iTRAQ analysis. Two control and two treatment samples were each labeled with one of the four iTRAQ tags as shown. The peptide samples were pooled, fractionated by two dimensions of liquid chromatography (cation-exchange and reverse-phase), and analyzed by MS. The iTRAQ sample was analyzed three times on an ESI-QqTOF mass spectrometer and once on a MALDI-TOF-TOF mass spectrometer. The image shows a sample MS/MS spectrum of a single peptide from which the amino acid sequence is deduced, and in addition, it reveals the four reporter ions (enlarged region) from the iTRAQ tags, in the low-mass region, whose intensity indicates the relative abundance of that peptide in the four samples. The two controls are labeled with tags 114 and 116, and show reporter ions at that m/z, while the two T3 treatment samples are labeled with tags 115 and 117, showing reporters at those m/z. This spectrum reveals an increase in that peptide due to T3.