et al. (2017) Significance estimation for large scale metabolomics annotations by spectral matching, Nat Commun 14;8(1):1494. doi: 10.1038/s41467-017-01318-5

    • Hosts: Evelyn Rampler (Uni Wien), Wolfram Weckwerth (Uni Wien)

11.11.2020

    • Manuscript: Searle et al. (2020), Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nat Comm, doi: 10.1038/s41467-020-15346-1

    • Hosts: Ruth Birner-Gruenberger (TUW), Matthias Schittmayer (TUW)

04.11.2020

    • Manuscript: Kong et al, (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Meth, doi:10.1038/nmeth.4256

    • Hosts: Ruth Birner-Gruenberger (TUW), Johannes Griss (MUW)

More Questions?

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All registered students and the lecturers of each university.