If you purify a protein by reverse phase HPLC, then reverse phase chromatography should not be used as your check of purity. Capillary electrophoresis, SDS PAGE, or isoelectric focusing would be more appropriate techniques in this example. Keep in mind that there is no absolute proof of purity. Demonstration of purity involves the accumulation of evidence. The more independent techniques you employ to demonstrate the purity of your sample the greater confidence you will have in its purity and the smaller the risk of an unsuccessful sequence.
Insufficient material is one of the most common reasons a protein sequence fails.
The reason for this is that most researchers tend to be overly optimistic when estimating the yield of their isolated protein. Many do not even attempt to determine the amount of protein in their sample material by assay. Preferring to calculate it based upon their knowledge of the protein concentration in the starting material and assumed recoveries for each step in their isolation protocol. These two problems of inaccurate estimates of protein concentration and inability to adequately adjust for sample handling losses during the isolation protocol lead to estimates of sample concentration that have little to do with reality. Consequently many samples are sequenced that do not contain sufficient protein to give a detectable sequence.