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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture CARIC Strategy

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rTANDEM, an R/Bioconductor package for MS/MS protein identification.

Frédéric Fournier¹, Charles Joly Beauparlant¹, René Paradis¹

¹Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.

Bioinformatics (Oxford, England)

|April 5, 2014

Summary

The rTANDEM and shinyTANDEM R/Bioconductor packages streamline proteomic data analysis. They provide tools for protein identification using X!Tandem and offer a graphical interface for results interpretation within R.

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Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Mass spectrometry-based proteomics generates large datasets requiring sophisticated analysis tools.
Integrating various analysis steps into a single environment enhances workflow efficiency.

Purpose of the Study:

To introduce rTANDEM, an R/Bioconductor package for interfacing the X!Tandem protein identification algorithm.
To present shinyTANDEM, an associated R package offering a web-based graphical user interface for results visualization and interpretation.
To establish a comprehensive MS/MS-based proteomic analysis pipeline within the R/Bioconductor ecosystem.

Main Methods:

The rTANDEM package enables direct execution of the multi-threaded X!Tandem algorithm on proteomic data files within R.
Functions are provided for seamless conversion of search parameters and results between R and X!Tandem.
Parameter manipulation and automated search capabilities are integrated into the package.

Main Results:

rTANDEM facilitates direct execution of X!Tandem searches from within the R environment.
The package supports efficient management and automation of proteomic search parameters.
shinyTANDEM provides an intuitive web-based interface for interactive exploration of identification results.

Conclusions:

rTANDEM and shinyTANDEM offer a powerful, integrated solution for MS/MS-based proteomic data analysis in R/Bioconductor.
These packages simplify the process of protein identification and result interpretation.
They serve as a foundational entry point for building complete proteomic analysis pipelines in R.