maxLFQ: The MaxLFQ algorithm for protein quantification
In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

maxLFQ

R Documentation

The MaxLFQ algorithm for protein quantification

Description

Estimates protein abundances by aiming to maintain the fragment intensity ratios between samples.

Usage

maxLFQ(X)

Arguments

`X`	A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.

Value

A list of two components is returned

`estimate`	A vector with length equal to the number of columns of the input containing the protein abundances in log2 space.
`annotation`	An empty string if all quantified samples are connected. Otherwise, a string of membership of the connected components is returned.

Author(s)

Thang V. Pham

References

Pham TV, Tran CTM, Henneman AA, Pham LHC, Le DG, Can AH, Bui PHL, Piersma SR, Jimenez CR. Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics. Journal of Proteome Research 2026 Feb 6; 25(2):1198–1203.

Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13(9):2513–2526.

Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.

iq documentation built on Oct. 28, 2026, 1:07 a.m.