Supplementary Figure 8: General workflow for single particle pre-processing.

A Data was acquired on a QE-UHMR. For the data shown in this work, scans were collected for 10 to 60 minutes. After acquisition, .RAW files were centroided and converted into the mzXML format. B Centroids were subjected to filtering. We rejected all centroids which were below a certain intensity value as well as centroids which have an adjacent peak within a certain m/z threshold above the noise limit (See red asterisk in rejected traces). C&D Effect of filtering on AaLS-neg dataset. C 2D histogram of single particle centroids before filtering. Ion intensities trail toward lower values, which is mainly attributed to the presence of split peaks (see Supplementary Fig. 1). D Dataset after noise filtering and removal of adjacent peaks. Filtered single particle centroids are more confined in the intensity domain and don’t show the trailing towards lower intensities anymore.