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Glossary

Mass Spectrometry

MS verifies which peptide is in a vial by comparing its measured mass with the mass calculated from the sequence. How to read the MS line on a certificate.

In mass spectrometry (MS), analyte molecules are ionised and sorted by mass-to-charge ratio, giving the molecular mass. For peptide certificates it answers what HPLC cannot: does this vial contain the sequence printed on the label? Electrospray ionisation (ESI-MS) is the most common technique on COAs, followed by MALDI-TOF.

Interpreting the MS result

Set the measured mass against the calculated mass derived from the sequence. The two should match within the tolerance stated for the instrument — on a modern ESI instrument well below one dalton, on MALDI-TOF within several daltons. ESI produces several charge states for one peptide ([M+2H]2+, [M+3H]3+), and deconvolution software combines them into a single neutral mass; a raw m/z figure quoted with no charge state leaves the result incomplete.

Telling mass shifts

Typical offsets carry meaning: +16 Da points to oxidation, most often at methionine; −0.98 Da is the gap between an amidated and a free-acid C-terminus; +42 Da signals acetylation; +1 Da may indicate deamidation. A discrepancy equal to exactly one residue mass suggests a missing or swapped amino acid.

Identity plus purity

An excellent HPLC value is meaningless if the molecule is the wrong one. A trustworthy COA needs both results — identity and purity — obtained from one and the same lot.

Full explainer: our guide to MS-based identity testing of peptides.

All glossary terms

Further reading

Guides that reference this term

Documentation

Nine Checks Before You Buy From a Research Peptide Supplier

You can work through eight of the nine before spending anything. The first few filter out most suppliers, and check four is the one buyers routinely skip.

Documentation

How to Read a Peptide Analysis Certificate: Identity, Purity and the Overlooked Line

The two things the document is there to prove, the one number that is routinely misunderstood, and a full walk-through of a realistic example.

Molecule guides

Peptide Antibodies and Antisera: Formats, Immunogens and Validation Controls

What a listing marked "antibody" really contains, why what it was raised against tells you most, and which controls let you stand behind a result.

Molecule guides

What Is 5-Amino-1MQ? NNMT Inhibition, Quinolinium Chemistry and Research Context

Why this quinolinium salt belongs in a different analytical world from the peptides beside it — its enzyme target, the NAD and methylation biology, and the salt-mass trap.