LC-MS-Based Global Metabolic Profiles of Alternative Blood Specimens Collected by Microsampling
Thaitumu MN, De Sá E Silva DM, Louail P, Rainer J, Avgerinou G, Petridou A, Mougios V, Theodoridis G,
DOI: 10.3390/metabo15010062
Metabolomics provides a real-time view of the metabolic state of the examined samples. The past decade the field showed strong growth, however limitations intrinsic to the field hinder further application in epidemiology level. Key obstacles include: variety of analyte molecular structures, slow marker identification, large differences in concentrations, poor validation, incomplete combination of data from different analyses and fragmentation of research. The consortium brings together scientists from different complementary disciplines and sectors to collaborate and set a research training network, combining infrastructure experience, knowledge and skills. The research scope is to identify the source of problems that hinder development, and recommend measures to overcome these. Training through
research will promote a new generation of omics researchers. Networking, joining forces via secondments will enhance research productivity transfer of knowledge. The project will train 10 ESRs in work-packages aiming toward improvement of design of experiment, harmonization of analytical methods, improved Data Mining and biochemical pathway analysis and translational research. Application will be in the study of blood metabolome of exhaustive physical exercise.
We aim to study sample stability & preparation (including blood and alternative forms such as dried blood spots), biomarker identification, exploitation of multiple datasets, promote standard procedures, develop robust pipelines, develop and implement machine searchable notations of metadata, central database for data storage, compare datasets, automate cross-laboratory data combination, develop novel algorithms for multidimensional data mining and reconstruct biochemical pathways. The overall goal is to train the ESRs in cutting edge metabolomics research and at the same time provide proof of concept of democratizing metabolomics by the use of patient centric sampling.

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Thaitumu MN, De Sá E Silva DM, Louail P, Rainer J, Avgerinou G, Petridou A, Mougios V, Theodoridis G,
DOI: 10.3390/metabo15010062
De Graeve M, Bittremieux W, Naake T, Huber C, Anagho-Mattanovich M, Hoffmann N, Marchal P, Chrone V,
Mass spectrometry (MS) is a key technology used across multiple fields, including biomedical research and life sciences. The data is often times large and complex, and analyses must be tailored to the experimental and instrumental setups. Excellent software libraries for such data analysis are available in both R and Python, including R packages from the RforMassSpectrometry initiative such as Spectra, MsCoreUtils, MetaboAnnotation, and CompoundDb (Rainer et al., 2022), as well as Python libraries like matchms (Huber et al., 2020), spectrum_utils (Bittremieux, 2020), Pyteomics (Goloborodko et al., 2013), and pyOpenMS (Röst et al., 2014). The reticulate R package (Ushey et al., 2025) provides an R interface to Python enabling interoperability between the two programming languages. The open-source SpectriPy R package builds upon reticulate and provides functionality to efficiently translate between R and Python MS data structures. It can convert between R’s Spectra::Spectra and Python’s matchms.Spectrum and spectrum_utils.spectrum.MsmsSpectrum objects and includes functionality to directly apply spectral similarity, filtering, normalization, etc. routines from the Python matchms library on MS data in R. SpectriPy hence enables and simplifies the integration of R and Python for MS data analysis, empowering data analysts to benefit from the full power of algorithms in both programming languages. Furthermore, software developers
can reuse algorithms across languages rather than re-implementing them, enhancing efficiency and collaboration.
DOI: 10.21105/joss.08070
Louail P, Brunius C, Garcia-Aloy M, Kumler W, Storz N, Stanstrup J, Treutler H, Vangeenderhuysen P,
DOI: 10.1021/acs.analchem.5c04338
Conference: European Bioconductor Conference 2026 (EuroBioC2026) | Turku | 3.6.2026 - 5.6.2026
More information: https://doi.org/10.5281/zenodo.20921564
Conference: Metabolomics in Life Science | Umea | 27.1.2026 - 28.1.2026
More information: https://doi.org/10.21105/joss.08070