Figure 1
From: Integrated multi-level quality control for proteomic profiling studies using mass spectrometry
QC tool output for section of study of patients with different levels of renal function using IMAC-Cu ProteinChips. Pair-wise plots of the first two principal components (PCs) and a dendrogram showing results of hierarchical clustering using Ward's agglomeration method and the Euclidean distance metric are shown in each panel. Panel (A) shows the plots with the chip ID number indicated by plotting character. The reference set chips are indicated with red, black and green plotting characters and subsequent projections described in the legend. Panel (B) shows the plots with the spot indicated. Panel (C) shows the plots with the reference set indicated by solid plotting characters (red, green and black as in panel (A)) and numbers plotted representing order of QC spectra on sample chips. Panel (D) shows the mean spectra obtained from samples in the reference set and also individual spectra which appear to be on the edge of the PC space in the PC plots in panel (C). The inset plot in panel (D) shows an expanded region of the spectra where the differences from the reference spectra can be observed.