A quantitative LC/MS proteomic analysis of the DS in the selected lines was performed to further identify protein expression patterns which could account for the various behavioral and electrophysiological differences previously reported in these selected lines. A total of 4,682 protein groups and 29,554 peptide groups were identified with 390 unique proteins being differentially expressed between lines (p<0.05). Table 3 lists the top 20 differentially expressed proteins in HAP relative to LAP mice. Although the magnitude of differential expression for any single protein appears relatively small, ratio compression is a known effect of MS2 quantification with TMT-labels (Rauniyar & Yates 2014); therefore, actual differences in concentrations may be higher. Additionally, due to the use of 8 biological replicates per line and the precision of tandem mass tag labeling for quantification, any proteins with significant (p<0.05) differential expression between lines can be considered of interest biologically.
