Analysis of in silico predicted protein masses verses in vivo measurements. Predicted (in silico) versus measured (in vivo) protein masses that were reconstructed in i JL1678-ME were categorized by function and compartment. Subgroups with zero values were removed from further calculations. (A) The linear model between in silico and in vivo protein mass predictions (p-value=6.6x10−3). The outliers had standardized residues that fell outside of the normal distribution curve as formed by the other points (Additional file 2: Figure S4). (B) The outliers were removed, and the linear model between in silico and in vivo protein mass predictions was recalculated (p-value=6.6x10−6).