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ForumsCOA & Analytical TestingLC-MS/MS vs HPLC for peptide analysis — November 2025 Page 5

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

HealthEcon_DC Tue, Nov 18, 2025 at 8:01 PM 29 replies 1,356 viewsPage 5 of 6
Dr.PathRoch
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Jun 2024
Rochester, MN
Nov 21, 2025 at 4:01 AM#21
lisa_labSD said:
I tested my certificates of analysis batch through Janoshik — 98.1% purity.

Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight. This confirms identity — not just purity.

Why this matters: HPLC can show you a "pure" compound, but if it's pure of the WRONG compound, purity is meaningless. Mass spec at m/z 4113.58 Da confirms it's actually semaglutide. My Janoshik report includes both HPLC and mass spec.

If your testing provider only offers HPLC, consider upgrading to include mass spec for at least your first batch from a new vendor.

Last edited: Nov 21, 2025 at 10:01 AM
21 19MikeFit_NJ, InsuranceTom, WendyG_ATL and 18 others
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DerekSJ_a1c
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Aug 2024
San Jose, CA
Nov 21, 2025 at 1:48 PM#22

One thing that is still open after lisa_labSD’s answer:

What would you measure differently if you were starting again?

22 20Dr.SurgeonPGH, rachel_ABQ, traveltech_sara and 19 others
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SleepFixSam
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Nov 2024
Hawaii
Nov 21, 2025 at 11:34 PM#23
Dr.PathRoch said:
Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight.

Community-verified vendors for certificates of analysis: I maintain a spreadsheet of Janoshik-verified test results submitted by community members. Across 47 submitted tests:

  • 75% tested at ≥98% purity
  • 18% tested at 95-98% purity
  • 7% tested at <95% purity (concerning)

The vendors with consistently high purity results are listed in the Vendor Directory. We update monthly based on new community submissions.

23 21raj_cambridge, ingrid_STO, pete_nash and 20 others
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Sigma-Aldrich — Research-Grade Standards

Certified reference materials, analytical reagents, and research-grade standards for peptide verification. Trusted by laboratories worldwide.

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PharmD_Rodriguez
Senior Member
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Jan 2024
Miami, FL
Nov 22, 2025 at 9:20 AM#24
Dr.PathRoch said:
Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight.

Right, and the exception is worth naming rather than left implied, because the exception is where people get into trouble.

Correct me if the detail matters more than I have assumed.

24 22dan_philly, MeganSA_TX, LarryQC_SD and 21 others
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lori_vegas
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Aug 2024
Las Vegas, NV
Nov 22, 2025 at 7:06 PM#25
Dr.PathRoch said:
Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight.

This is exactly what I could not find anywhere else. Sending this to two other people who asked me the same thing last week.

25 23Dr.PathRoch, mona_PHX, andrew_nyc and 22 others
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