De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4

Methods Mol Biol. 2020;2104:185-207. doi: 10.1007/978-1-0716-0239-3_11.


SIRIUS 4 is the best-in-class computational tool for metabolite identification from high-resolution tandem mass spectrometry data. It offers de novo molecular formula annotation with outstanding accuracy. When searching fragmentation spectra in a structure database, it reaches over 70% correct identifications. A predicted fingerprint, which indicates the presence or absence of thousands of molecular properties, helps to deduce information about the compound of interest even if it is not contained in any structure database. Here, we present best practices and describe how to leverage the full potential of SIRIUS 4, how to incorporate it into your own workflow, and how it adds value to the analysis of mass spectrometry data beyond spectral library search.

Keywords: Annotation; LC–MS/MS; Metabolite identification; Metabolomics; Molecular formula; SIRIUS; Structure prediction.

Publication types

  • Review

MeSH terms

  • Chromatography, Liquid
  • Computational Biology* / methods
  • Databases, Factual*
  • Humans
  • Metabolomics* / methods
  • Molecular Structure
  • Software*
  • Spectrometry, Mass, Electrospray Ionization
  • Structure-Activity Relationship
  • Tandem Mass Spectrometry
  • User-Computer Interface
  • Workflow