Chromatographic purity is calculated by integrating every peak in an HPLC chromatogram and dividing the area of the main peak by the total. A result of 99.0% means that, of everything the detector saw at that wavelength, 99.0% of the signal came from the main peak.
It is a relative measure. It does not count anything the detector cannot see, such as water, counter-ions and inorganic salts, and it cannot separate an impurity that elutes at exactly the same time as the main component. For that reason it is read alongside mass spectrometry, which confirms identity, and net peptide content, which accounts for the non-peptide mass.
Because it depends on the column, gradient and wavelength used, a purity figure is most meaningful when the method is stated with it.
See also
For in vitro laboratory research only. Not for human or veterinary use. This library describes chemistry, analytical methods and published laboratory research; it gives no guidance on use in people or animals.