Saturation transfer difference (STD) methods recently have been proposed to be a promising tool for self-recognition mapping at residue and atomic resolution in amyloidogenic peptides. Despite the significant potential of the STD approach for systems undergoing oligomer/monomer (O/M) equilibria, a systematic analysis of the possible artifacts arising in this novel application of STD experiments is still lacking. Here, we have analyzed the STD method as applied to O/M peptides, and we have identified three major sources of possible biases: offset effects, intramonomer cross-relaxation, and partial spin-diffusion within the oligomers. For the purpose of quantitatively assessing these artifacts, we employed a comparative approach that relies on 1-D and 2-D STD data acquired at different saturation frequencies on samples with different peptide concentrations and filtration states. This artifact evaluation protocol was applied to the A beta(12-28) model system, and all three types of artifacts appear to affect the measured STD spectra. In addition, we propose a method to minimize the biases introduced by these artifacts in the H alpha STD distributions used to obtain peptide self-recognition maps at residue resolution. This method relies on the averaging of STD data sets acquired at different saturation frequencies and provides results comparable to those independently obtained through other NMR pulse sequences that probe oligomerization, such as nonselective off-resonance relaxation experiments. The artifact evaluation protocol and the multiple frequencies averaging strategy proposed here are of general utility for the growing family of amyloidogenic peptides, as they provide a reliable analysis of STD spectra in terms of polypeptide self-recognition epitopes.