Fig. 3: Performance evaluation of directDIA, LFQ-DDA, and TMT on the spike-in metaproteome samples with 6 species added to feces.

a Overlap of proteins and peptides shared in at least 2/3 replicates in each sample group by different methods. b Measured fold change (FC) values of protein abundance between sample 2 (as numerator) and sample 1 (as denominator) for each species calculated based on the average of the replicates of each sample. c Measured FC values between sample 3 (as numerator) and sample 1 (as denominator). d Measured FC values between sample 3 (as numerator) and sample 2 (as denominator). Only proteins quantified in at least 2/3 replicates of each sample group and uniquely belonging to one species were taken into consideration. Numbers (n) of quantified 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 mark 2.5% and 97.5% percentile; 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. The DDA data were analyzed by PEAKS, and the TMT data were analyzed by MaxQuant. Source data are provided as a Source Data file.