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What the HPLC trace, purity percentage, endotoxin figure and mass-spec confirmation on a peptide certificate of analysis actually tell you, and what they do not.
A certificate of analysis is the analytical record for one specific synthesis batch. It is not a statement about the product line - it is a statement about the material in your vial, identified by lot number.
This distinction matters more than anything else on the document. A supplier who publishes one certificate per product rather than one per lot is telling you what some other batch looked like.
Reverse-phase high-performance liquid chromatography separates the components of a sample by how strongly they bind to a hydrophobic column. The output is a chromatogram: retention time along the horizontal axis, detector response on the vertical.
A clean peptide gives one dominant peak. The purity figure is that peak's area as a percentage of total peak area. At 99% purity, the main peak accounts for 99% of everything the detector saw.
Small peaks either side of the main peak are usually synthesis-related: deletion sequences missing a residue, or incompletely deprotected material. A peak that is very close to the main peak often indicates a diastereomer.
Purity by HPLC is a relative area measurement. It says what proportion of the detected material is the target compound. It does not, on its own, confirm that the target compound is what you think it is - that is what mass spectrometry is for.
It also says nothing about water content, residual solvent or counterion mass. A vial labelled 10 mg at 99% purity contains 10 mg of net peptide by the supplier's fill specification, but the gross contents include the acetate or trifluoroacetate counterion.
Bacterial endotoxin is lipopolysaccharide from Gram-negative cell walls. It survives autoclaving, it is biologically active at very low concentrations, and it is a common confound in cell-based assay work.
The Limulus amebocyte lysate assay measures it, reported in endotoxin units per milligram. Below 0.5 EU/mg is the usual specification for research-grade material.
Where HPLC answers how much of the sample is one compound, mass spectrometry answers which compound. The observed mass is compared against the calculated mass for the sequence.
A match within the instrument's tolerance confirms identity. A mass low by roughly the weight of one residue points to a deletion sequence; a mass high by 16 usually means oxidation, typically of a methionine.
The lot number printed on the crimp label is the key. Enter it into the PeptideSeed certificate lookup and it returns the purity and endotoxin reports generated against that specific synthesis.
If a lot number does not resolve, do not assume the certificate for a neighbouring lot applies. Contact the supplier.
This guide is general laboratory reference material relating to the handling of research compounds. It is not medical, veterinary or clinical guidance, and it does not describe or imply any use in humans or animals. All PeptideSeed material is supplied for in-vitro laboratory research only — see the terms of supply.