Figure 4.

Parent protein expression of distinct peptide matches (per LC–MS/MS run) detected in the a/b/y ion screen alone, the b/y ion screen alone, or both a/b/y and b/y ion screens. Protein expression values (PE; estimated molecules per cell) were obtained from genomic-scale Western analyses in yeast.¹³ Proteins of unknown PE values or values of zero (undetected) are not included. Distribution lines represent parent-protein PE values of peptides detected by the SEQUEST (A) and OMSSA parameter set 0 (B) screens. Also see Supplementary Figure 3.