Cross-Disease Breathomics by PTR-TOF-MS: Multiclass Machine Learning and Network Remodeling Across Asthma, COPD, Cystic Fibrosis, and Lymphangioleiomyomatosis

Malika Mustafina, Artemiy Silantyev, Aleksandr Suvorov, Stanislav Krasovskiy, Marina Makarova, Alexander Chernyak, Olga Suvorova, Anna Shmidt, Daria Gognieva, Aleksandra Bykova, Nana Gogiberidze, Andrei Akselrod, Andrey Belevskiy, Sergey Avdeev, Vladimir Betelin, Abram Syrkin, Philipp Kopylov

Chronic obstructive and inflammatory lung diseases share overlapping clinical manifestations and spirometric features, complicating differential diagnosis and monitoring. In this study, we performed an integrative real-time proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS) breathomics analysis to assess whether exhaled volatile organic compound (VOC) profiles enable multiclass discrimination among bronchial asthma (BA), chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and lymphangioleiomyomatosis (LAM), with healthy individuals as controls. Breath VOC data from 843 subjects were analyzed using a stratified 70/30 train/test split. An ensemble feature selection strategy based on gradient boosting (XGBoost with SMOTE within cross-validation) identified stable VOC panels (top 25% selection probability), yielding 29 VOCs and 31 features including clinical covariates. On the independent test set, the VOC-only model achieved a macro-averaged one-vs-one (OvO) AUC of 0.866 (95% CI 0.829–0.903), while the combined model improved to 0.888 (95% CI 0.853–0.919), indicating modest value of clinical variables. Pairwise analysis demonstrated highest discrimination for CF (AUC up to 0.988), whereas BA and LAM showed lower sensitivity (<0.60), likely reflecting heterogeneity and limited sample size. Given differences in age, sex, BMI, and smoking status across cohorts, confounding effects were assessed, confirming that VOC signatures retain independent diagnostic information. Disease-specific VOC interaction networks revealed distinct remodeling patterns, with central metabolites not captured by univariate analysis. Overall, PTR-TOF-MS breathomics demonstrates proof-of-concept multiclass discrimination across chronic lung diseases.