The example peaks of two labels A and B are depicted

Copyright information:Taken from "Precise protein quantification based on peptide quantification using iTRAQ™"http://www.biomedcentral.com/1471-2105/8/214BMC Bioinformatics 2007;8():214-214.Published online 21 Jun 2007PMCID:PMC1940031. The area of the peaks is not proportional to the sum of intensities if peak distances and peak count are not equal. This has effects on the quantification results yielding notable differences. The summed intensities of the example above are 15.0000 and 20.000, respectively. The trapezoid integrals amount to 1.500 (A) and 2.000 (B). The corresponding ratios are 1.3333 (summed) and 1.3333 (area). Suppose an additional peak at 115.0600 m/z with an intensity of 7.6000. Then, the area of B would be the identical, whereas the summed intensities will change to 27.6000, yielding a ratio of 1.8400. This yields a difference in relative quantification of 38%. In the former case, the ratio would not reflect the ion count of the three peaks detected by the mass spectrometer, but the latter does as the intensity of each signal represents the amount of ions detected and counted by the mass spectrometer.