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Next Meeting Details

Invited Seminar: 23.06.2021 – 16:30

Host: Evelyn Rampler

Meeting Link: Zoom
Meeting number: 882 3669 0961
Password: HQQRu9

Speaker: Prof. Ian Lewis, University of Calgary, Canada
Title: Harnessing mass spectrometry as a rapid diagnostic platform for detecting infectious


The APMA Journal club will start again in the summer semester 2021. Our first date is 03. March at 3pm.


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, and University of Vienna. If you are there, you can book the course to get credits for it.

All others 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.

The person presenting the paper will also be asked to write a short summary of the paper which will be published in a dedicated section on this website.

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

Previous Meetings


  • 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.