Fig. 1

Established proteomic approaches used for investigation of RCC biological samples. Comparative two-dimension electrophoresis (left) assesses protein abundance differences based on spot intensity (Quantitation), with subsequent mass spectrometry analysis identifying the proteins from the excised spot (Identification). Label-free quantitation (middle) entails mass spectrometry analysis of individual samples, with peptides identified at the MS2 level (Identification), and peptide abundance based on peak intensity determined at the MS1 level (Quantitation). Protein abundance is inferred from peptide abundance measurements. In some label-free quantitation-based experiments, spectral counting is employed, wherein protein abundance is inferred by the number of mass spectrometry spectra generated for each peptide derived from the precursor protein. Isobaric labeling (right) methods involve the labeling of peptides derived from individual samples with mass tags that include reporter ions and mixing of samples prior to mass spectrometry analysis. Peptide Identification and Quantitation information is obtained at the MS2 level in the same spectra. Protein abundance is inferred from peptide abundance measurements