Prague Workshop for Computational Mass Spectrometry

Focused on non-target LC-MS metabolomics data processing, this workshop is suited for beginners and expert users and software developers. We aim for a high percentage of hands-on lectures.

The workshop is in-person and free of charge.

Organizers:

• Dr. Tomáš Pluskal: tomas.pluskalinvalid-email-name@invalid-email-domainuochb.cas.cz, www.pluskal-lab.org
• Dr. Robin Schmid: rschmid1789invalid-email-name@invalid-email-domaingmail.com, robinschmid.github.io

• Download here
  

• Watch here
  

Downloads

• Download the whole Google Drive folder, especially the important dataset folder, which is ~500 MB. And unzip the file. The zip contains mzml data files and a spectral library: download here (alternative link).
• Spectral library: The Google Drive dataset already contains the MoNA (LC-MS2 pos) library (alternative link if downloading from MassIVE).

Installations

• mzmine: Download and install the latest version (current mzmine 4.0.2).
  
  There are platform-specific installers for Windows, Mac, and Linux. There is NO need to install any other tool or Java Virtual Machine (JVM): Refer to the documentation for installation instructions and post issues on GitHub.

• Cytoscape: Download and install the latest version.

• matchms and python consorts: Make sure you have a Google account and can log into Google Colab.

Dataset information

The dataset is constituted of HRMS/MS data acquired over Pseudomonas strains.

It contains wild type or mutant strains together with medium blanks and QCs. More background on the dataset is available here.

We will use this Google document as a live document to post information about the ongoing workshop. Feel free to comment and ask questions there if something is unclear.

• Dr. Tomáš Pluskal (IOCB Prague, Czechia) – Plant specialized metabolism, biosynthesis
• Dr. Corinna Brungs (IOCB Prague, Czechia) – Pharmacist and Analytical Chemist focused on reference data and plant metabolism
• Dr. Robin Schmid (IOCB Prague, Czechia) – Food Chemist and Analytical Chemist focussed on computational mass spectrometry; Lead Architect of MZmine 
• Dr. Louis-Félix Nothias (Université Côte d’Azur, ICN, CNRS, Nice, France) – Experimental & computational mass spectrometry-based metabolomics
• Prof. Matej Orešic (University of Turku, Finland) – Professor of medicine (systems medicine), professor of biochemistry (metabolomics)
• Prof. Sebastian Böcker (FSU Jena, Germany) – Bioinformatician, computational mass spectrometry and computational metabolomics
• Dr. Marcus Ludwig (FSU Jena & Bright Giant GmbH, Germany) – Bioinformatician, computational mass spectrometry and computational metabolomics
• Dr. Adriano Rutz (ETH Zürich, Switzerland) – Pharmacist, computational metabolomics & open science, LOTUS initiator
• Dr. Yasin El Abiead (UC San Diego, USA) – Analytical Chemist focused on computational mass spectrometry
• Niek de Jonge (Wageningen University, the Netherlands) – Computational mass spectrometry focussed on software development
• Steffen Heuckeroth (University of Münster, Germany) – Analytical chemist focussed on ion mobility spectrometry-mass spectrometry and computational mass spectrometry
• Dr. Ansgar Korf (IOCB Prague, Czechia) – Food Chemist and Analytical Chemist focussed on computational mass spectrometry