What Is Mass Spectrometry?

Mass spectrometry is an analytical technique that measures the mass-to-charge ratios of ionized molecules in order to determine what they are and how much of them is present. In peptide testing, that measurement answers the identity question — is this molecule the sequence on the label — with unmatched specificity.

Every mass spectrometer has three functional sections. The ion source converts molecules into gas-phase ions (electrospray for liquid samples; MALDI for matrix-dried samples). The mass analyzer separates ions by m/z — quadrupoles, time-of-flight, Orbitrap, each trading speed, resolution, and cost differently. The detector registers the separated ions and their abundances, producing the spectrum.

Three things: the molecular weight, which must match the theoretical mass of the labeled sequence; the isotope and charge envelope, which carries information about the molecule's size and heterogeneity; and with fragmentation (MS/MS), the sequence itself. Together these anchor the identity half of a peptide COA, while HPLC anchors the purity half — the interlock is explained in the characterization pillar.

Chromatography first separates a mixture in time; MS then measures each separated component. Coupled LC-MS is the modern standard for peptide batch analysis: HPLC provides the purity chromatogram and MS confirms the identity of the main peak and flags mass-differentiated impurities. The separation chemistry is covered in the purification pillar.

m/z: mass-to-charge ratio, the x-axis of a spectrum. Deconvolution: recovering the neutral mass from a multi-charge envelope. Isotope envelope: the family of peaks from natural isotopes. MS/MS: fragmenting a selected ion to read the sequence. Adduct: an ion plus a salt companion (Na+, K+). The deeper characterization workflow continues in mass spectrometry for peptide characterization.