Noise Filtering Algorithm Using Gaussian Mixture Models for High-Resolution Mass Spectra of Natural Organic Matter

High-resolution mass spectra of natural organic matter (NOM) contain a large number of noise signals. These signals interfere with the correct molecular composition estimation during nontargeted analysis because formula-assignment programs find empirical formulas for such peaks as well. Previously proposed noise filtering methods that utilize the profile of the intensity distribution of mass spectrum peaks rely on a histogram to calculate the intensity threshold value. However, the histogram profile can vary depending on the user settings. In addition, these algorithms are not automated, so they are handled manually. To overcome the mentioned drawbacks, we propose a new algorithm for noise filtering in mass spectra. This filter is based on Gaussian Mixture Models (GMMs), a machine learning method to find the intensity threshold value. The algorithm is completely data-driven and eliminates the need to work with a histogram. It has no customizable parameters and automatically determines the noise level for each individual mass spectrum. The algorithm performance was tested on mass spectra of natural organic matter obtained by averaging a different number of microscans (transients), and the results were compared with other noise filters proposed in the literature. Finally, the effect of this noise filtering approach on the fraction of peaks with assigned formulas was investigated. It was shown that there is always an increase in the identification rate, but the magnitude of the effect changes with the number of microscans averaged. The increase can be as high as 15%.