Fig. 5

Variation among laboratories. A SNR distribution of 24 datasets produced by the nine types of mass spectrometers in 15 laboratories. S: site; D: dataset. B Number of proteins identified in S8D2 and S3D1 (left panel) and the Venn diagram of proteins identified from the two datasets (right panel). C Reproducibility of detected proteins in low-intensity, medium-intensity, high-intensity, and global groups from the two datasets (left panel: S8D2; right panel: S3D1). D Pie chart presenting the percentage of proteins with different identification frequency (IDF) in a specific experiment with three repeats; these proteins are divided into low-intensity, medium-intensity, and high-intensity groups (left panel: S8D2; right panel: S3D1). E Pearson’s correlation coefficients matrix representing the correlations between different replicates from two laboratories. F Sankey plot (top panel) depicting the flow direction of reproducibility for proteins within different (low, medium, high) intensity groups from S8D2 to S3D1. The corresponding and detailed percentages are summarized in the bottom table. G CVs for proteins within different intensity groups and the global group of S8D2 and S3D1. H Principal component analysis and SNR scoring for S8D2 and S3D1 using proteins within different intensity groups and the global group