CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification

TLDR

Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). The authors developed CFM‑ID to predict ESI‑MS/MS spectra from chemical structures and to aid compound identification, and they present significant improvements to its performance and speed. The updated CFM‑ID 3.0 incorporates a rule‑based lipid fragmentation model, integrates experimental spectra and metadata, introduces new scoring functions that raise accuracy by 21.1 %, and adds a chemical classification algorithm that correctly classifies unknowns in over 80 % of cases. CFM‑ID 3.0 demonstrates markedly improved spectral prediction accuracy, faster processing, and enhanced compound identification, and is freely available as a web server with open‑source code.

Abstract

Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was developed to accurately predict electrospray ionization-MS/MS (ESI-MS/MS) spectra from chemical structures and to aid in compound identification via MS/MS spectral matching. While earlier versions of CFM-ID performed very well, CFM-ID’s performance for predicting the MS/MS spectra of certain classes of compounds, including many lipids, was quite poor. Furthermore, CFM-ID’s compound identification capabilities were limited because it did not use experimentally available MS/MS spectra nor did it exploit metadata in its spectral matching algorithm. Here, we describe significant improvements to CFM-ID’s performance and speed. These include (1) the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID; (2) the inclusion of experimental MS/MS spectra and other metadata to enhance CFM-ID’s compound identification abilities; (3) the development of new scoring functions that improves CFM-ID’s accuracy by 21.1%; and (4) the implementation of a chemical classification algorithm that correctly classifies unknown chemicals (based on their MS/MS spectra) in >80% of the cases. This improved version called CFM-ID 3.0 is freely available as a web server. Its source code is also accessible online.