Photo by Patrick Tomasso on Unsplash

Next Meeting Details

7.12.2022– 3pm

Host: Sarah Theiner (UniWien)

Meeting Link:

23.11.2022 – 3 pm


It is hosted through an online meeting system. The used system will change depending on the hosting institution.

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. Important: The link will change for every meeting.


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 per week.

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

Previous Meetings


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).

Host: Sarah Theiner (Uni Vienna)


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).

Host: Sarah Theiner (Uni Vienna)


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).

Host: Tamara Tomin (TU Wien)


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).

Host: Sarah Theiner (Uni Vienna)


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).

Host: Marcel Kwiatkowski (Uni Innsbruck)


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;

Host: Ruth Birner-Gruenberger (TU Vienna)


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


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).

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).

Host: Katharina Hohenwallner, Evelyn Rampler (Uni Vienna)


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).

Host: Ruth Birner-Gruenberger (TU Vienna)


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).

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

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


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

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).

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. 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), 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

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 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.

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.

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).

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).

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.

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).

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).

Host: Evelyn Rampler (Uni Vienna)


Title: Y. He et al. Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis. Anal Chem 93, 9, 4217-4222 (2021).

Host: Marcel Kwiatkowski (Uni Innsbruck)


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).

Host: Marcel Kwiatkowski (Uni Innsbruck)


Manuscript: Tripathi et al. Chemically informed analyses of metabolomics mass spectrometry data with Qemistree, Nature Chemical Biology , 17, 146–151, 2021.

Host: Evelyn Rampler (Uni Wien)


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)


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)


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


  • Manuscript: Single-cell lipidomics with high structural specificity by mass spectrometry, 2021, Nature Communication, 12:2869,
  • Host: Evelyn Rampler (Uni Wien)


  • Manuscript: Dugourd et al. Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses. Mol Syst Biol (2021)17:e9730.
  • Host: Marcel Kwiatkowski (Uni Innsbruck)


  • 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)


  • 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)


  • 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)



  • 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)


  • 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).
  • Host: Johannes Griss (MUW)


  • 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)


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


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



  • Manuscript: Medina, C.B., Mehrotra, P., Arandjelovic, S. et al. Metabolites released from apoptotic cells act as tissue messengers. Nature 580, 130–135 (2020).
  • Hosts: Evelyn Rampler (Uni Wien), Johannes Griss (MUW)


  • 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


  • 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)


  • 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)


  • Manuscript: Meier et al., (2020) Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage. bioRxiv
  • Hosts: Ruth Birner-Gruenberger (TUW), Johannes Griss (MUW)


  • 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)


  • 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)


  • 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)


  • 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?

In case you have more questions about the APMA Journal Club don’t hesitate to contact us at office [at] apma [dot] at.