create_protein_table: Protein quantification for a list of proteins

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Protein quantification for a list of proteins

Description

Travels through the input list and quantifies all proteins one by one.

Usage

create_protein_table(protein_list, method = "maxLFQ", ...)

Arguments

protein_list	The input protein list
method	Possible values are "maxLFQ", "median_polish", "topN", and "meanInt".
...	Additional parameters for individual quantitation methods.

Value

A list of two components is returned

estimate	A table of protein abundances for all samples in log2 space.
annotation	A vector of annotations, one for each protein.

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.

See Also

create_protein_list, maxLFQ, median_polish, topN, meanInt

Examples

data("spikeins")
# This example set of spike-in proteins has been 'median-normalized'.
norm_data <- iq::preprocess(spikeins, median_normalization = FALSE, pdf_out = NULL)
protein_list <- iq::create_protein_list(norm_data)
result <- iq::create_protein_table(protein_list)
head(result)

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