Figure 5.

Quantitative variance per protein within and across cell lines. (A) Proteins with three peptides are included in the comparison and distributions of coefficient of variation (CV) among peptides per protein per cell line are plotted. Ideally, peptides for a particular protein and cell line should have identical quantitative values. Larger CV indicates more variation for the measurement of a protein within a given cell line, most likely due to interference from coisolated ion species. (B) Variance of relative abundance per protein across 11 cell lines. Quantitative proteomics reveals distinct composition of the 11 cell lines (Figure S3), so consequently a substantial fraction of proteins is expected to have large variation across cell lines. Reduced variations from HRMS2 relative to SPS90, SPS180, and RTS indicate ratio compression toward uniform values. Variance for the HRMS2 analysis was on average 1.7-fold lower than the other three methods.