Comparative analysis of label-free and 8-plex iTRAQ approach for quantitative tissue proteomic analysis

MS-based approaches have been successfully utilized for the comprehensive characterization of the cell proteome. However, in the case of quantitative proteomics the open question still remains, which quantification method is more suitable for identification of proteins with the altered abundance, particularly for the highly complex clinical samples. In this study, a thorough comparison of label-free method (intensity-based) and 8-plex iTRAQ was conducted as applied to the analysis of tumor samples from non-muscle invasive and muscle-invasive bladder cancer. In the case of the label-based approach, the results obtained for the unfractionated and fractionated sample were included. To obtain representative results from each approach, both experiments were conducted according to routinely applicable protocols. Additionally, the sampling procedure was standardized to reduce the effect of biological and analytical variability on the quantification results.