Purity and identity are two questions
Analytical characterization answers two separate questions: is this the right molecule (identity), and how much of the sample is that molecule versus impurities (purity). A responsible certificate of analysis addresses both, because a sample can be highly pure yet be the wrong compound, or correctly identified yet heavily contaminated.
HPLC for purity
High-performance liquid chromatography (HPLC) separates a sample's components and reports the target peak as a percentage of total peak area. A stated purity figure is only meaningful alongside the actual chromatogram, the method, and a batch identifier. A bare “99% pure” claim with no trace or lot number is a marketing statement, not analytical data.
Mass spectrometry for identity
Mass spectrometry measures the molecular mass of the peptide and confirms whether it matches the theoretical mass of the intended sequence. This is how identity is verified. A COA that reports a purity percentage but shows no mass-spec confirmation leaves the most basic question—what is this actually?—unanswered.
Net peptide content and the TFA counterion
Reported HPLC purity does not equal how much peptide is in the vial. Lyophilized peptides carry water, salts, and counterions. Peptides purified by common methods often retain trifluoroacetic acid (TFA) as a counterion, which adds mass that is not peptide. Net peptide content, sometimes from amino-acid analysis, tells you the actual peptide fraction—an important distinction from purity.
Red flags on a certificate of analysis
Warning signs include a COA with no batch or lot number, no chromatogram, no method described, a mass that does not match the sequence, identical “template” documents reused across products, or figures that look too clean to be real data. A COA can be generic or even falsified, so treat it as one input, not proof. This is educational lab literacy, not a purchasing endorsement.
Sources and what they cover
These primary studies, official records and standards cover the topics linked below. The scope notes distinguish laboratory findings, human trials and regulatory records. This is a selected bibliography, not a systematic review or verification of every sentence; absence of a study here does not prove that no study exists.
- ICH Q2(R2) — Validation of Analytical Procedures (FDA guidance)
Analytical validation framework. A chromatogram alone does not validate identity, content, sterility or fitness for human use.
Relevant sections: Purity and identity are two questions · HPLC for purity · Mass spectrometry for identity · Net peptide content and the TFA counterion · Red flags on a certificate of analysis
FAQ
Does HPLC purity tell me how much peptide is in the vial?+
No. HPLC purity is a percentage of chromatographic peak area, while net peptide content tells you the actual peptide fraction after accounting for water, salts, and counterions like TFA. They are different measurements.
How is a peptide's identity confirmed?+
Primarily by mass spectrometry, which checks whether the measured molecular mass matches the theoretical mass of the intended sequence. A purity figure alone does not confirm identity.
Can a certificate of analysis be misleading?+
Yes. A COA can be generic, incomplete, or falsified, and independent testing has found mislabeled or contaminated materials. Look for a batch ID, an actual chromatogram, a described method, and mass-spec confirmation, and treat the document as one input rather than proof.