Results from full LC-MS/MS files were searched using a new version of MetaMorpheus in which importing MsAlign files had been enabled, as described in the Supplemental Methods (SM8). For each of the six TDP files, MS2 MsAlign files were generated using IsoDec (both 4and 8-bin models), FLASHDeconv, and TopFD. MsAlign files from each tool were searched separately but using the same search parameters. Comparison of IsoDec to the native deconvolution implemented in MetaMorpheus was also performed (Figure , Supplemental Discussion SD2). Details on how proteoform-spectrum matches (PrSMs) were calculated and compared are provided in the Supplemental Methods (SM9). Additional Supplemental Methods detail assessing deconvolution quality (SM10), performance on synthetic spectra (SM11), and statistical methods (SM12).