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Fabian Aicheler, Jia Li, Rainer Lehmann, Guowang Xu, and Oliver Kohlbacher (2015)

Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches

Anal. Chem., 87(15):7698-704.

Identification of lipids in non-targeted lipidomics based on liquid-chromatography coupled to mass spectrometry (LC-MS) is still a major issue. While both accurate mass and fragment spectra contain valuable information, retention time (RT) information can be used to augment this data. We present a retention time model based on machine learning approaches which enables an improved assignment of lipid structures and automated annotation of lipidomics data. In contrast to common approaches we used a complex mixture of 201 lipids originating from fat tissue instead of a standard mixture to train a support vector regression (SVR) model including molecular structural features. The cross-validated model achieves correlation coefficients between predicted and experimental retention times of r = 0.989. Of note, as few as 50 reference lipids of different classes are sufficient to adapt to different chromatographic setups. Combining our retention time model with identification via accurate mass search (AMS) of lipids against the comprehensive LIPID MAPS database, retention time filtering can significantly reduce the rate of false positives in complex data sets like adipose tissue extracts. In our case, filtering with retention time information removed more than half of the potential identifications, while retaining 95 % of the correct identifications. Combination of high-precision retention time prediction and accurate mass can thus significantly narrow down the number of hypotheses to be assessed for lipid identification in complex lipid pattern like tissue profiles.