What does greater than 99% purity actually mean?

Chromatographic purity usually compares the integrated area of the principal peak with the total integrated peak area under specified conditions. Column chemistry, gradient, wavelength, integration choices, detection limits, and the treatment of unreported peaks all influence the number.

A greater-than-99% result does not mean that 99% of the vial's total weight is active peptide. It also cannot establish molecular identity, net fill, water or counterion content, bacterial endotoxin, sterility, or stability after storage. Those are different questions requiring other measurements or records.