Mass Spectrometry and Machine Learning Reveal Stool-Based Multi-Signatures for Diagnosis and Longitudinal Monitoring of Inflammatory Bowel Disease
Confirmed Presenter: Elmira Shajari, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
Room: 02F
Format: In person
Moderator(s): Wout Bittremieux
Authors List: Show
- Elmira Shajari, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- David Gagné, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- Patricia Roy, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- Mandy Malick, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- Maxime Delisle, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- François-Michel Boisvert, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- Marie Brunet, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
- Jean-François Beaulieu, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada, Canada
Presentation Overview: Show
Background:
Monitoring inflammation activity in Inflammatory Bowel Disease (IBD) is essential for guiding treatment and preventing long-term complications. While fecal calprotectin is a common non-invasive biomarker, its diagnostic reliability declines significantly within the “gray zone” (50–300 µg/g), limiting its clinical utility. To address this challenge, we developed a stool-based proteomic biomarker panel for precise classification of inflammation activity in this diagnostically ambiguous range.
Methods:
We analyzed 155 stool samples from IBD patients for model training and reserved 53 samples for blind testing. The proteomic profiling was performed using SWATH-MS, a data-independent acquisition (DIA) mass spectrometry technique known for its reproducibility and depth. Protein- and peptide-level datasets were preprocessed separately. Feature selection was conducted using Boruta, LASSO, RF, and RFE. Features identified consistently across both data levels were prioritized. Six machine learning models (SVM, Random Forest, Naïve-Bayes, KNN, GLMnet, and XGBoost) were evaluated with 10-fold cross-validation, focusing on gray zone performance. Model interpretability was assessed using SHAP values and GO enrichment analysis explored the biological relevance of selected features.
Results:
We identified 19 protein-level and 14 peptide-level discriminatory features, with five robust overlapping markers selected for final modeling. The Support Vector Machine (SVM) model achieved the highest performance: 0.96 precision and 0.88 recall during training, and 1.00 precision and 0.86 recall in blind testing. SHAP analysis confirmed biomarker contribution, and enriched GO terms were linked to immune and inflammatory pathways.
Conclusion:
This proteomic signature offers a promising non-invasive tool for resolving diagnostic uncertainty in IBD monitoring within the gray zone.
Rapid Deployment of Interactive and Visual Web Applications for Computational Mass Spectrometry
Confirmed Presenter: Tom David Müller, University of Tübingen, Germany
Room: 02F
Format: In person
Moderator(s): Wout Bittremieux
Authors List: Show
- Tom David Müller, University of Tübingen, Germany
- Arslan Siraj, University of Tübingen, Germany
- Justin Cyril Sing, University of Toronto, Canada
- Joshua Charkow, University of Toronto, Canada
- Axel Walter, University of Tübingen, Germany
- Samuel Wein, University of Tübingen, Germany
- Ayesha Feroz, University of Tübingen, Germany
- Matteo Pilz, University of Tübingen, Germany
- Kyowon Jeong, University of Tübingen, Germany
- Mingxuan Gao, University of Toronto, Canada
- Wout Bittremieux, University of Antwerp, Belgium
- Hannes Luc Röst, University of Toronto, Canada
- Oliver Kohlbacher, University of Tübingen, Germany
- Timo Sachsenberg, University of Tübingen, Germany
Presentation Overview: Show
Mass Spectrometry (MS) is a highly versatile bioanalytical technique with a myriad of experimental approaches, instrumentation, and computational tools. If a desired analysis is not already supported by existing desktop applications, bioinformaticians often integrate scripts and tools to produce custom analyses and visualizations. While effective, this approach requires specialized expertise and limits accessibility for non-technical users. Traditional workflow systems can standardize and scale such analyses, but often lack user-friendly interfaces, visualization capabilities, and support for interactive decision-making during execution.
To address these limitations, we present two freely available open-source solutions designed to streamline MS workflow development and deployment. pyOpenMS-viz enables rapid creation of publication-ready visualizations, such as spectra, chromatograms, and peak maps with a single line of code, directly from pandas DataFrames, a common data structure in Python-based MS tools. Straightforward use cases that do not require complex development, are well supported by Jupyter notebooks enhanced with pyOpenMS-viz.
For broader accessibility and reuse, the OpenMS WebApp template offers a lightweight framework to develop interactive web applications with minimal effort. These apps guide users through uploading files, setting parameters, executing workflows involving arbitrary scripts and command line tools, and visualizing results interactively. Visualizations from pyOpenMS-viz and other libraries are fully supported. Applications can be deployed online allowing users to share results (e.g. with collaborators) via website URLs or offline via automatically generated windows executables.
Together, pyOpenMS-viz and the OpenMS WebApp template empower rapid prototyping, streamline deployment, and make MS workflows accessible to a wider scientific audience, promoting collaboration and reproducibility.