New Method Developed for Comprehensive Analysis of Dipeptides

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Dipeptides have gained significant attention due to their biological functions and potential as disease biomarkers. Analyzing dipeptides in complex matrices can provide insight into their functions and aid in biomarker discovery. Researchers at the University of Alberta have developed a method for high-coverage detection and accurate relative quantification of dipeptides using differential chemical isotope labeling (CIL) of dipeptides with dansylation and liquid chromatography orbital trap tandem mass spectrometry (LC–orbital trap-MS).

The team used an optimized LC gradient to separate dansyl-dipeptides, including positional isomers. They optimized MS/MS collision energy in orbital trap MS to provide characteristic fragment ion information to sequence dansyl-dipeptides. A CIL standard library consisting of retention time, MS, and MS/MS information of a whole set of 400 dansyl-dipeptides was constructed to facilitate rapid dipeptide identification.

For qualitative analysis of dipeptides in real samples, IsoMS data processing software's parameters were tuned to improve the coverage of dipeptide annotation. Data-dependent acquisition was carried out to improve the reliability of dipeptide identification. The method was successfully used to identify a total of 321 dipeptides in rice wines and 105 dipeptides in human serum samples.


For quantitative analysis, the researchers demonstrated that the intensity ratios of the peak pairs from 96% of the dansyl-dipeptides detectable in a 1:1 mixture of 12C- and 13C-labeled rice wine samples were within ±20% of an expected value of 1.0. More than 90% of dipeptides were detected with a relative standard deviation of less than 10%, showing good performance of relative quantification.

This newly developed method provides a comprehensive analysis of dipeptides and can be applied to the detection and quantification of dipeptides in complex matrices. The study is published in Analytical Chemistry and was conducted by Zhan Cheng and Liang Li from the Department of Chemistry at the University of Alberta. The research opens up new opportunities for investigating the roles of dipeptides in biological systems and the potential use of dipeptides as biomarkers for various diseases.


Cheng, Z.; Li, L. Development of Chemical Isotope Labeling Liquid Chromatography Orbitrap Mass Spectrometry for Comprehensive Analysis of Dipeptides. Anal. Chem. 2023. DOI: