IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets.

Poor chemical annotation of high-resolution mass spectrometry data limit applications of untargeted metabolomics datasets. Our new software, the Integrated Data Science Laboratory for Metabolomics and Exposomics â€" Composite Spectra Analysis (IDSL.CSA) R package, generates composite mass spectra libraries from MS1-only data, enabling the chemical annotation of LC/HRMS peaks regardless of the availability of MS2 fragmentation spectra. We demonstrate comparable annotation rates for commonly detected endogenous metabolites in human blood samples using IDSL.CSA libraries versus data dependent acquisition (DDA) MS2 libraries in validation tests. IDSL.CSA can create and search composite spectra libraries from any untargeted metabolomics dataset generated using high-resolution mass spectrometry coupled to liquid or gas chromatography. The cross-applicability of these libraries across independent studies can improve overall annotation rates in metabolomics and exposomics projects, providing access to new biological insights that may be missed due to the lack of MS2 fragmentation data. The IDSL.CSA package is available in the R CRAN repository ( https://cran.r-project.org/package=IDSL.CSA . Detailed documentation and tutorials are provided at https://github.com/idslme/IDSL.CSA .