TraianProt is a web-based, user-friendly proteomics data analysis platform, that enables the analysis of label free and TMT labelled data from data-dependent or data-independent acquisition mass spectrometry mode supporting MaxQuant, MSFragger, DIA-NN, ProteoScape and Proteome Discoverer output formats. Among its functionalities preprocessing of data, differential expression analysis, functional and protein interaction analysis are included along with the visualization of each of the aforementioned stages.

TraianProt can be accessed through the following url: https://samueldelacamara.shinyapps.io/TraianProt/

The tutorial which covers how to analyze data in every single module can be found in a .pdf format and a vignette in vignettte folder.

If you are bound to analyze data generated by Proteome Discoverer or Fragpipe we recommend you to use the "Unique peptides extractor" app for a unique peptides filter: https://samueldelacamara.shinyapps.io/Unique_peptides_extractor/

Requisites

• R version >= 4.2
• Rstudio

• ProteinGroups.txt file from MaxQuant. a test dataset can be found on "Data_test/MaxQuant" folder.
• combined_protein.tsv file from MSFragger.
• report.pg.matrix.tsv file along with report.tsv if you are using the local version.
• Output file from Proteome Discoverer.
• Metadata whose format is explained in the Tutorial which can be found in the vignette folder.

Installation for Shiny app locally:

• Download the local version functions.R located in the R folder and app.R, Downstreaming_Analysis_report.Rmd and traianprot.png files located in the inst/shiny/TraianProtApp folder and load them into you R session.
• Click Run app.
• Or instead users can access through the url provided above.

Installation for TraianProt R package:

You can install TraianProt from Bioconductor with:

# Install the package (if needed)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TraianProt")

Alternatively you can install the development version from GitHub. First, make sure to install devtools with:

if (!require("devtools")) {
  install.packages("devtools")
}

And install the development version

devtools::install_github('SamueldelaCamaraFuentes/TraianProt')

Test dataset

Test datasets discussed in the manuscript are available in inst/extdata folder

Reference:

[1] de la Cámara-Fuentes, S., Gutiérrez-Blázquez, D., Hernáez, ML., Gil, C. (2024). TraianProt: a user-friendly R shiny application for wide format proteomics data downstream analysis. arXiv:2412.15806.