Mass spectrometry (MS) ionises a sample and measures mass-to-charge ratios, from which the molecular mass is calculated. On a peptide certificate it answers the identity question that chromatography cannot: is the molecule in this vial the sequence on the label? Electrospray ionisation (ESI-MS) and MALDI-TOF are the two methods usually cited.
Reading the MS line
Compare the observed mass with the theoretical mass computed from the sequence. They should agree to within the instrument's stated tolerance — typically a fraction of a dalton on a modern ESI instrument, a few daltons on MALDI-TOF. ESI spectra of peptides show a series of multiply charged ions ([M+2H]2+, [M+3H]3+) that software deconvolutes into a single neutral mass; a certificate that reports only a raw m/z without stating the charge state is incomplete.
Diagnostic mass differences
Common offsets are informative: +16 Da suggests oxidation, typically at methionine; −0.98 Da distinguishes a C-terminal amide from the free acid; +42 Da indicates acetylation; +1 Da can mean deamidation. A mismatch of exactly one residue's mass points to a deletion or substitution.
Why it matters
A high HPLC figure on the wrong molecule is worthless. Identity plus purity on the same lot is the minimum credible pair on a certificate of analysis.