Figure 3.

Protein spot quantification and identifications for breast cancer samples (whole tumor slices): ER positive versus ER-negative samples. Spot numbers correspond to those in Figure 2. 'n.i.' means 'not identified'. Genbank Identities are from the NCBI database (version of 4 April 2004). Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) peptide mass fingerprinting (PMF) scores are from MASCOT. The average spot fraction for ER-positive and ER-negative are given as percentage of the normalized total spot volume for each spot (= [ER-positive × 100%]/[ER-positive + ER-negative]) across all patient pools based on two-color ProteoTope analysis for the indicated most significant protein spots. These values were obtained using a least square fit for a model based on all replicates and attributing pool variability as a random effect. The t-test P value for this model is also given. P values < 0.01 are bold, and P values < 0.001 are designated as such. The bars at the right depict average percent abundance of each protein across the ER-positive (black) and ER-negative (gray) pools as indicated above the column with bars (0% to 50% to 100%). Error bars show standard error of means. Protein spots between numbers 1–32 and 1–24 (indicated by a patterned field) are not presented, having failed to meet selection criteria of either abundance difference ratio of 1.5 or significance at the 5% level. ER, estrogen receptor; NCBI, National Center for Biotechnology Information.