Protein Quantification in Mass Spectrometry-Based Proteomics

An implementation of the maximal peptide ratio extraction module of the MaxLFQ algorithm by Cox et al. (2014) in a complete pipeline for processing proteomics data in data-independent acquisition mode. It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).