Liquid-chromatography retention order prediction for metabolite identification

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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2018-09-01
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Language
en
Pages
9
875-883
Series
Bioinformatics, Volume 34, issue 17
Abstract
Motivation: Liquid Chromatography (LC) followed by tandem Mass Spectrometry (MS/MS) is one of the predominant methods for metabolite identification. In recent years, machine learning has started to transform the analysis of tandem mass spectra and the identification of small molecules. In contrast, LC data is rarely used to improve metabolite identification, despite numerous published methods for retention time prediction using machine learning. Results: We present a machine learning method for predicting the retention order of molecules; that is, the order in which molecules elute from the LC column. Our method has important advantages over previous approaches: We show that retention order is much better conserved between instruments than retention time. To this end, our method can be trained using retention time measurements from different LC systems and configurations without tedious pre-processing, significantly increasing the amount of available training data. Our experiments demonstrate that retention order prediction is an effective way to learn retention behaviour of molecules from heterogeneous retention time data. Finally, we demonstrate how retention order prediction and MS/MS-based scores can be combined for more accurate metabolite identifications when analyzing a complete LC-MS/MS run.
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Keywords
TANDEM MASS-SPECTRA, TIME PREDICTION, FRAGMENTATION, METABOLOMICS, PERFORMANCE, REGRESSION, DATABASES
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Citation
Bach, E, Szedmak, S, Brouard, C, Boecker, S & Rousu, J 2018, ' Liquid-chromatography retention order prediction for metabolite identification ', Bioinformatics, vol. 34, no. 17, pp. 875-883 . https://doi.org/10.1093/bioinformatics/bty590