create_protein_list: Creating a list of matrices of fragment ion intensities for...

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Creating a list of matrices of fragment ion intensities for all proteins

Description

For each protein, a numerical matrix is formed where the columns are samples and rows are fragment ions.

Usage

create_protein_list(preprocessed_data)

Arguments

preprocessed_data

A data frame of four components as output of the preprocess function.

Value

A list where each element contains the quantitative data of a protein. The column names are sample names and the row names fragment ions.

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

preprocess

Examples

data("spikeins")
head(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)

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