Migration time correction for dual pressure capillary electrophoresis in semi‐targeted metabolomics study

Abstract

Migration time fluctuation strongly affects peak alignment and identification of unknown compounds, making migration time correction an essential step in capillary electrophoresis (CE)-based metabolomics. To obtain more reliable information, metabolites with different apparent mobilities are analyzed by tandem mass spectrometry. Applying a small pressure is a common practice for reducing the analysis time of anions in a positive mode CE, known as the pressure-assisted CE. However, applying pressure may reduce the separation efficiency and can be undesirable for cation analysis. A simple way to address this issue is to increase the pressure after a certain time, during the separation. We term this practice as dual pressure CE. However, changing the pressure during the CE separation complicates migration time correction. Previous migration time correction methods were established based on a consistent electroosmotic flow and a constant pressure-driven bulk-flow velocity. We proposed a new correction method to support the peak alignment when dual pressure CE is used. A Python-based script was developed to implement dual pressure CE migration time correction for semi-targeted metabolomics study performed by a multiple reaction monitoring-based method. This script can help select suitable endogenous metabolites as correction markers, perform migration time correction, and conduct peak alignment. A case study showed that migration time precision of 156 metabolites in 32 samples can be improved from 4.8 to 11.4%RSD (relative standard deviation) to less than 1.8%RSD.

Capillary Electrophoresis: A Three-Year Literature Review

“…A.; Tan, J.; Li, Y.; Miao, S.; Scotland, K. B.; Chew, B. H.; Lange, D.; Chen, D. D. Y. Electrophoresis , Vol. 43 , Issue 15 (ref ). Copyright 2022 Wiley.…”

“…Huang et al introduced a migration time correction method for a semitargeted metabolomics study using a homemade Python script (Figure 6). 194 This method facilitated peak alignment among CE-MS runs with varying bulk BGE velocities, leading to a substantial improvement in the precision of migration time applied in the subsequent steps of metabolomic data processing.…”

Simultaneous Quantitation and Discovery (SQUAD) Analysis: Combining the Best of Targeted and Untargeted Mass Spectrometry-Based Metabolomics

“…In another example, MS 2 spectra of metabolites resulting from a QTRAP instrument were compared with references MS 2 spectra for the confident annotation of potential biomarkers of fertility decline in elderly women, which might help in finding the corresponding traditional Chinese medicine treatment and exploring its mechanism of action [ 60 ]. Moreover, a method that used tandem MS coupled to the capillary electrophoresis (CE) technique was used for improved annotation of unknown compounds utilizing both the MS/MS fragmentation patterns and CE migration time [ 61 ], yet the authors called the approach semi-targeted metabolomics. Bayle et al, on the other hand, performed a multi-platform approach using both liquid and gas chromatography coupled to MS to improve the coverage of the physiochemical diverse nutrient markers in plasma.…”

Using variable data independent acquisition for capillary electrophoresis-based untargeted metabolomics

“…However, the use of DIA coupled with chromatogram deconvolution has not been validated for untargeted metabolomics using CE-MS/MS. Additionally, large MT drift between samples often results in MT differences of more than 1.0 min, making peak annotation and alignment challenging 12,13,14 . In fact, high reproducibility of chromatographic peak elution time (less than 0.2 min between sample injections) increases confidence in peak alignments and reduces false peak calls in the alignment result.…”