High-resolution tandem mass spectrometry is a key technology for generating peptide tags in partial amino acid sequences, which confirm the presence of proteins and enable accurate quantification of their abundance. Peptides generated from proteins via trypsin proteolysis are typically separated by their hydrophobicity using reverse-phase chromatography and then introduced into the mass spectrometer through a nanospray interface directly connected to the outlet of the chromatography column. After their molecular weights are determined, peptides are either isolated (in Data-Dependent Acquisition mode, DDA) or pooled (in Data-Independent Acquisition mode, DIA) and subsequently fragmented. The molecular weights of the resulting fragments are then measured. The initial peptide mass data helps to narrow down potential sequence candidates, while the fragmentation patterns enable precise identification of the amino acid sequence.