Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.Isobaric labeling has the promise of combining high sample multiplexing with precise quantification.  Here, we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes.  All novel tools and algorithms are available with the regular MaxQuant and Perseus releases, which are downloadable at http://maxquant.org.
MaxQuant
Furthermore, we provide many novel processing and normalization options in Perseus, the companion software for the downstream analysis of quantitative proteomics results.  All novel tools and algorithms are available with the regular MaxQuant and Perseus releases, which are downloadable at http://maxquant.org.
Perseus