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iq (version 2.0.0)

Protein Quantification in Mass Spectrometry-Based Proteomics

Description

An implementation of the MaxLFQ algorithm by Cox et al. (2014) in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 ). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, the median polish algorithm by Tukey (1977, ISBN:0201076160), and a robust linear model. In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.

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Install

install.packages('iq')

Monthly Downloads

1,907

Version

2.0.0

License

BSD_3_clause + file LICENSE

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Repository

https://github.com/tvpham/iq

Maintainer

Thang Pham

Last Published

October 6th, 2025

Functions in iq (2.0.0)

create_protein_list

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

long_format_to_iq_format

Long format input data to iq format

fast_preprocess

Data filtering and normalization

The MaxLFQ algorithm

The meanInt algorithm for protein quantification

Reading data from an input file

connected_component

Group connected samples

Data preprocessing for protein quantification

process_wide_format

Merging rows with identical values in a particular column in a table

Rescale relative quantification

process_iq_format

Process data in the iq format

A wrapper for the R implementation of the median polish algorithm

Process individual matrix

process_long_format

Long format to a wide format table using the MaxLFQ algorithm

Plotting the underlying quantitative data for a protein

The topN algorithm for protein quantification

An example dataset of 12 spike-in proteins

The MaxLFQ algorithm for protein quantification

create_protein_table

Protein quantification for a list of proteins

extract_annotation

Protein annotation extraction