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