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ForumsCOA & Analytical TestingLC-MS/MS vs HPLC for peptide analysis — November 2025

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

Dr.SportsMedIN Mon, Jul 22, 2024 at 3:37 PM 51 replies 2,260 viewsPage 1 of 11
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Dr.SportsMedIN
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Jul 22, 2024 at 3:37 PM#1
Got my latest Janoshik results back and I realized a lot of people in this community don't actually know how to read an HPLC report. I work in analytical chemistry (pharma sector) so let me break this down. What you'll see on a Janoshik HPLC report: 1. Chromatogram — the actual graph with peaks. X-axis is retention time (minutes), Y-axis is signal intensity (mAU) 2. Peak table — lists each detected peak, its retention time, area, and area % 3. Purity percentage — the main peak area as a % of total peak area 4. Identity confirmation — whether the main peak's retention time matches the reference standard What "good" results look like for GLP-1 peptides: - Purity ≥ 95% = excellent, pharmaceutical grade territory - Purity 90-95% = acceptable for research peptides - Purity 85-90% = borderline, I'd want to know what the impurities are - Purity < 85% = return/discard, not worth the risk The purity number is the single most important figure. But don't ignore the rest of the data. 📊
28 23lucas_SP_BR, lisa_labSD, adam_van and 25 others
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laura_annarbor
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Jul 22, 2024 at 3:43 PM#2
This is so helpful. I just got my first result back — tirzepatide from [vendor]. Report says 97.3% purity with a main peak at retention time 12.4 min. There are two small impurity peaks at 8.2 min (1.1%) and 14.7 min (1.6%). Is this good? Should I be worried about those impurity peaks?
Last edited: Jul 22, 2024 at 5:43 PM
27 22emily_PDX, Dr.SleepRoch, laura_annarbor and 24 others
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KevinCompounds
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Jul 22, 2024 at 3:49 PM#3
97.3% is excellent — that's genuinely pharmaceutical grade purity. For context, the FDA approval for Mounjaro (brand tirzepatide) requires ≥95% purity. Those small impurity peaks at 1.1% and 1.6% are completely normal and expected in peptide synthesis. They're most likely: - Truncated sequences — shorter versions of the peptide that didn't fully synthesize - Oxidized forms — the peptide with a slightly modified amino acid - Deletion peptides — missing one amino acid in the chain None of these are dangerous at those levels. They're just inactive or minimally active fragments. You'd need impurities above 5% before I'd start asking questions about what they actually are. Your vendor did well on this batch. 👍
26 21MikeKY_noInsulin, Dr.RaviCardio, jennifer_SEA and 23 others
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mike_nyc
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Jul 22, 2024 at 3:55 PM#4
Good breakdown. Let me add something about retention time because this is how identity is confirmed. Every compound has a characteristic retention time on a given HPLC column under specific conditions. Janoshik runs reference standards alongside your sample. If your sample's main peak elutes at the same time (±0.2 min typically) as the reference standard, that confirms identity. > If the purity is 98% but the retention time doesn't match the reference standard, you have a very pure sample of the wrong compound. This has happened. I've seen a result where someone sent in "semaglutide" and it came back 96% pure — but the retention time matched BPC-157, not semaglutide. The vendor had mislabeled the vials. Without the identity confirmation, you'd think everything was fine. Always check the identity match, not just the purity number.
25 20pete_RVA, CarlaRPh_TPA, steph_laguna and 22 others
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kevin_tulsa
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Jul 22, 2024 at 4:24 PM#5
Wow, that's terrifying. So a bad actor could sell literally anything and if you only looked at purity %, you'd never know?
24 19NurseLeah_Nash, gary_naperville, sean_dublin and 21 others
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