qPLEXanalyzer is an R package available in Bioconductor that provides a toolkit for statistical analysis of quantitative proteomics data. It was developed by Kamal Kishore, Ashley Sawle and Matt Eldridge in the Bioinformatics Core in collaboration with the Proteomics Core and Jason Carroll‘s and Florian Markowetz‘s groups. Also available is a companion package, qPLEXdata, that contains several experimental datasets to test the functionality of the qPLEXanalyzer package.

The qPLEXanalyzer package provides a comprehensive workflow consisting of importing, quality control, statistical analysis and visualization of proteomics data.

  • Import quantitative dataset: pre-processed data from MaxQuant, Proteome Discoverer or other proteomic software consisting of peptide intensities with associated features and sample metadata can be imported by qPLEXanalyzer

  • Quality control: computes and displays quality control statistics plots of the quantitative dataset

  • Data normalization: quantile normalization, central tendencies scaling and linear regression based normalization

  • Data aggregation: summarization of peptide intensities into protein intensities

  • Differential statistical analysis: limma based analysis to identify differentially abundant proteins and visualization of the results