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QFeaturesGUI

Léopold Guyot

10 March 2026

Source: vignettes/QFeaturesGUI.Rmd
QFeaturesGUI.Rmd

QFeaturesGUI

QFeaturesGUI is a collection of Shiny applications that provide graphical user interfaces for the analysis of MS-based proteomics data using the Bioconductor ecosystem. It builds on the functionality of the QFeatures and scp package (Vanderaa and Gatto (2021)), offering user-friendly tools for both bulk and single-cell proteomics (SCP) data analysis.

The suite leverages the power of Shiny and shinydashboardPlus to deliver interactive, modular applications. Rather than a single monolithic app, QFeaturesGUI is composed of multiple applications, each dedicated to a specific aspect of proteomics data analysis. These applications are documented in separate vignettes, making it easy for users to navigate and find information relevant to their needs.

Currently available applications include:

  • Data import
  • Data processing

Additional applications will be added in future releases.

The QFeatures and scp Packages

QFeaturesGUI serves as a graphical interface to core Bioconductor data infrastructures for proteomics. To use the GUI applications effectively, it is recommended to understand how the underlying packages handle proteomics data. This section provides a brief overview; refer to the respective package documentations for more detailed information.

The QFeatures Package

The QFeatures package is a data framework specifically designed to manipulate and process MS-based quantitative proteomics data, with a primary focus on bulk proteomics workflows (Gatto (2020)).

It preserves the relationships between different levels of information, such as peptide to spectrum match (PSM) data, peptide data, and protein data. Additionally, the QFeatures package provides an interface to various utility functions that streamline common MS data processing tasks.

For further details on MS data analysis tools, refer to the RforMassSpectrometry project.

The scp Package

The scp package extends QFeatures to support single-cell proteomics (SCP) data analysis (Vanderaa and Gatto (2021)). It operates on a specialized data structure that wraps QFeatures objects around SingleCellExperiment objects (Amezquita et al. (2020)).

This data structure can be conceptualized as Matryoshka dolls, where SingleCellExperiment objects are the smaller dolls contained within the larger QFeatures object.

The SingleCellExperiment class provides a dedicated framework for single-cell data, acting as an interface to cutting-edge methods for processing, visualizing, and analyzing single-cell data. By combining SingleCellExperiment and QFeatures, the scp package enables principled handling of SCP-specific challenges while maintaining compatibility with the broader MS-based proteomics ecosystem.

Before You Start

Before diving into proteomics data analysis using QFeaturesGUI, it is important to note that these applications act as interfaces to the underlying QFeatures and scp packages.

When errors occur during an analysis, QFeaturesGUI reports the corresponding error messages in a dropdown menu at the top right of the application interface. These messages originate from the underlying package functions. Users are therefore encouraged to consult the documentation of the associated QFeatures or scp functions to identify and resolve issues.

The error messages provide valuable clues, and searching the package documentation will often help users troubleshoot effectively.

Installation and Launch

Installation 

# Check if remotes is installed. Otherwise install it.
if (!require("remotes", quietly = TRUE)) {
    install.packages("remotes")
}
# Install the package
remotes::install_github("UCLouvain-CBIO/QFeaturesGUI")
# Load the package
library(QFeaturesGUI)

Applications launch

QFeaturesGUI is composed of multiple Shiny applications, each dedicated to a specific step of the proteomics data analysis workflow. Applications are launched independently, depending on the task to be performed.

For example, the application dedicated to importing data into a QFeatures object can be launched as follows:

app <- importQFeatures()

if (interactive()) {
    shiny::runApp(app)
}

Similarly, the application dedicated to data processing can be launched using:

app <- processQFeatures(qfeaturesObject)

if (interactive()) {
    shiny::runApp(app)
}

Applications overview

Rather than a single application with multiple sections, QFeaturesGUI provides a set of dedicated applications. Each application addresses one step of the proteomics workflow and exposes functionality through a focused graphical interface.

The use of each application is described in a corresponding vignette:

Additional applications will be introduced in future releases and documented in their own vignettes.

Citation

References

Amezquita, Robert A, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, et al. 2020. “Orchestrating Single-Cell Analysis with Bioconductor.” Nat. Methods 17 (2): 137–45.
Gatto, Laurent. 2020. “QFeatures: Quantitative Features for Mass Spectrometry Data.”
Vanderaa, Christophe, and Laurent Gatto. 2021. “Replication of Single-Cell Proteomics Data Reveals Important Computational Challenges.” Expert Review of Proteomics, 1–9.