Just apply CONSTANd (the normalization algorithm used in QCQuan) to your matrix of (aggregated) quantification values. If you have multiple experiments, you need to normalize each matrix separately.
Initial Publication: Maes, E., Hadiwikarta, W. W., Mertens, I., Baggerman, G., Hooyberghs, J., & Valkenborg, D. (2016). CONSTANd: A normalization method for isobaric labeled spectra by constrained optimization. Molecular & Cellular Proteomics, 15(8), 2779-2790.

Upload a csv-file containing only the matrix of quantification values (may contain header and ID column. Delimiters may be ',' or '\t' or ';'):
We recommend using non-transformed intensities as input values. Do not use log2(ratio) values: CONSTANd only works on positive values.
File contains header (first row).
File contains row identifiers (first column).

Found a bug? Send us the details and job ID at qcquan@vito.be.