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Identity first: how LC-MS shows what is in the vial

Liquid chromatography separates the sample, mass spectrometry measures the mass of each part, and a match with the expected mass confirms the compound.

By Published Last updated 3 min read

Uses the lab reports of the 11 tested lots on this site

A mass spectrometer with its vacuum chambers and magnet, seen from above
A mass spectrometer with its vacuum chambers and magnet, seen from above. Photo: Radiogenic, CC0, via Wikimedia Commons

Key takeaways

  • Mass spectrometry measures the mass of molecules; the expected mass confirms identity.
  • Liquid chromatography first separates the sample, so each component is measured on its own.
  • Some differences do not change the mass, such as mirror-image amino acids, and need extra techniques.

A very pure sample of the wrong compound is still the wrong compound. Identity is the first question a report should answer.

Why identity comes first

Peptide quality specifications cover identification, purity and assay[1]. Every number after identity assumes the sample is what the label says. A purity of 99% describes the main peak, whatever that peak is.

Laboratories confirm identity with methods such as nuclear magnetic resonance, mass spectrometry and chromatography, and measure purity and content with HPLC[2].

What LC-MS does

LC-MS joins two instruments. Liquid chromatography (LC) separates the sample in time, as in an HPLC purity test. The mass spectrometer (MS) then measures the mass of each component as it leaves the column. Matching a measured mass to the mass a compound should have is evidence of what that component is. Mass spectrometry is increasingly used to characterise the impurities of synthetic peptides[3].

mass Amass Bmass C123
  1. Liquid chromatography separates the sample: each component leaves the column at its own time.
  2. The mass spectrometer measures the mass of what leaves the column at each moment.
  3. Each measured mass is matched to what it can be: the peptide, a bulking agent, a degradation product.
Figure 1. How LC-MS works, in three steps. A schematic, not a real spectrum. Schematic drawn by BP.

What the lab found in our lots

Each lot on this site has an LC-MS screening report. In the comment the lab names what it identified. For 9 of the 11 lots it adds "No significant contamination detected". The reports for R3T4, T1RZ3P4T1D3, from Nov 2025, do not carry that sentence[4].

ProductWhat the lab identified
3P1TH4L0NLot EP-470mannitol, 3P1TH4L0N, degradation productsPass
6HK-CULot GH-692mannitol, 6HK‑CU, degradation productsPass
8PC Wolverine StackLot BT-317mannitol, T8‑500 (T84), 8PC‑157, degradation productsPass
8PC-157Lot BP-482mannitol, 8PC‑157, degradation productsPass
C1C-1295 + 1P4M0R3L1NLot CI-741mannitol, 1P4M0R3L1N, C1C‑1295, degradation productsPass
M0TS-CLot MC-823mannitol, M0TS‑C, degradation productsPass
R3T4Batch 2029/1mannitol, R3T4, degradation productThe comment lists what was found, without a contamination sentence
S3L4NKLot SL-547mannitol, S3L4NK, degradation productsPass
S3M4XLot SM-381mannitol, S3M4X, degradation productsPass
T1RZ3P4T1D3Batch 2029/1mannitol, T1RZ3P4T1D3, degradation productThe comment lists what was found, without a contamination sentence
T3S4M0R3L1NLot TE-156mannitol, T3S4M0R3L1N, degradation productsPass
Figure 2. What the lab identified in each lot, and whether its comment adds "No significant contamination detected". Taken from the lab's comments, with product names in their code. Source: Janoshik Analytical LC-MS screening reports in the COA library.

Mannitol and degradation products

Two names come up on every report. Mannitol is used as a bulking agent in freeze-drying[5]. Degradation products are molecules formed as a peptide slowly breaks down; synthetic peptides change through their starting materials, their manufacture and their storage[3].

What mass alone cannot tell

Two molecules can share a mass. Some amino acids have the same mass as another, and a mirror-image amino acid weighs the same as the original. Characterising those needs additional techniques[2,3]. A screening comment confirms what the lab identified; it is not a full structural analysis.

Check it on real reports. The COA library has the full lab reports for 11 lots, with the original PDFs and links to the lab's own copies. Open the COA library

Sources

  1. Vergote V, Burvenich C, Van de Wiele C, De Spiegeleer B. Quality specifications for peptide drugs: a regulatory-pharmaceutical approach. Journal of Peptide Science 2009;15(11):697-710. doi.org/10.1002/psc.1167
  2. McCarthy D, Han Y, Carrick K, Schmidt D, Workman W, Matejtschuk P, Duru C, Atouf F. Reference standards to support quality of synthetic peptide therapeutics. Pharmaceutical Research 2023;40(6):1317-1328. Open access. doi.org/10.1007/s11095-023-03493-1
  3. Lian Z, Wang N, Tian Y, Huang L. Characterization of synthetic peptide therapeutics using liquid chromatography-mass spectrometry: challenges, solutions, pitfalls, and future perspectives. Journal of the American Society for Mass Spectrometry 2021;32(8):1852-1860. doi.org/10.1021/jasms.0c00479
  4. Bali Peptide Supply. COA library: every lab report for the lots sold on this site. Reports issued by Janoshik Analytical, with their task numbers, keys and original PDFs. balipeptidesupply.com/coa/
  5. Liao X, Krishnamurthy R, Suryanarayanan R. Influence of the active pharmaceutical ingredient concentration on the physical state of mannitol: implications in freeze-drying. Pharmaceutical Research 2005;22(11):1978-1985. doi.org/10.1007/s11095-005-7625-x

Each source was read in its own document on 16 Oct 2026. Numbers about BP's lots come from the reports in the COA library.

How this article was made

Written by Bali Peptide Supply from the sources listed above, each read in its own document on 16 Oct 2026. Every number about our lots comes from the Janoshik Analytical reports in the COA library, read by the site build, not typed by hand. The lead photo is from Wikimedia Commons under a free licence.

BP sells research materials for laboratory use only. This article explains laboratory testing and lab reports. It is not medical advice and not instructions for use.

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