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Evidence-based GLP-1 & peptide discussion since 2023
ForumsCOA & Analytical TestingLC-MS/MS vs HPLC for peptide analysis — which is more reliable?

LC-MS/MS vs HPLC for peptide analysis — which is more reliable?

HPLC_Greg Wed, Jun 3, 2026 at 8:25 AM 19 replies 492 viewsPage 1 of 4
HPLC_Greg
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Jun 3, 2026 at 8:25 AM#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. 📊
22 17SallyK_inj, CryptoCarl, MariaRD and 19 others
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HealthEcon_DC
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Jun 3, 2026 at 8:44 AM#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: Jun 3, 2026 at 10:44 AM
21 16JessicaH_TX, KevinCompounds, TirzTom and 18 others
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JennaRN
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Jun 3, 2026 at 9:04 AM#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. 👍
20 15BiostatsBrad, PeptideSynthNJ, Dr.KarenChen and 17 others
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NeuroNate
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Jun 3, 2026 at 9:23 AM#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.
19 14kim_atl_prep, sarah_TO, wendy_avl and 16 others
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AussieAnna
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Jun 3, 2026 at 11:09 AM#5
Wow, that's terrifying. So a bad actor could sell literally anything and if you only looked at purity %, you'd never know?
Last edited: Jun 3, 2026 at 12:09 PM
18 13pete_manc_UK, anna.melb_AU, mark_tokyo and 15 others
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