Hands-on I - Metabolomics (bio)sample Description
Resources
12 papers from plant, health and nutrition domains:
- Discovery and Validation of Banana Intake Biomarkers Using Untargeted Metabolomics in Human Intervention and Cross-sectional Studies - Vázquez-Manjarrez et al - https://doi.org/10.1093/jn/nxz125
- Manual annotation combined with untargeted metabolomics for chemical characterization and discrimination of two major crataegus species based on liquid chromatography quadrupole time-of-flight mass spectrometry - Li et al - https://doi.org/10.1016/j.chroma.2019.460628
- A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato- Jeon et al - https://doi.org/10.1016/j.cell.2019.11.037
- Cerebrospinal fluid metabolomics highlights dysregulation of energy metabolism in overt hepatic encephalopathy - Weiss et al - https://dx.doi.org/10.1016/j.jhep.2016.07.046
- Dietary bioac ves increase gut microbiome diversity and alter host and microbial metabolite profiles- Duncan et al - https://doi.org/10.1101/2025.10.16.25338140
- An online atlas of human plasma metabolite signatures of gut microbiome composition - Dekkers et al - https://doi.org/10.1038/s41467-022-33050-0
- Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species - Roch et al - https://doi.org/10.1093/jxb/eraa302
- Metabolomic and Lipidomic Alterations in Patients with Atopic Dermatitis with Dupilumab-Associated Ocular Surface Disease - Patra et al - https://doi.org/10.1016/j.xjidi.2025.100361
- Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites - Balcke et al - https://doi.org/10.1105/tpc.17.00060
- Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - Torta et al - https://doi.org/10.1038/s41467-024-52087-x
- High-confidence structural annotation of metabolites absent from spectral libraries - Hoffmann et al - https://doi.org/10.1038/s41587-021-01045-9
- Specialized metabolome and transcriptome atlas of developing Arabidopsis thaliana seed under warm temperatures - Barreda et al - https://doi.org/10.1038/s41597-025-04563-2
Checklists Version 0.0
Instructions
Exercice 01
- Identify/list the entities that, in your opinion, characterize the information available in your case study!
- We will focus on two groups of entities:
- those used to describe biological samples (e.g., species)
- and those used to describe the results of the metabolomics study (e.g., metabolite name).
- 1 type of entity —> 1 sticky note
Exercice 02
- Fill in the checklist document for your case study, particularly
- the “Value In your Paper” columns for the given term
- and according to whether it is mandatory/optional for describing the biological sample given in a metabolomics study
Format of the deliverable
- Paper 01: Sticky notes of Entities identified (Biosample Group & Results Group) in use cases
- Paper 02: Sticky note with your Feedback about the exercise - 1 comment —> 1 sticky note
- Filled Checklist(s)