DIAgui: a Shiny application to process the output from DIA-NN

Marc-Antoine Gerault; Luc Camoin; Samuel Granjeaud

doi:10.1093/bioadv/vbae001

DIAgui: a Shiny application to process the output from DIA-NN

Bioinform Adv. 2024 Jan 13;4(1):vbae001. doi: 10.1093/bioadv/vbae001. eCollection 2024.

Authors

Marc-Antoine Gerault^{1

2}, Luc Camoin¹, Samuel Granjeaud¹

Affiliations

¹ Aix-Marseille University, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille F-13009, France.
² Centrale Marseille School, Marseille F-13013, France.

Abstract

Summary: DIAgui is an R package to simplify the processing of the report file from the DIA-NN software thanks to a Shiny application. It returns the quantification of either the precursors, the peptides, the proteins, or the genes thanks to the MaxLFQ algorithm. In addition, the latest version provides the Top3 and iBAQ quantification and the number of peptides used for the quantification. In the end, DIAgui produces ready-to-interpret files from the results of DIA mass spectrometry analysis and provides visualization and statistical tools that can be used in a user-friendly way.

Availability and implementation: Code and documentation are available on GitHub at https://github.com/marseille-proteomique/DIAgui. The package is written in R and also uses C++ code. A vignette shows its use in an R command line workflow.