Fig. 4

Variation among nine conventional instruments. A Number of proteins identified in sample D5 (one of the twin daughters) from the Quartet using nine conventional instruments. B Venn diagram of proteins quantified from the same series of MS instruments, corresponding to Orbitrap Fusion series, Orbitrap QE series, TOF series, and ion mobility series. C Sankey plot (top panel) depicting the flow direction of reproducibility for proteins within different (low, medium, high) intensity groups along with upgraded instruments. The corresponding and detailed percentages are summarized in the bottom table. This assessment involved the same four series of MS instruments as described for B. For a specific experiment, low intensity refers to the < 33.33th percentile, medium intensity refers to the 33.33–66.7th percentile, and high intensity refers to the > 66.67th percentile. D Coefficients of variation (CVs) for proteins within different intensity groups and the global group for the nine conventional instruments (also see Fig. S2B). E Definition of signal-to-noise ratio (SNR, top panel) and the SNR distribution of the nine conventional instruments (bottom panel)