Nontargeted screening of aldehydes and ketones by chemical isotope labeling combined with ultra-high performance liquid chromatography-high resolution mass spectrometry followed by hybrid filtering of features

Aldehydes and ketones are important carbonyl compounds that are widely present in foodstuffs, biological organisms and human living environment. However, it is still challenging to comprehensively detect and capture them using liquid chromatography - mass spectrometry. In this work, a chemical isotope labeling (CIL) coupled with ultra-high performance liquid chromatography - high resolution mass spectrometry (UHPLC-HRMS) strategy was developed for the capture and detection of this class of compounds. 2,4-Dinitrophenylhydrazine (DNPH) and isotope-labeled DNPH (DNPH-d3) were utilized to selectively label the target analytes. To address the difficulties in processing UHPLC-HRMS data, a post-acquisition data processing method called MSFilter was proposed to facilitate the screening and identification aldehydes and ketones in complex matrices. The MSFilter consists of four independent filters, namely statistical characteristic-based filtering, mass defect filtering, CIL paired peaks filtering, and diagnostic fragmentation ion filtering. These filters can be used individually or in combination to eliminate unrelated interfering MS features and efficiently detect DNPH-labeled aldehydes and ketones. The results of a mixture containing 48 model compounds showed that although all individual filtering methods could significantly reduce more than 95% of the raw MS features with acceptable recall rates above 85%, but they had relatively high false positive ratios of over 90%. In comparison, the hybrid filtering method combining four filters is able to eliminate massive interfering features (> 99.5%) with a high recall rate of 81.25% and a much lower false positive ratio of 15.22%. By implementing the hybrid filtering method in MSFilter, a total of 154 features were identified as potential signals of CCs from the original 45,961 features of real tobacco samples, of which 70 were annotated. We believe that the proposed strategy is promising to analyze the potential CCs in complex samples by UHPLC-HRMS.