Peptide Normalization Increases Sensitivity of Label-Free Quantification of Proteins

摘要

Estimation of relative protein abundance from label-free quantitative proteomic analysis requires the assembly of peptide ion current (IC) values that correspond to individual proteins. Since the ICs from different peptides are not directly comparable due to different ionization potentials, the peptide ICs must be normalized with either difference or ratio techniques. The normalized peptide ICs can then be compared using ANOVA. In order for the ANOVA approach to be applied, repeated injection and repeated digestion of samples must generate consistent IC values. We used z score normalization on the aligned peptide ICs from the nano-LC-MS-FTICR analysis of peptides produced from human red blood cell (RBC) ghosts to determine the effects on sensitivity of increasing digestion and injection replicates.