Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z, starting from z=1, and colour-coding z in m/z spectra. CHARDA combines the analysis of ion signal decay rates in the time-domain data (transients) in Fourier transform (FT) MS with the interrogation of mass defects of biopolymers. Being applied to individual isotopic peaks in a complex protein tandem (MS/MS) dataset, CHARDA facilitates charge state deconvolution of large ionic species in crowded regions, estimating z even in the absence of isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust and consistent with conventional FT MS and FT MS/MS data acquisition procedures. An effective charge state resolution Rz≥6 is obtained, with potential for further improvements.