In mass spectrometry bottom-up proteomics, proteins in complex biological samples are enzymatically digested into peptides, which undergo at least two rounds of mass spectrometry analysis . First, populations of intact peptides are analyzed (the MS1 scan), and then, populations of peptide fragments are examined (the MS2 scan). This process results in a collection of mass spectra, and the immediate analysis challenge posed by each MS2 spectrum is to identify the amino acid sequence of the peptide responsible for generating the spectrum.