Identification of serum proteins by immunodepletion and western blotting. Proteins representing peaks at m/z 6624, m/z 8916 and m/z 13870 were immunodepleted from serum extracts using monoclonal antibodies against (A) apolipoprotein CI (ApoCI), (B) C3a/ C3a des-arginine anaphylatoxin (C3a-desArg) or (C) transthyretin. The starting material (Starting, upper panel), the immunodepleted sample (Depleted, middle panel) and the eluted fraction (Recovered, lower panel) were analyzed on NP20 arrays by surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS). (D) Western blotting for ApoCI, C3a/C3a-desArg and transthyretin were performed on four healthy volunteer (HV) samples and four breast cancer patient (BC) samples. (E) Mean band densities (+standard deviation (SD)) derived from the blots shown in panel D (n = 4 for all groups). (F-H) Association between SELDI peak intensities and western blotting band densities for individual HV and BC serum samples (n = 8), indicating strong correlations for (F) ApoCI, (G) C3a-desArg and (H) transthyretin.