Next, we tested how IsoDec performed on large TDP LC-MS/MS data sets consisting of thousands of individual scans and millions of features. We selected a set of six files from replicate injections of intact E. coli lysate and benchmarked the performance of IsoDec against FLASHDeconv and TopFD. In addition to sensitivity and accuracy, speed also becomes a concern when working with large files, so we first compared the total time to deconvolve the selected files.