Why it matters
Mass spectrometry is the definitive way to confirm a synthetic peptide’s molecular identity. HPLC quantifies purity; MS confirms the molecule is the intended target — correct molecular weight, correct sequence.
That matters because several synthesis errors produce molecules of similar hydrophobicity to the target, so they hide inside what looks like a single “pure” HPLC peak:
- Deletion sequences — a missing amino acid
- Insertion sequences — an extra residue
- Racemization products — wrong stereochemistry
- Incompletely deprotected species — leftover protecting groups
Only MS catches these, by showing the measured mass deviates from the theoretical value.
For anyone relying on peptide identity for experimental validity, MS data on a Certificate of Analysis isn’t optional — it’s the confirmation that the vial matches the label.
ESI-MS vs. MALDI-TOF
Two ionization methods dominate. They’re complementary, not interchangeable — each wins in different conditions.
ESI-MS
Multiply-charged ions; couples directly to liquid chromatography (LC-MS). Best for solution-phase work and running identity + purity in one method.
MALDI-TOF
Mostly singly-charged ions. Fast, tolerant of mixtures and salts, and well-suited to larger peptides where a simple mass readout is the goal.
What to check on a COA
Whatever method the lab uses, the verification logic is identical. Look for: