Peptides are in great demand in the pharmaceutical arena and a majority of these peptides contain 20 or more amino acids. They are infrequently synthesised using the fragment condensation approach. A key limitation in adopting this approach more commonly is that protected peptide fragments with high purity are often required prior to the final condensation steps. It is hypothesized that understanding the hydrophobic nature of the protected amino acids will assist with designing optimal fragment purification processes when needed. Whilst a myriad of hydrophobicity indices are reported in the literature for unprotected amino acids, the literature lacks any data regarding the protected amino acids which form the key precursor for the fragment condensation task. In this current study, hydrophobicity indices for protected amino acids with common α-amino and sidechain protecting groups were experimentally determined. Different positions for each amino acid within the peptide chain were considered, namely at the C-terminal and N-terminal as well as internal positions. These data give deep insights on the hydrophobicity of each amino acid with respect to its position in the peptide chain. The data acquired in this research facilitated the prediction of the retention time of protected peptide fragments with an uncertainty of less than ±1.5%.