After comparing speed, we next compared deconvolution reproducibility. The six selected files are replicate injections under the same chromatographic conditions, so the same species should be found at approximately the same retention time in each file. Features were constructed by aggregating clusters with similar masses from nearby scans, as described in the Supplemental Methods (SM10). Each possible pairwise combination of the six files was compared from the same deconvolution algorithm, and we calculated the percentage of features that agreed between the files. Here, IsoDec slightly outperformed FLASHDeconv and TopFD, matching an average of over 75% of features (Figure and Supplemental Discussion SD3). However, all algorithms performed similarly with respect to feature intensity, with over 95% of total feature intensity matched between replicate injections. These data suggest all algorithms perform well on abundant features, and the differences lie in the less abundant proteoforms.