Measurements of mass spectral peak intensities and spectral counts are promising methods
for quantifying protein abundance changes in shotgun proteomic analyses. We describe
Serac, software developed to evaluate the ability of each method to quantify relative
changes in protein abundance. Dynamic range and linearity using a three-dimensional ion
trap were tested using standard proteins spiked into a complex sample. Linearity and good
agreement between observed versus expected protein ratios were obtained after …