Improving accuracy of peak-pair intensity ratio measurement in differential chemical isotope labeling LC–MS for quantitative metabolomics

Abstract

High-performance chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC–MS) has become a powerful platform for quantitative metabolomic analysis. With differential isotope labeling of individual samples (e.g., 12C2-labeling) and a control sample (e.g., 13C2-labeling), the resulting mixtures (12C2-labeled sample and 13C2-labeled control) can be analyzed using LC–MS to detect peak pairs of labeled metabolites from which the peak-pair intensity ratios can be measured to provide the basis of relative quantification of metabolites in different samples. Depending on the mass difference of the light and heavy reagents used and the number of reagent tags attached to a metabolite, the mass difference within a peak pair can be as low as 2 Da. With 2-Da difference, the natural isotopologue of the light labeled molecular ion can overlap with that of the heavy labeled molecular ion of the same metabolite, causing potential interference in the measurement of the heavy peak intensity. In this work, we report our study of the natural isotope relative peak intensity of the most common elements in human endogenous metabolites, including carbon, hydrogen, oxygen, nitrogen, phosphor and sulfur, and their contributions to the intensity of the 2-Da-heavier labeled peak. We propose a simple data processing method to estimate and remove the natural isotope interference for improving the measurement accuracy of peak-pair intensity ratios.