Continuing and expanding the tradition of the University of Athens within the subject, starting from Zervas of Bergmann-Zervas carbobenzoxy method fame, Photaki initially worked on further refinement of suitable protecting groups for oligopeptide synthesis. She investigated with Zervas new types of protection such as N-protection with benzyl phosphate esters (N-phosphamide derivatives), S-protection using trityl, benzhydryl or benzoyl groups (as part of the greater effort for the synthesis of asymmetric cysteine-containing peptides), N-protection using the o-nitrophenylsulfenyl (NPS) group discovered in their Athens laboratory, or S-protection using the p-methoxycarbobenzoxy group (a modification of the Z group).
With the above methodologies she embarked on the synthesis of complex polypeptides, especially fragments of enzyme active sites and peptide hormones. Some notable achievements in papers Photaki co-authored include the first synthesis of the 20-membered insulin intra-chain ring or –following her research under du Vigneaud– several previously inaccessible oxytocin analogues (e.g. 4-deamido-oxytocin) and a novel oxytocin synthesis via a different route than the du Vigneaud synthesis.
In later years she also examined the preparation of biologically active atypical peptides such as N-arginine or lanthionine-containing peptides.