Mass spectrometry (MS) turns molecules into ions and separates them by mass-to-charge ratio (m/z). For peptides the two common ionisation methods are electrospray ionisation (ESI), which typically produces a series of multiply protonated ions, and matrix-assisted laser desorption/ionisation (MALDI), which mostly produces singly charged ions.
Identity is confirmed when the observed mass matches the mass calculated from the sequence and its modifications. Coupled to HPLC (LC-MS), it can also give the masses of impurity peaks, which helps identify them: a +16 Da peak suggests oxidation, a +1 Da shift on an asparagine-containing peptide suggests deamidation, and a missing-residue mass suggests a deletion sequence.
MS does not establish purity on its own, and it cannot distinguish molecules of identical mass, such as a peptide and its D-amino-acid epimer.
See also
For in vitro laboratory research only. Not for human or veterinary use. This library describes chemistry, analytical methods and published laboratory research; it gives no guidance on use in people or animals.