We developed a novel method for non-targeted screening of metabolites by high performance liquid chromatography-mass spectrometry with paired homologous double neutral loss scan mode after in vitro isotope labelling (IL-HPLC-PHDNL-MS). As a proof of concept, we investigated the carboxylic acid metabolite profiling in plant samples by the IL-HPLC-PHDNL-MS method. To this end, N , N -dimethylaminobutylamine (DMBA) and d 4 - N , N -dimethylaminobutylamine (d 4 -DMBA) were synthesized and utilized to label carboxylic acids. Our results show the MS response of carboxylic acids was enhanced by 20- to 40-fold after labelling. As for the IL-HPLC-PHDNL-MS analysis, DMBA and d 4 -DMBA labelled samples were mixed equally before MS analysis. Because the isotope labelled moieties (dimethylamino moiety, Me 2 N) of DMBA and d 4 -DMBA are easily ruptured and lost as neutral fragments (NL 45 and NL 49) under collision induced dissociation (CID), two neutral loss scans can be carried out simultaneously to record the signals of DMBA and d 4 -DMBA labelled samples, respectively. In this respect, the metabolites from two samples labelled with different isotope reagents are ionized at the same time but recorded separately by mass spectrometry, which can eliminate the MS response fluctuation and mutual interference. Using this method, six potential biomarkers involved in wounded tomato leaves were identified, and their structures were further elucidated by product ion scan and high resolution mass spectrometry analysis. Taken together, the IL-HPLC-PHDNL-MS method demonstrated good performance on the identification as well as relative quantification of metabolites with a carboxyl group in biological samples. The development of a method for non-targeted screening of metabolites with a carboxyl group by high performance liquid chromatography-mass spectrometry with paired homologous double neutral loss scan mode after in vitro isotope labelling was reported.