Interpreting the charge state assignment in electrospray mass spectra of bioparticles

In electrospray ionization mass spectra of heterogeneous protein complexes and other bioparticles, accurate mass determination is often hampered by the inaccuracy in determination of the charge states for individual signals. Here, we describe an algorithm that automatically minimizes the standard deviation in a series of related ion peaks with varying numbers of charges. The algorithm assumes that the mass is invariant and allows the determination of the correct charge state in a peak series. The analysis results in a periodic pattern, which can be interpreted as a harmonic oscillator, when the minimum standard deviation of a charge state series is found. We observed that a mass resolution of much less than 1000 in the acquired mass spectra is sufficient to achieve a correct charge state assignment. Moreover, the boundaries of mixed species can be identified by examining the loss of periodicity in the pattern of the analysis. We tested our algorithm successfully on novel spectra and on spectra reported in the literature with sample masses up to several million Dalton, e.g., viral particles, polyethylene glycol polymers, and polystyrene nanoparticles.