Fig. 1

Quantification of proteins in the breast tissues. a Mass spectrometry-based proteomics workflow. b Dynamic range of protein expression in our study. c Overlap in the identified proteins between our study (Tang et al.) and Mertins et al. [13]. d Abundance of individual proteins correlates between our study and Mertins et al. (Spearman’s rank correlation rho = 0.56). Correlation is better for high than low abundance proteins. Scaled total spectral counts (z-scaled log converted PSMs) were plotted on the x- and y-axes. e A principal component analysis (PCA) based on the abundance of 7141 proteins in 118 tissues (breast tumors n = 65; adjacent non-cancerous tissues n = 53). The two-dimension PCA plot shows distinct clustering of the tumor (red) and non-cancerous (blue) tissues