topN: The topN algorithm for protein quantification

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

The topN algorithm for protein quantification

Description

Estimates protein abundances using the N most intense ions.

Usage

topN(X, N = 3, aggregation_in_log_space = TRUE)

Arguments

X	A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.
N	The number of top ions used for quantification.
aggregation_in_log_space	A logical value. If FALSE, data aggregation is performed in the original intensity space.

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	Reserved, currently an empty string.

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.

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.