If my peptide is 95% pure, what is the other 5%?

Peptide purity is usually determined by HPLC using a gradient of 1% acetonitrile per minute. During the synthesis process, the cross-linking efficiency between amino acids cannot always reach 100%, thus producing a series of impurities with missing amino acids. Most of these amino acid-deleted impurities were removed during purification, but a few had chromatographic profiles that closely resembled the target peptide. Contaminant peptides with these amino acid deletions remaining in the peptide sample make up the remaining few percent.