Fig. 4: The qualitative and quantitative performance across 20 LC-MS platforms.

The number of proteins identified (with 1% FDR) from the 10 platforms without LC-SOP (a, orange) and with LC-SOP (e, blue). Three technical replicates were collected in each platform. The average number was shown at the bottom of the bar, and the individual data points were indicated by purple dot points (n = 3), with error bars representing +/− SD. Horizontal dashed lines were added at 3000, as a reference value. b and f The upset plot showed the numbers of proteins co-identified across various combinations of 10 platforms without LC-SOP (b) and with LC-SOP (f) (vertical bars). The colored vertical bar reflected the number of proteins co-identified by all 10 platforms without LC-SOP (b, orange) and with LC-SOP (f, blue). The horizontal bars reflected the number of proteins identified in total at each platform. c, g The distribution of the coefficients of variation (CV) obtained on the quantified protein intensity across the three technical replicates was plotted for each platform. All box plots indicated the median and the first and third quartiles as the box ends. Whiskers were positioned 1.5-times in the interquartile range. Horizontal dashed lines were added at 20% CV, as a reference value. The Pearson correlation matrix based on log2 protein intensity of the common proteins from 10 platforms without LC-SOP (d) and with LC-SOP (h). The color-scale indicated the magnitude of the Pearson correlation coefficient. 20 platforms arranged in chronological order based on the MS release dates. Source data are provided as a Source Data file.