An automatic peak finding method for LC‐MS data using Gaussian second derivative filtering

A highly automated procedure for localising and characterising peaks in the chromatographic time domain of LC‐MS data has been developed. The work was initiated by an identified need to facilitate the detection and tracking of chromatographic peaks during method development for the analysis of impurities in pharmaceutical products. The algorithm is mainly based on a digital filter for which the settings are automatically adapted to the data set under study. The procedure was evaluated for synthetic data sets with various S/N levels, peak widths and baseline properties. It was found that even for the worst case tested with S/N=10 and a high variability in the baseline, 94% of the simulated analytical peaks could be detected without producing any false‐positive identifications. Furthermore, the number of correctly estimated peak heights and peak widths falling within a 10% error of the true values were 94 and 91%, respectively. For experimental data sets, peak height, and width estimations were more difficult, but the processed reconstructions showed an excellent agreement with the analytical signals of the raw data, and also a clearly improved visualisation in total ion‐ and base‐peak chromatograms.