extract_annotation: Protein annotation extraction

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Protein annotation extraction

Description

Extracts annotation columns from a long-format input

Usage

extract_annotation(protein_ids, quant_table, primary_id = "PG.ProteinGroups",
                   annotation_columns = NULL)

Arguments

protein_ids	A vector of protein ids.
quant_table	A long-format input table. The input is typically the same as input to the preprocess function.
primary_id	The column containing protein ids.
annotation_columns	A vector of columns for annotation.

Value

A table of proteins and associated annotation extracted from the input.

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")
extra_names <- iq::extract_annotation(levels(spikeins$PG.ProteinGroups),
                                      spikeins,
                                      annotation_columns = c("PG.Genes", "PG.ProteinNames"))

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