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Metabolites 2013, 3(2), 440-462; doi:10.3390/metabo3020440
Article

Small Molecule Identification with MOLGEN and Mass Spectrometry

1
 and
2,*
Received: 28 March 2013 / Revised: 16 May 2013 / Accepted: 17 May 2013 / Published: 28 May 2013

Abstract

This paper details the MOLGEN entries for the 2012 CASMI contest for small molecule identification to demonstrate structure elucidation using structure generation approaches. Different MOLGEN programs were used for different categories, including MOLGEN–MS/MS for Category 1, MOLGEN 3.5 and 5.0 for Category 2 and MOLGEN–MS for Categories 3 and 4. A greater focus is given to Categories 1 and 2, as most CASMI participants entered these categories. The settings used and the reasons behind them are described in detail, while various evaluations are used to put these results into perspective. As one author was also an organiser of CASMI, these submissions were not part of the official CASMI competition, but this paper provides an insight into how unknown identification could be performed using structure generation approaches. The approaches are semi-automated (category dependent) and benefit greatly from user experience. Thus, the results presented and discussed here may be better than those an inexperienced user could obtain with MOLGEN programs.
Keywords: CASMI; mass spectrometry; MOLGEN; MOLGEN–MS; MOLGEN–MS/MS; small molecule identification; structure generation; structure elucidation CASMI; mass spectrometry; MOLGEN; MOLGEN–MS; MOLGEN–MS/MS; small molecule identification; structure generation; structure elucidation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Meringer, M.; Schymanski, E.L. Small Molecule Identification with MOLGEN and Mass Spectrometry. Metabolites 2013, 3, 440-462.

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