Degree of sampling of SILAC peptide pairs. Yeast was SILAC labeled as explained in Figure 7 and one gel band was analyzed. In principle, SILAC peptide pairs should both be recognized and sequenced as they are equally abundant. (a) Proteins identified were binned according to decreasing Mascot score. Blue bars indicate the peptide in which both members of SILAC pairs were sequenced and red bars indicate the proportion of peptides in which only one member of the SILAC pair was sequenced. (b) Complete analysis of the LCMS experiment for all SILAC pairs extracted by their mass differences. Peptide pairs are ordered by the number of consecutive mass spectrometry scans that they appear in, thus greater or equal than three means that the pair was detected in three or more scans.