![Alt text](TraianProt.png) 

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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/
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# 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.

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# Installation for Shiny app locally:

* Download the local version `functions.R` file the `app.R`, `Downstreaming_Analysis_report.Rmd` and `traianprot.png ` files located in the `inst` 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:
```r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("TraianProt")

```

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

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# 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.
