Photo by Patrick Tomasso on Unsplash

Next Meeting Details

1.12.2021 – 15:00

Host: Marcel Kwiatkowski (Uni Innsbruck)

Meeting Link: https://univienna.zoom.us/j/95599980433?pwd=eExvNEcrR093KzIvYmZvMHdzU2cxUT09
Meeting number: 955 9998 0433
Password: 914907

Who?

Speaker: Thomas Mair (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). https://doi.org/10.1038/s41467-020-17916-9.

When?

1.12.2021 – 3 pm

Where?

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.

All others can join the meeting through the link posted at the top of the page. Important: The link will change for every meeting.

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 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

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

  • Manuscript: Single-cell lipidomics with high structural specificity by mass spectrometry, 2021, Nature Communication, 12:2869, doi.org/10.1038/s41467-021-23161-5
  • 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

20.01.2021

  • Manuscript: Medina, C.B., Mehrotra, P., Arandjelovic, S. et al. Metabolites released from apoptotic cells act as tissue messengers. Nature 580, 130–135 (2020). https://doi.org/10.1038/s41586-020-2121-3
  • 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

  • Manuscript: Meier et al., (2020) Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage. bioRxiv https://www.biorxiv.org/content/10.1101/656207v1
  • 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?

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