The issue of automated peak selection in time-of-flight secondary ion mass spectrometry (ToF-SIMS) spectra is examined in relation to the hierarchical nature of the experimental design and the related existence of observations which are not statistically independent.To avoid unreliable results, the presence of pseudoreplication should be taken into account correctly. A combination of the recommended univariate peak selection approachwith some multivariate techniques, namely principal component analysis and heatmap data representation, is proposed to highlight and analyze obtained results for a set of ToF-SIMS spectra from copper phthalocyanine thin films grown on TiO2 substrates by a supersonic beam deposition apparatus. New insight is obtained on the effectiveness of the deposition for different working parameters of the process.