Fig. 1: Performance comparison of different DIA data analysis software tools.

a Construction of the benchmarking samples and the evaluated data analysis strategies. b Numbers of quantified proteins per run. The bars indicate the mean values and the error bars indicate the standard deviations. Significant differences (t-test p-value < 0.05, two-sided, no multiple comparison adjustments) are indicated. c Numbers of proteins quantified in at least specified percentages (data completeness) of runs. d Overlap of the proteins quantified in at least 50% runs. e Measured fold change (FC) values of protein quantities using sample S3 as reference. FC values were calculated only for proteins quantified in at least 3 runs for each sample of the comparison. Numbers (n) of proteins are indicated for each species. The boxes mark the first and third quantile and the lines inside the boxes mark the median; the whiskers extend from the box to the farthest point lying within 1.5 times the inter-quartile range; outliers are not shown. The theoretical ratios are highlighted as dashed lines. Differences between the measured median FC values and theoretical values are indicated, among which the smallest ones are darkened. Significant differences (t-test p-value < 0.05 and Cohen’s |d | > 0.2, two-sided, no multiple comparison adjustments) are indicated. In b–e, the data was analyzed using the library free strategy. Source data are provided as a Source Data file.