How Well Can We Predict Mass Spectra from Structures? Benchmarking Competitive Fragmentation Modeling for Metabolite Identification on Untrained Tandem Mass Spectra

Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID) is a machine learning tool to predict in silico tandem mass spectra (MS/MS) for known or suspected metabolites for which chemical reference standards are not available. As a machine learning tool, it relies on both an underlying statistical model and an explicit training set that encompasses experimental mass spectra for specific compounds. Such mass spectra depend on specific parameters such as collision energies, instrument types, and adducts which are accumulated in libraries. Yet, ultimately prediction tools that are meant to cover wide expanses of entities must be validated on cases that were not included in the initial training and testing sets. Hence, we here benchmarked the performance of CFM-ID 4.0 to correctly predict MS/MS spectra for spectra that were not included in the CFM-ID training set and for different mass spectrometry conditions. We used 609,456 experimental tandem spectra from the NIST20 mass spectral library that were newly added to the previous NIST17 library version. We found that CFM-ID's highest energy prediction output would maximize the capacity for library generation. Matching the experimental collision energy with CFM-ID's prediction energy produced the best results, even for HCD-Orbitrap instruments. For benzenoids, better MS/MS predictions were achieved than for heterocyclic compounds. However, when exploring CFM-ID's performance on 8,305 compounds at 40 eV HCD-Orbitrap collision energy, >90% of the 20/80 split test compounds showed <700 MS/MS similarity score. Instead of a stand-alone tool, CFM-ID 4.0 might be useful to boost candidate structures in the greater context of identification workflows.