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The growing use of intact protein mass analysis,
top-down proteomics, and native mass spectrometry have created a need for
improved data analysis pipelines for deconvolution of electrospray (ESI) mass
spectra containing multiple charge states and potentially without isotopic
resolution. Although there are multiple deconvolution algorithms, there is no
consensus for how to judge the quality of the deconvolution, and many scoring
schemes are not published. Here, an intuitive universal score (UniScore) for
ESI deconvolution is presented. The UniScore is the weighted average of
deconvolution scores (DScores) for each peak. Each DScore is composed of separate
components to score 1) the uniqueness and fit of the deconvolution to the data,
2) the consistency of the peak shape across different charge states, 3) the
smoothness of the charge state distribution, and 4) symmetry and separation of
the peak. Example scores are provided for a range of experimental and simulated
data. By providing a means of judging the quality of the overall deconvolution
as well as individual mass peaks, the UniScore scheme provides a foundation for
standardizing ESI data analysis of larger molecules and enabling the use of ESI
deconvolution in automated data analysis pipelines.