Figure 2

Comparison with XPRESS and Mascot Distiller. (a-c) Correlation of log₂ ratios between distinct peptides from the same protein obtained by Mascot Distiller (a) [16], XPRESS (b) [10], and our method (c). Peptides from each protein were randomly assigned to two groups for this comparison of log₂ ratios of peptides in group 1 versus log₂ ratios of peptides in group 2. Multiple measurements (for example, charge states) of the same peptide, when present, were collated and given a median log₂ ratio prior to forming the peptide groups. Black points designate proteins identified and quantified by both methods, and red points designate proteins identified and quantified that were specific to each method. The diagonal gray line designates perfect correlation.