We developed a novel dissociation strategy in the data acquisition process, the Mesh strategy to dissociate multiple charge states of one proteoform with stepped HCD (high collision energy dissociation). We proved that the ‘Mesh’ strategy could generate fragments with improved sequence coverage and it could also improve identification rate in top-down proteomics analysis for complicated samples. The strategy is implemented within an an open source real-time instrument control software program called MetaDrive to perform real time deconvolution and precursor selection.