Computational prediction of electron ionization mass spectra to assist in GC-MS compound identification
- Felicity Allen
- Allison Pon
- Russ Greiner, Dept of Computing Science; PI of AICML
- David S. Wishart, Departments of Computing Science and Biology, University of Alberta
We describe a tool, Competitive Fragmentation Modeling for Electron Ionization (CFM-EI) that, given a chemical structure (e.g. in SMILES or InChI format), computationally predicts an electron ionization mass spectrum (EI-MS) – i.e. the type of mass spectrum commonly generated by gas chromatography mass spectrometry (GC-MS). The predicted spectra produced by this tool can be used for putative compound identification, complementing measured spectra in reference databases by expanding the range of compounds able to be considered when availability of measured spectra is limited. The tool extends CFM-ESI, a recently developed method for computational prediction of electrospray tandem mass spectra (ESI-MS/MS), but unlike CFM-ESI, CFM-EI can handle odd-electron ions and isotopes, and incorporates an artificial neural network. Tests on EI-MS data from the NIST database demonstrate that CFM-EI is able to model fragmentation likelihoods in low resolution EI-MS data, producing predicted spectra whose dot product scores are significantly better than full enumeration ’bar-code’ spectra. CFM-EI also outperformed previously reported results for MetFrag, MOLGEN-MS and Mass Frontier on one compound identification task. It also outperformed MetFrag in a range of other compound identification tasks involving a much larger data set, containing both derivatized and non-derivatized compounds. While replicate EI-MS measurements of chemical standards are still a more accurate point of comparison, CFM-EI’s predictions provide a much-needed alternative when no reference standard is available for measurement. CFM-EI is available at https://sourceforge.net/projects/cfm-id/ for download and http://cfmid.wishartlab.com as a web service.
Citation
F. Allen, A. Pon, R. Greiner, D. Wishart. "Computational prediction of electron ionization mass spectra to assist in GC-MS compound identification". Analytical Chemistry, 88(15), pp 7689-7697, July 2016.| Keywords: | Mass Spec, CFM, chemical informatics, machine learning |
| Category: | In Journal |
| Web Links: | DOI |
| Journal URL |
BibTeX
@article{Allen+al:16,
author = {Felicity Allen and Allison Pon and Russ Greiner and David S.
Wishart},
title = {Computational prediction of electron ionization mass spectra to
assist in GC-MS compound identification},
Volume = "88",
Number = "15",
Pages = {7689-7697},
journal = {Analytical Chemistry},
year = 2016,
}Last Updated: February 10, 2020Submitted by Sabina P
