In the field of quantitative proteomics, the Isobaric Tags for Relative & Absolute Quanti-tation (iTRAQ) technology has demonstrated efficacy for proteome monitoring despite its lack of a consensus for data handling. In this study, after peptide and protein identification, we com-pared the widespread quantitation method based on the calculation of MS/MS reporter ion peaks areas ratios (Protein Pilot) to the alternative method based on the calculation of ratios of the sum of peak intensities (jTRAQx (Quant)) and we processed output data with the in-house Customi-zable iTRAQ Ratios Calculator (CiR-C) algorithm. Quantitation based on peak area ratios dis-played no significant linear correlation with Western blot quantitation. On the contrary, quantita-tion based on the sum of peak intensities displayed a significant linear association with Western blot quantitation (non-zero slope; Pearson correlation coefficient test, r = 0.2962, p = 0.0099 **) with an average bias of 0.08747 ± 0.5004 and 95% Limits of Agreement from - 0.8932 to 1.068. We proposed the Mascot-jTRAQx-CiR-C strategy as a simple yet powerful data processing ad-junct to the iTRAQ technology