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

Small Molecule Identification with MOLGEN and Mass Spectrometry

DLR: German Aerospace Center, Earth Observation Center (EOC), Münchner Strasse 20, D-82234 Oberpfaffenhofen–Wessling, Germany
Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
Author to whom correspondence should be addressed.
Received: 28 March 2013 / Revised: 16 May 2013 / Accepted: 17 May 2013 / Published: 28 May 2013


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. View Full-Text
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

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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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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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