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Training courses: Metabolomics Approaches for ‘One Health’


Important Dates

  • Deadline for application: 30th April 2024
  • Deadline for abstract submission (see below): 30th April 2024
  • Selected abstract will be notified by: 4th May 2024
  • Workshop date: 30-31 May 2024


University of Milano-Bicocca
Department of Biotechnology and Bioscience
Piazza della Scienza 2, Milano


Academic: EUR 130
Industry: EUR 130
Undergraduate and PhD students: EUR 70
The fee covers coffee-breaks and lunches.
Participants are expected to pay their own travel and accommodation costs (if any).
Social “Aperitivo”:
Participants who wish to attend the social Aperitivo on Thursday 30th May, should add 30 EUR to the fee.

Abstract submission for flash presentations

Participants who wish to present a research topic and have the chance to discuss their metabolomics issues/approach with
the speakers can submit an abstract (maximum 150 words).
The organising Committee will select 10 abstracts for a flash presentation (5 min, 2 slides) and discussion with the speakers.
Please send you abstract at the following e-mail:
Deadline for abstract submission: 30th April 2024

(Invited) Speakers

  • Marco Vanoni, University of Milano-Bicocca, ISBE-IT, Italy
  • Marcella Bonanomi, National Research Council – IBFM, ELIXIR-IT, Italy
  • Flavio A. Franchina, University of Ferrara, Italy
  • Luigi Lucini, Università Cattolica del Sacro Cuore, Italy
  • Anna Calì, Agilent
  • Maria Klapa, FORTH, ELIXIR-GR, Greece
  • Lilia Alberghina, University of Milano-Bicocca, ISBE-IT, Italy
  • Claire O ‘Donovan, EMBL-EBI, United Kingdom
  • Leilei Zhang, Università Cattolica del Sacro Cuore, Italy
  • Pascual Garcia-Perez, Università Cattolica del Sacro Cuore, Italy
  • Michael Zimmerman, EMBL, Germany
  • Duccio Cavalieri, University of Florence, Italy
  • Davide Seveso, University of Milano-Bicocca, Italy
  • Francesca Scolari, National Research Council – IGM, Italy
  • Valentina Pasquale, University of Milano-Bicocca, Italy
  • Fabrizio Mastrorocco, National Research Council – IBIOM, Italy


  • Daniela Gaglio, ELIXIR-IT, National Research Council – IBFM, Milan, Italy
  • Sergio Giannattasio, ELIXIR-IT, National Research Council – IBIOM, Bari, Italy
  • Federica Baldassari, National Research Council – IBFM, Italy
  • Clara Musicco, ELIXIR-IT, National Research Council – IBIOM, Bari, Italy
  • Allegra Via, ELIXIR-IT, National Research Council - IBPM, Rome, Italy
  • Marco Vanoni, University of Milano-Bicocca, ISBE-IT, Italy
  • Danilo Porro, ELIXIR-IT, National Research Council – IBFM, Italy


For all kinds of queries, please contact the organisers

Course Description

Metabolomics is the large-scale study of small molecules known as metabolites which constitute the metabolom, the downstream effect of an organism’s genome and its interaction with the environment. This young field of the Life Sciences arena has widespread applications across the medical, clinical, biological, environmental and agricultural sciences fitting precisely into the #OneHealth approach.
We will show how exciting and multi-colored Metabolomics can be including the challenges and its current limits. Special attention will be given to the following topics

  1. Practice and theory in metabolomic applications;
  2. Study design and sample collection;
  3. Stable isotope-resolved metabolomics;
  4. Metabolic Flux Analysis;
  5. Latest research in One Health metabolomics.

Target audience

This workshop is designed for scientists approaching metabolomics and those who want to improve their knowledge and competencies through open discussions with experts in this field.

Aims of the workshop

This workshop focuses on experimental design and sample preparation matrix enabling junior and senior scientists to apply metabolomics approaches to a research-based context.
Attendees will be guided through mass spectrometry-based experiment designs, learning about cutting-edge equipment and different technical procedures for metabolomics.

Learning Outcomes

By the end of this workshop the participants will be able to:

  1. Describe what Metabolomics is and what it is used for.
  2. Design a metabolomics experiment in all its steps.
  3. Know different kinds of sample preparation.
  4. Discern the importance of Metabolomics in a specific research context.

Course prerequisites

Participants are expected to have basic knowledge of biology and/or biochemistry


Application Form


Tuesday - 30st May, 2024

09:00 - 10:00 Registration
10:00 - 10:10 Welcome
Graziano Pesole Head of Elixir Italian Node
10:10 - 10:50 Metabolomics: a primus inter pares among the omic sciences?
Marco Vanoni (UNIMIB, ISBE-IT)
10:50 - 11:20 Experimental design and best practice for mass-spectrometry based metabolomics
Marcella Bonanomi (CNR, ELIXIR-IT)
11:20 - 11:30 Coffee Break
11:30 - 12:15 Sampling and GC-MS analysis of specialised metabolites from "uncommon" biofluids: the case of sweat and exhaled breath
Flavio A. Franchina (UNIFE)
12:15 - 13:00 Untargeted profiling of polyphenols: a screening of functional compounds and their metabolites in raw and in vitro digested cereals
Luigi Lucini (Università Cattolica del Sacro Cuore)
13:00 - 14:00 Lunch Break
14:00 - 14:45 Unknown compound identification through GC and LC/QTOF technologies.
Anna Calì (Agilent)
14:45 - 15:30 Heart metabolic profiling of an adult-onset-hypothyroidism mouse model reveals sex-specific differences
Maria Klapa (FORTH)
15:30 - 16:15 Data and Networks in Systems Biology
Lilia Alberghina (UNIMIB, ISBE-IT)
16:15 - 16:30 Coffee Break
16:30 - 17:15 Metabolomics global open data annotation and management - from the MetaboLights perspective.
Claire O 'Donovan (EMBL-EBI)
17:15 - 18:00 Chemometric interpretation of metabolomics signatures: from unsupervised to supervised statistics and deep learning approaches.
Pascual Garcia-Perez, Leilei Zhang (Università Cattolica del Sacro Cuore)
18:00 - 20:00 Social Aperitivo

Friday - 31st May, 2024

09:15 - 10:00 Metabolomics approaches to systematically investigate microbiome-mediated biotransformation.
Michael Zimmerman (EMBL)
10:00 - 10:45 Case study - Integrating microbiome, transcriptome and metabolome data in African families as a tool to investigate the role of globalisation in the rise of non-communicable disorders.
Duccio Cavalieri (University of Florence)
10:45 - 11:15 Case study: The stress response and metabolomic profiling of corals in a changing ecosystem
Davide Seveso (UNIMIB)
11:15 - 11:30 Coffee Break
11:30 - 12:00 Case study - Exploring the metabolomes of insect agricultural pests: innovative approaches for effective control
Francesca Scolari (CNR-IGM)
12:00 - 12:30 Case study - Cancer heterogeneity in spheroids, a training ground for omics integration
Valentina Pasquale (UNIMIB)
12:30 - 13:00 Case study - Yeast untargeted metabolomics of mitochondrial stress response: a model organism-focussed system for metabolome annotation and integration.
Fabrizio Mastrorocco (IBIOM-CNR)
13:00 - 14:00 Lunch Break
14:00 - 15:00 ONE-ON-ONE: mentoring session with lecturers
15:00 - 16:30 Abstract presentations
16:30 - 16:40 Greetings