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ForumsCOA & Analytical TestingLC-MS/MS vs HPLC for peptide analysis — which is more reliable? Page 2

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 2 of 4
Dr.AddMedPHL
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Jun 3, 2026 at 12:55 PM#6
Exactly right, which is why I always recommend the Identity + Purity test (~$180) rather than purity alone ($120). The extra $60 gives you confirmation that the compound actually IS what it claims to be. Some other things to look for on your Janoshik report: Peak shape matters: - A nice, symmetrical, sharp peak = clean compound - A broad, tailing, or fronting peak = potential issues with formulation or degradation - Multiple peaks clustered together = possible degradation products What "related substances" means: Sometimes Janoshik will list "related substances" separately from impurities. Related substances are structurally similar compounds — for peptides, these are usually synthesis byproducts. They're reported individually if they exceed 0.5%. The limit of detection (LOD): Janoshik's HPLC typically has an LOD of ~0.1%. Anything below that won't show up on the report. This is standard for the method.
Last edited: Jun 3, 2026 at 2:55 PM
17 12FitDadDave, RunnerRach, TrialNerd_Beth and 14 others
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TrialTracker_MD
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Jun 3, 2026 at 2:41 PM#7
One more critical point: concentration/potency testing. Purity tells you what percentage of the sample is your target compound. But it doesn't tell you how much compound is in the vial. Example: A vial labeled "5mg tirzepatide" could test at 98% purity but only contain 2.5mg total. It's pure — there's just not enough of it. For concentration testing, you need a quantitative assay, which is a different (more expensive) test. Janoshik offers this at ~$250. It will tell you the actual mg content. > My rule of thumb: test purity + identity on first order from a new vendor (~$180). If that passes, test quantitative on the second order (~$250) to verify dosing accuracy. If both pass, you've got a reliable vendor.
Last edited: Jun 3, 2026 at 7:41 PM
16 11stefan_berlin, Dr.EM_Chicago, pete_RVA and 13 others
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chris_chi24
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Jun 3, 2026 at 4:27 PM#8
What about the solubility notes I see on some reports? My result has a note that says "sample fully soluble in analytical solvent." Does that matter?
15 10MaxMetOK, MounjBrad, nick_newbie and 12 others
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DataDave
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Jun 3, 2026 at 6:13 PM#9
It's a minor quality indicator but worth noting. If the sample doesn't fully dissolve in the analytical solvent, it means: 1. The HPLC result may not represent the entire sample (insoluble portions aren't measured) 2. There could be non-peptide contaminants (fillers, excipients, residual salts) For reconstituted peptide solutions, full solubility is expected and normal. For lyophilized powders, it's a good sign that the synthesis was clean. If you ever see "sample partially soluble" or "turbid solution" on a Janoshik report, that's a yellow flag. It doesn't necessarily mean the peptide is bad, but it warrants further investigation. Great questions from everyone. Understanding your test results is just as important as getting them in the first place. Knowledge is power in this space. 🔬
14 9amsterdam_pete, LondonLisa, mike_nyc and 11 others
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Admin
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Jun 4, 2026 at 2:43 AM#10
Excellent thread. Adding this to the wiki under Testing & Analytics. For anyone who wants to learn more, Janoshik occasionally publishes educational content on their site explaining methodology. They use a C18 reverse-phase column with UV detection at 220nm for most peptide work, which is the industry standard approach. If you have a specific result you want help interpreting, feel free to start a new thread with the PDF (redact your sample ID) and tag it with [Result Interpretation]. Several of our members with analytical chemistry backgrounds are happy to help.
22 20PeptideSynthNJ, Dr.KarenChen, Dr.NateNeph and 19 others
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