Systems and methods are provided for obtaining raw mass spectrometry data from samples, determining signals present across the samples, and separating the raw mass spectrometry data into discrete intervals in each of the samples. At each interval of the discrete intervals of the raw mass spectrometry data, a local highest intensity signal, relative to any other signal within each interval, is determined, and a frequency of occurrence of each local highest intensity signal across the samples is determined. A subset of local highest intensity signals is retrieved based on respective frequencies of occurrence of the local highest intensity signals. The subset of the local highest intensity signals is ingested into a machine learning model.