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.
Abstract
Mass spectrometry-based metabolomics is rapidly evolving, challenging us to process and interpret complex multi-dimensional data. There are many computational mass spectrometry projects to aid in this process - but mastering or even starting to use them can be a challenge of its own. Therefore, we want to provide a platform in Prague to meet, discuss, and learn how to move MS-based metabolomics forward.
Who we are:
Our presenters comprise software developers and power users of various open source projects, including MZmine, SIRIUS, matchms, MS2Query, LOTUS, GNPS, MassQL, MASST, Cytoscape
Who you are:
You are a “beginner” or “expert” in the field open to network and dive deeper into MS tools, data processing, and compound annotation.
Our goals for the workshop:
- Introduce MS-based metabolomics and data processing
- Provide hands-on experience with various computational tools
- Connect users and developers - to better understand trends and needs
- Socializing & networking
We are opening this to all experience levels - no prior knowledge is required as we are starting with some basics, but the workshop will be fast-paced.
Organizers:
Dr. Tomáš Pluskal
- Email: [email protected]
- Web: www.pluskal-lab.org
Dr. Robin Schmid
- Email: [email protected]
- Web: robinschmid.github.io
Registration
- Deadline to register: 31 January 2024
- Registration form
Presenters
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
Program
Monday (April, 15th 2024)
8.30 - 9.00 Registration and Coffee
9.00 - 9.05 Welcome
9.05 - 9.20 20th Anniversary - MZmine History
9.20 - 9.30 Future of MZmine
9.30 - 10.00 Talk: Brief Intro to Mass Spectrometry
10.00 - 10.30 Talk: Computational Mass Spectrometry Basics
10.30 - 11.00 Coffee Break
11.00 - 11.30 Research Talk(s)
11.30-12.00 Hands-On: Exploring MS Data in MZmine
12.00 - 13.00 Hands-On: MZmine I - LC-MS/MS Data Processing
13.00 - 14.00 Lunch at IOCB
14.00 - 14.30 Talk: Introduction to Molecular Networking
14.30 - 15.00 Talk: Automatic Spectral Library Generation
15.00 - 16.00 Coffee Break
16.00 - 17.30 Hands-On: MZmine II - LC-MS/MS Results
17.30 - ?? Social time
Tuesday (April, 16th 2024)
8.30 - 9.00 Coffee
9.00 - 9.15 Introduction to matchms, MS2Deepscore and MS2Query.
9.15 - 9.30 Introduction to Jupyter Notebooks (Colab)
9.30-10.30 Hands-On: matchms, MS data in Python
10:30-11:00 MS2Query; Predicting analogues
11.00 - 11.30 Coffee Break
11:30 - 12:00 GNPS2 introduction and setting up accounts
12:00 - 13:00 Hands-On: Feature-based molecular networking
13.00 - 14.00 Lunch at IOCB
14:00 - 15:30 MassQL and modification site localization
15.30 - 16.30 Coffee Break
16.30 - 17.30 Hands-On: MASST for microbes, foods, plants
17.30 - ?? Social time
Wednesday (April, 17th 2024)
8.30 - 9.00 Coffee
9.00 - 9.20 Talk: Introduction to SIRIUS
9.20 - 11.00 Hands-On: SIRIUS, CSI:FingerID, and CANOPUS
11.00 - 11.30 Coffee Break
11.30 - 12.00 Talk: SIRIUS behind the scenes: How it works
12.00 - 13.00 Hands-On: LOTUS and Wikidata
13.00 - 14.00 Lunch at IOCB
13.30 - 14.00 Ask the Developers Q&A
15.00 - 16.00 Coffee Break
16.00 - 17.30 Hands-On: Cytoscape - Fusion of Results
- MZmine
- GNPS2
- matchms
- MASST
- MassQL
- LOTUS
- SIRIUS
17.30 - 17.45 Farewell
17.45 - ?? Time to explore Prague
Prague Workshop for Computational Mass Spectrometry: Poster
