Protein Quantification in Mass Spectrometry-Based Proteomics

An implementation of the MaxLFQ algorithm by Cox et al. (2014) using least-squares analysis in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 , and a new algorithm using the conjugate gradient method Pham et al. 2026 ). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, the median polish algorithm by Tukey (1977, ISBN:0201076160), a robust linear model, and fragment weighting. A new iq format enables the processing of large-scale datasets. In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.