Chemical isotope labeling-assisted liquid chromatography-mass spectrometry enables sensitive and accurate determination of dipeptides and tripeptides in complex biological samples

Small peptides have attracted increasing attention for their unique features and diverse biological functions. Achieving rapid separation and accurate quantification, however, remains a challenge because of their low abundance and the co-existence of numerous structural isomers. In this study, we developed a novel approach using isotope chemical labeling for ultrasensitive determination of di/tripeptides in biological samples. We successfully synthesized a novel derivatization reagent, 4-(2-(ethoxymethylene)-3-oxobutanamido)-N,N,N-trimethylbenzenaminium iodide (EOTMBA) as well as its deuterium-labeled isotope reagent (d3-EOTMBA). A total of 97 small peptides, including 89 dipeptides and 8 tripeptides, could be completely derivatized in methanol within 1.5 h at 60°C. After EOTMBA labeling, analysis of these di/tripeptides were achieved within 22 min by LC-MS/MS analysis. The method demonstrated 86.3-113% accuracy and the limit of quantification ranged from 0.25 fmol/L to 5 nmol/L. Using this method, we achieved ultrasensitive and accurate quantification of di/tripeptides in 147 plasma, 49 urine and 46 bile samples obtained from healthy individuals and patients with biliary tract diseases. The identified differential di/tripeptide biomarker panels showed promising diagnostic performance for patients with biliary tract cancer with area under the receiver operating curve values from 0.870 to 0.996. Furthermore, this method was successfully applied to quantify di/tripeptides in the extract of an animal-derived traditional Chinese medicine, Eupolyphaga sinensis Walker. These findings highlight the possible application of the analytical method in clinics and for the purposes of quality control of traditional Chinese medicines.