Accepted answer
97.1 and 95.2 are 1.9 percentage points apart, which sounds small until you restate it as impurity. VendorInvestigate is leaving 2.9 per cent of the detected area unassigned and PeptideMeter 4.8 per cent — a factor of 1.66 between them. The impurity fraction is the quantity that moves when a method changes, and it is the one worth arguing about; the headline is just its complement. Comparable means same column chemistry, same gradient slope, same detection wavelength, same integration convention. Until you have those four from both laboratories, 97.1 and 95.2 are two measurements of slightly different quantities that happen to share a unit.
The short answer is that two competent laboratories on identical material will disagree, and the disagreement is almost always explainable by method differences.
Temperature affects the dynamics of molecular conformation, and if a peptide has proline residues that interconvert on the chromatographic timescale, the peak will split or shoulder at low temperature and collapse at high temperature.
Put another way, detection wavelength matters because 214 nm sees the peptide backbone while 280 nm sees only aromatic side chains — so truncation impurities lacking a tryptophan are invisible at 280 nm.
The ICH Q3A impurity thresholds and the relevant pharmacopoeial chapters all specify method validation requirements that almost no research-grade certificate claims to meet.
Compare purity within a single laboratory on the same method, never across laboratories.