Accepted answer
Coupling the chromatography to mass spectrometry adds identity information but trades chromatographic quality for ionisation efficiency.
Proline-rich sequences are particularly problematic because the isomerisation kinetics are in the same timescale as the separation, leading to split or broadened peaks at low temperature.
Acetonitrile is the organic modifier of choice because it has a good UV cutoff, a reasonable viscosity and a refractive index that minimises baseline noise.
Peptide impurities from solid-phase synthesis include deletion sequences, truncations from premature cleavage, racemised residues from epimerisation and oxidised variants, each of which may have different chromatographic behaviour.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.
edited 16 Nov 2024 by klara_novotna — clarified the distinction between purity and content