Non-targeted analysis (NTA) is a growing approach to uncover the known and unknown unknowns in complex samples, containing thousands of chemical constituents. Due to the complexity of the samples, coming from, for example, environmental or biological background, adequate data processing approaches are required for resolving the information belonging to unique chemical constituents. One of the most commonly used approaches to perform NTA is liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). LC-HRMS, even though powerful in separating chemical constituents, is not able to fully resolve complex samples. This lack of full separation may result in overlapping signals from multiple chemicals (e.g. matrix signal). These overlapping signals potentially result in noisy MS/MS spectra, particularly in data-independent acquisition (DIA) experiments.