We recommend N-terminal acetylation for peptide scans because: (1) peptides are more stable to degradation, (2) the uncharged N-ac better represents the region in the native antigen than a charged NH3+-group.
Note on Cys/Ser substitution: Cysteine containing peptides are sensitive to oxidation and cyclization. Therefore, substituting cysteine with serine residues increases the quality of the peptide. Cysteine is very rarely an essential residue in antibody epitopes.