An implementation of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>). 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). In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.
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