The evaluation of protein structural change is crucial for the study of protein-protein interactions and protein conformational changes. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) was used to detect pH dependent structural change in staphylococcal protein A (SpA), which is well known to the bind Fc region of immunoglobulins. TOF-SIMS spectra of SpA-immobilized samples in a pH 7 solution, in an acidic solution, and in a pH 7 solution after having been soaked in an acidic solution, respectively, were compared to select fragment ions specific to normal SpA at pH 7 using spectral analysis techniques such as principal component analysis (PCA) and the mutual information method. A fragment ion depending on change in the B and E domains of SpA were detected with this method. These findings demonstrate that structural change of SpA depending on pH change can be evaluated with TOF-SIMS together with spectrum analysis methods for the multivariate data. [DOI: 10.1380/ejssnt.2009.715]