ToF-SIMS analysis of adsorbed proteins: Principal component analysis of the primary ion species effect on the protein fragmentation patterns

In time-of-flight secondary ion mass spectrometry (ToF-SIMS), the choice of the primary ion used for analysis can influence the resulting mass spectrum. This is because different primary ion types can produce different fragmentation pathways. In this study, analysis of single-component protein monolayers were performed using monatomic, triatomic, and polyatomic primary ion sources. Eight primary ions (Cs ⁺, Au ⁺, Au ₃ ⁺, Bi ⁺, Bi ₃ ⁺, Bi ₃ ⁺⁺, C ₆₀ ⁺, and C ₆₀ ⁺⁺) were used to examine the low mass (m/z < 200) fragmentation patterns from five different proteins (bovine serum albumin, bovine serum fibrinogen, bovine immunoglobulin G, and chicken egg white lysozyme) adsorbed onto mica surfaces. Principal component analysis (PCA) processing of the ToF-SIMS data showed that variation in peak intensity caused by the primary ions was greater than differences in protein composition. The spectra generated by Cs ⁺, Au ⁺, and Bi ⁺ primary ions were similar, but the spectra generated by monatomic, triatomic, and polyatomic primary ions varied significantly. C ₆₀ primary ions increased fragmentation of the adsorbed proteins in the m/z < 200 region, resulting in more intense low m/z peaks. Thus, comparison of data obtained by one primary ion species with that obtained by another primary ion species should be done with caution. However, for the spectra generated using a given primary ion beam, discrimination between the spectra of different proteins followed similar trends. Therefore, a PCA model of proteins created with a given ion source should only be applied to data sets obtained using the same ion source. The type of information obtained from PCA depended on the peak set used. When only amino acid peaks were used, PCA was able to identify the relationship between proteins by their amino acid composition. When all peaks from m/z 12-200 were used, PCA separated proteins based on a ratio of C ₄H ₈N ⁺ to K ⁺ peak intensities. This ratio correlated with the thickness of the protein films, and Bi ₁ ⁺ primary ions produced the most surface sensitive spectra.