For the 500 ms data set we identified a total of 28,230 PSMs using MS 2 Rescore for post-processing. This represents a substantial increase of 8,526 PSMs compared to the 19,704 PSMs initially identified by MS Amanda. Furthermore, it surpasses the results from Percolator by an additional 1,837 PSMs, as Percolator identified 26,393 PSMs in total (26,482 when providing a combined input pin file to Percolator). Similarly, in the context of the 750 ms data set, MS 2 Rescore showed superior performance by identifying the highest number of PSMs, totaling at 20,681. This is an increase of 1,254 PSMs compared to Percolator's count of 19,427 PSMs (19,695 for the combined input pin file) and MS Amanda's count of 15,578 PSMs (an increase of 5,103 PSMs). Additionally, Venn diagrams in Supplementary Figure show that there is a substantial overlap between the PSMs of the three workflows.