Mass spectrometry: how a peptide's identity is confirmed

What a mass spectrometer measures

A mass spectrometer turns molecules into charged ions and measures their mass-to-charge ratio (m/z). Peptides usually pick up more than one charge, so one peptide can show several peaks, each at its mass divided by its charge. Software combines them into a single molecular mass.

LC-MS runs liquid chromatography first, so each separated component goes into the mass spectrometer on its own. That ties the mass to a specific peak in the chromatogram.

Reading expected vs observed mass

The expected mass is calculated from the peptide's sequence. The observed mass is what the instrument found. A report should give both, or at least state that identity was confirmed and by which method. A small difference is normal; how small depends on the instrument, and the report should name the method.

What a matching mass does and doesn't prove

A match shows the main component has the right mass, which rules out most wrong-compound mix-ups. It does not measure purity or quantity, and two different sequences with the same amino acids in another order can share a mass. That is why identity, purity and net content are three separate lines on a complete report.

Common questions