LC-MS/MS vs HPLC for peptide analysis — November 2025

Clinical perspective, offered as context rather than as advice.

HPLC results interpretation for certificates of analysis: when you get your Janoshik report back, here's what the numbers mean:

• Purity %: Should be >97%. Below 95% is concerning.
• Retention time: Should match reference standard for the peptide
• Related substances: Degradation products should be <2% total
• Single impurity: No individual impurity should exceed 1%

My last batch: 99.2% purity, 0.2% total related substances. Clean chromatogram with single sharp peak at expected retention time. Exactly what you want to see.

PeptideChemSF said:

Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight.

Thank you — that is the clearest version of this I have read, and I have read a lot of them. Taking it to my next appointment.

From the other side of the consultation, briefly.

Vendor quality matters when discussing certificates of analysis. I've tested my last 5 batches through Janoshik and purity has ranged from 98.6% 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.

Dr.NateNeph said:

Vendor quality matters when discussing certificates of analysis.

Same pattern here, and in the same order.

Moderator note: a post naming a supplier has been edited. Discuss suppliers in the review sections, not here. Thread quality here is what the rules are for. Keep it up.