Figure 1: General workflow for patient sampling, iTRAQ labeling, and protein quantification. All patient samples are depleted and trypsin digested separately. Each sample is then labeled with a different iTRAQ mass tag whereafter the samples are pooled. The pooled samples are fractionated with strong cation exchange and reverse-phase chromatography and analyzed by quadrupole time-of-flight mass spectrometry. The resulting Mascot peptide fragmentation spectra (upper spectra image) provide the peptide sequence and the low mass end (highlighted in lower spectra) shows the iTRAQ reporter ion region used for quantification.