---
title: "SpacePath expands spatial metabolomics and lipidomics analysis while preserving annotation ambigui"
id: "biorxiv-9-spacepath-enables-pathway-and-molecular-family-analysis-beyond-annotation"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-9-spacepath-enables-pathway-and-molecular-family-analysis-beyond-annotation"
content_type: "clinical_feed_article"
specialty: "Radiology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1?rss=1"
published_at: "2026-10-22T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# SpacePath expands spatial metabolomics and lipidomics analysis while preserving annotation ambigui
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-9-spacepath-enables-pathway-and-molecular-family-analysis-beyond-annotation
- **Specialty:** [Radiology](https://medichelpline.com/clinical-feed/radiology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1?rss=1)
- **Published At:** 2026-10-22T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- SpacePath is a computational framework designed for **spatial metabolomics** and **lipidomics** that preserves ion-to-compound assignment ambiguity rather than forcing single annotations. - The pipeline scores canonical biochemical **pathways** at each tissue location while retaining multiple candidate compound matches per ion; investigators reported this approach increases pathway-covered assignments versus strict mapping. - Authors observed that conventional pathway mappings accounted for about 1% of molecular assignments on average; the combined SpacePath representation covered 24% of pooled assignments, indicating broader spatial biochemical coverage. - SpacePath also groups unmapped MS1 assignments into de novo molecular families based on chemical similarity, allowing spatial analysis of related features that fall outside canonical pathways. - Benchmarking used four public spatial lipidomics datasets: healthy mouse brain, cerebellum, a demyelination model, and human bladder cancer; the study team observed recovery of previously reported spatial patterns in those data. - In newly acquired glioblastoma xenograft datasets, the cohort showed distinct lipid programs separating tumor from surrounding brain regions; the study team reported independent SpiderMass-MS/MS confirmation of four tumor-associated features drawn from a de novo family. - The authors made code and data available via Zenodo and GitHub links provided in the preprint; the preprint has not been peer reviewed and authors declared no competing interests.
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Johanna Galvis 1 University of Bordeaux, CNRS, IBGC UMR 5095, 1 rue Camille Saint Saens, Bordeaux, 33077, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Johanna%2BGalvis%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Galvis%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJohanna%2BGalvis%2B) * [ORCID record for Johanna Galvis](http://orcid.org/0000-0001-9852-3798 "Open in new tab") Mélanie Moreau 2 Univ. Bordeaux, CNRS, Bordeaux Proteome, UAR 2046, F-33076, Bordeaux, 33076, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=M%C3%A9lanie%2BMoreau%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Moreau%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AM%25C3%25A9lanie%2BMoreau%2B) * [ORCID record for Mélanie Moreau](http://orcid.org/0000-0003-4030-9654 "Open in new tab") Sebastian Lillo 1 University of Bordeaux, CNRS, IBGC UMR 5095, 1 rue Camille Saint Saens, Bordeaux, 33077, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Sebastian%2BLillo%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Lillo%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASebastian%2BLillo%2B) * [ORCID record for Sebastian Lillo](http://orcid.org/0009-0005-1702-6869 "Open in new tab") Doriane Bomont 1 University of Bordeaux, CNRS, IBGC UMR 5095, 1 rue Camille Saint Saens, Bordeaux, 33077, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Doriane%2BBomont%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Bomont%20D&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ADoriane%2BBomont%2B) Léa Ledoux 3 PRISM Laboratory, University of Lille, Campus Cite Scientifique, Bat SH2, Villeneuve d Ascq, 59655, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=L%C3%A9a%2BLedoux%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Ledoux%20L&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AL%25C3%25A9a%2BLedoux%2B) * [ORCID record for Léa Ledoux](http://orcid.org/0009-0007-8963-7073 "Open in new tab") Yanis Zirem 3 PRISM Laboratory, University of Lille, Campus Cite Scientifique, Bat SH2, Villeneuve d Ascq, 59655, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Yanis%2BZirem%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Zirem%20Y&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AYanis%2BZirem%2B) * [ORCID record for Yanis Zirem](http://orcid.org/0009-0003-1237-4448 "Open in new tab") Michel Salzet 3 PRISM Laboratory, University of Lille, Campus Cite Scientifique, Bat SH2, Villeneuve d Ascq, 59655, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Michel%2BSalzet%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Salzet%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AMichel%2BSalzet%2B) * [ORCID record for Michel Salzet](http://orcid.org/0000-0001-9875-9004 "Open in new tab") Isabelle Fournier 3 PRISM Laboratory, University of Lille, Campus Cite Scientifique, Bat SH2, Villeneuve d Ascq, 59655, France; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Isabelle%2BFournier%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Fournier%20I&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AIsabelle%2BFournier%2B) * [ORCID record for Isabelle Fournier](http://orcid.org/0000-0003-1096-5044 "Open in new tab") Nicolas Desbenoit 4 Univ. 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University of Bordeaux, Bordeaux Bioinformatics Center CBiB, 146 rue Leo Saignat, Bordeaux, 33076, France * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Macha%2BNikolski%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Nikolski%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AMacha%2BNikolski%2B) * [ORCID record for Macha Nikolski](http://orcid.org/0000-0001-6059-577X "Open in new tab") * For correspondence: macha.nikolski@u-bordeaux.fr * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5894117/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5894117/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5894117/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5894117/1) * [Data/Code](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1.external-links)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_data_code/node:5894117/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.16.759546v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5894117/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Mass spectrometry imaging (MSI) maps metabolites and lipids in tissue with spatial resolution, but molecular identity remains partly resolved: single ions match multiple candidate compounds, and most detected metabolites and lipids fall outside canonical biochemical pathways. We developed SpacePath, a computational framework that retains ion-to-compound ambiguity, scores canonical pathways across tissue locations, and groups assignments that were unmapped to pathways into de novo molecular families by chemical similarity. Pathway mappings covered on average only 1% of molecular assignments, whereas the combined SpacePath representation covered 24% of pooled assignments. Benchmarking on four public spatial lipidomics datasets (healthy mouse brain, cerebellum, a demyelination model, and human bladder cancer) recovered previously reported spatial patterns. In newly acquired glioblastoma xenograft datasets, SpacePath identified lipid programs specific to tumor and surrounding brain, and SpiderMass-MS/MS independently confirmed four tumor-associated features from a de novo family, refining the initial MS1 assignments. SpacePath extends the spatial interpretation of MSI data beyond canonical pathways while preserving annotation uncertainty. ### Competing Interest Statement The authors have declared no competing interest. ## Footnotes * * ## Funder Information Declared PLBIO 2021 “Biologie et Sciences du Cancer” of the Institut National du Cancer (INCA), France, 221284 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. [Donate to openRxi
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