Dr.LipidDallas said:

They are not contradictory, they measure different things, and this is the single most common misreading of a certificate.

Vendor quality matters when discussing certificates of analysis. I've tested my last 5 batches through Janoshik and purity has ranged from 97.4% to 99.2%. Consistency is key.

For anyone new: always request the COA, and consider independent verification. The $300 for a Janoshik test is worth the peace of mind.

A narrower follow-up, since the general answer is now clear:

Why two laboratories report different purity for the same batch, and which number to believe?

bri_stats said:

Vendor quality matters when discussing certificates of analysis.

Third-party testing services for certificates of analysis besides Janoshik:

• Janoshik: Gold standard for peptide community, ~$151, 10-14 day turnaround
• Valitech: US-based, ISO 17025 accredited, ~$201
• Eurofins: Full pharmaceutical testing suite, more expensive but comprehensive
• ChemTox: Basic identity and purity testing, ~$101

Janoshik is the community standard but any ISO-accredited analytical lab can verify peptide identity and purity. The key is independence — don't rely solely on the vendor's own testing.

OP back with an update, since a thread like this is useless without one.

Purity and content being different measurements was the piece I was missing. The vial was overfilled and pure, which is a very different problem from the one I thought I had.

Dr.NephBHM_UK said:

Third-party testing services for certificates of analysis besides Janoshik: Janoshik: Gold standard for peptide community, ~$151, 10-14 day turnaround…

Agreed, and mass spec answers a question purity does not: identity. High purity tells you one thing dominates the chromatogram, not that it is the molecule you ordered. A mass within about a dalton of expected is the identity check.