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HPLC vs Mass Spec: what each one actually measures

Purity and identity are different questions. A real QC program answers both.

Peptech Lab·Jun 12, 2026
learnhplcquality
HPLC vs Mass Spec: what each one actually measures
Research use only. Not for human or animal consumption. All products and content are for laboratory research purposes only.

Research use only. Not for use in humans or animals. All products and information on this site are provided strictly for in-vitro laboratory research purposes. They are not for use in humans or animals, and are not drugs, foods, cosmetics, or medical devices.

HPLC measures purity

Reverse-phase HPLC (RP-HPLC) separates the components of a sample by hydrophobicity. The detector counts how much of the eluted material is the target peptide vs. impurities. Purity is reported as a percentage of total peak area.

  • Industry minimum: >=98% by area
  • Research grade: >=99%
  • Pharmaceutical grade: >=99.5% with specific impurity profiles

HPLC tells you nothing about what the molecule actually is — only what fraction of the sample is the major peak.

Mass spectrometry verifies identity

ESI-MS measures the mass-to-charge ratio of ionized molecules. A peptide theoretical mass is calculable from its sequence. The observed mass should match within +/-1 Da.

A common failure mode: HPLC shows 99.5% purity, but the major peak is not actually the target peptide. Without MS confirmation, you cannot tell.

What a complete report shows

  • HPLC chromatogram with purity percentage and method (column, gradient, detector wavelength)
  • MS spectrum with observed mass, theoretical mass, and the matching adduct ion
  • Both done on the same lot, on the same or sequential days

What we publish

Every Peptech batch ships with HPLC + MS in a single COA. We do not release a batch with one but not the other.