It tells you 99.1 per cent of the integrated area came off a C18 column where ecnoglutide comes off, and the remaining 0.9 per cent did not. That is an area statement at one wavelength, not a mass statement about the vial: 0.9 per cent of area is only 0.9 per cent of mass if every impurity absorbs exactly as strongly as the parent, which none of them do. It also says nothing about how many milligrams are in the glass — water, counter-ion and a short fill are all invisible to it. What a C18 column does add is a constraint on what could be hiding: a column that retains by hydrophobicity separates deletion sequences well and separates isomers of identical hydrophobicity not at all.
Stated carefully, the chemistry of peptides at low pH and high organic-solvent concentration is not something most users have intuition for, which is why published methods exist.
Reverse-phase stationary phases use C18 or C8 chains bonded to silica, and the pore size of the silica matters more for a peptide of this chain length than the ligand length does.
Reconciling gross mass to label claim
| Component | Typical share | Counted in purity? | Counted in content? |
|---|
| Target peptide | 88–94 % | Yes, as main peak | Yes |
| Related impurities | 1–3 % | Yes, as other peaks | No |
| Counter-ion (TFA or acetate) | 2–8 % | No | No |
| Residual water | 2–6 % | No | No |
| Bulking agent, if present | 0–40 % | No | No |
Concretely, mobile phase pH at the point where you inject must match the mobile phase pH at the start of the gradient, or the sample will not be focused at the column head.
I would caution against over-interpreting small differences between runs, because the noise floor of the method is larger than most people assume.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.