Figure 2: Comparison of sample preparation methods across proteins. Bar graphs emphasizing the denaturant- and protein-dependent response encountered in peptide-based quantifications. Data represent the mean ± S.E.M. for three transitions measured for each peptide by LC-MS/MS for 44 hr digestions. All samples were processed from the same initial pellet for each transfected cell line to rule out variability in starting material. Membrane fractions were initially denatured in 25 mM ABC alone or 25 mM ABC containing 7 M Gdn, 0.2% PMAX, or 10% DOC prior to alkylation, dilution, and digestion. Repeated measures ANOVA followed by Dunnett’s Multiple Comparison Test were performed to compare each preparation method with control (designated as heat with ABC buffer alone). *Differences were considered significant at the level of p = 0.05.