2. Software for Proteomics Data Analysis 2021 (PDA21)

• Install [R version 4.1 or higher] (https://cran.r-project.org/)
• Install Rstudio
• Install msqrob2, start R and run the following command.

if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
BiocManager::install("msqrob2")

• check if your installation is working with the following example library(msqrob2)

data(pe)
pe <- aggregateFeatures(pe,i="peptide",fcol="Proteins",name="protein")
pe <- msqrob(pe,i="protein",formula=~condition,modelColumnName="rlm")
getCoef(rowData(pe[["protein"]])$rlm[[1]])

• Participants who want to use the graphical user interface (GUI) can install the msqrob2gui shiny app, start R and run the following commands

if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
BiocManager::install("statomics/msqrob2gui")

• Launch the GUI. Run

library(msqrob2gui)
launchMsqrob2App()