Session: Session 1

DIANN_MaxQ_process.rmd and Shiny_PROTEOM_IC.R : Two R tools that accelerate descriptive and statistical proteomic analysis.

Johanna BRUCE¹, Guilhem CLARY¹, Emilie-Fleur GAUTIER¹, Pierre SOHIER¹, Marjorie LEDUC¹

¹Proteom’IC facility, Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris, France

In the aim of accelerating and avoiding mistakes during statistical analysis of label free quantitative proteomics data, we have developed two user-friendly interface tools allowing an automatic analysis of the data in only few minutes without need of any programming background.

DIANN_MaxQ_process.rmd is a markdown R script that analyses data files obtained from Maxquant and DIA-NN softwares. It generates descriptive plots including barplot of the number of proteins per sample, principal component analysis, heatmaps, before making Student tests and generates volcano plot and heatmap showing significant proteins. This script finally exports 4 files:

a Word report with these plots (this report can be manually modified easily) ;

an Excel file with proteins identification and intensities, Student results and number of peptides per protein (this export can be modified easily) ;

a text file that contains the same data as an Excel file ;

a .rds file that can be used as input for Shiny_PROTEOM_IC.R script.

Shiny_PROTEOM_IC.R script allows to custom plots made using DIANN_MaxQ_process.rmd and to further more investigate data with supplemental plots such as scatterplot of different samples or conditions, individual protein expression plot and associated peptides plot.

Finally, these 2 scripts allow rapid and automatic data analysis of Maxquant and DIA-NN outputs without need of any programming background. They are freely available on https://github.com/MarjorieLeduc.