A chemometric strategy to automatically screen selected ion monitoring ions for gas chromatography–mass spectrometry-based pseudotargeted metabolomics

The pseudotargeted metabolomics based on gas chromatography-mass spectrometry (GC-MS) has the advantage of filtering out artifacts originating from sample treatment and accurately quantifying underlying compounds in the analyzed samples. However, this technique faces the problem of selecting high-quality selective ions for performing selected ion monitoring (SIM) on instruments. In this work, we proposed AntDAS-SIMOpt, an automatic untargeted strategy for SIM ion optimization that was accomplished on the basis of an experimental design combined with advanced chemometric algorithms. First, a group of diluted quality control samples was used to screen underlying compounds in samples automatically. Ions in each of the resolved mass spectrum were then evaluated by using the developed algorithms to identify the SIM ion. A Matlab graphical user interface (GUI) was designed to facilitate routine analysis, which can be obtained from http://www.pmdb.org.cn/antdassimopt. The performance of the developed strategy was comprehensively investigated by using standard and complex plant datasets. Results indicated that AntDAS-SIMOpt may be useful for GC-MS-based metabolomics.