A synthetic MALDI-TOF MS atlas for microbial classification across hospitals

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Abstract Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI–TOF) mass spectrometry (MS) is central to routine clinical microbiology for species identification. Its combination with machine learning is constrained by fragmented public datasets, species imbalance and acquisition-related variability. Synthetic datasets could provide more training data, but they must preserve the spectral information needed to make predictions on real samples. Here, we present an open, synthetic MALDI–TOF MS atlas comprising 4.3 million spectra across 43 clinically relevant bacterial species. To construct the atlas, we harmonised public repositories from three countries and trained a species- and institution-conditioned concept-bottleneck generative variational autoencoder (CBGM-VAE) on 179,086 measured spectra. We assessed the atlas as both a stand-alone training resource and a complement to real data, using bacterial species classification as a functional benchmark. Evaluation comprised 7,269 real spectra from more than 7 countries, 24 institutions and multiple acquisition platforms, covering: temporal, technical, biological and combined shifts. A neural network trained only on synthetic spectra achieved F1 scores ranging from 0.788 to 1.000 across external cohorts. When synthetic spectra were combined with real training data, classification performance improved or matched using real data only. These findings demonstrate that the atlas retains transferable information and can complement measured data. The openly released atlas provides a reusable resource for supervised learning and benchmarking. It can also be explored for pretraining representation-learning and foundation models in MALDI–TOF MS research.