The effect of alternating fragmentor voltages of LC-MS in full scan mode on data quality: A comparative study

Abstract

The use of chemometrics for liquid chromatography-full scan mass spectrometry data analysis has become popular in untargeted metabolomics and targeted quantitative analysis. However, MS parameters that affect data quality are often neglected by researchers. The present study aims to investigate the effect of in-source fragmentor voltage, a key parameter in full scan mode, on the quality of LC-MS data mainly from the perspective of quantitative analysis. Published full scan LC-MS data recorded at four alternating fragmentor voltages were analyzed by self-weighted alternating trilinear decomposition (SWATLD) algorithm. Predicted results and analytical figures of merit of analytes were selected as key indicators for evaluating data quality. Fragmentor voltage indirectly affects figures of merit of an analyte by changing its total ion current chromatogram (TIC) intensity and extent of in-source fragmentation (ISF). No significant correlation is observed between selectivity (SEL) and fragmentor voltage. Sensitivity (SEN) and limit of detection (LOD) are mainly influenced by the TIC intensity of the analyte. Hence, considering the uncertainty effect of fragmentor voltage on SEL, as a compromise, fragmentor voltage at which the analyte has the maximum TIC intensity will be selected as the optimum one, which can ensure better SEN and LOD results. This work may provide new insights into the quality evaluation of full scan LC-MS data recorded at different fragmentor voltages, and help researchers to achieve the best analytical performance when conducting targeted quantitative analysis.