  In comparative proteomics studies, LC-MS/MS data is generally quantified
using one or both of two measures: the spectral count, derived from the
identification of MS/MS spectra, or some measure of ion abundance derived from
the LC-MS data. Here we contrast the performance of these measures and show
that ion abundance is the more sensitive. We also examine how the conclusions
of a comparative analysis are influenced by the manner in which the LC-MS/MS
data is `rolled up' to the protein level, and show that divergent conclusions
obtained using different rollups can be informative. Our analysis is based on
two publicly available reference data sets, BIATECH-54 and CPTAC, which were
developed for the purpose of assessing methods used in label-free differential
proteomic studies. We find that the use of the ion abundance measure reveals
properties of both data sets not readily apparent using the spectral count.
