MaxQuant: To evaluate each tool's parameter combinations and algorithms for data processing and protein quantification analysis, we analyzed the PXD000279 dataset with MaxQuant . Raw data were processed with MaxQuant (version v1.6.10.43) before the downstream analysis with each tool. MaxQuant was used with default parameters except that "the min ratio of LFQ" was set as 1 and "matching between runs" was enabled. Result parameters from MaxQuant analysis and the parameters file used can be downloaded from the following repository ().