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

Frédéric Fournier; Charles Joly Beauparlant; René Paradis; Arnaud Droit

doi:10.1093/bioinformatics/btu178

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

Bioinformatics. 2014 Aug 1;30(15):2233-4. doi: 10.1093/bioinformatics/btu178. Epub 2014 Apr 3.

Authors

Frédéric Fournier¹, Charles Joly Beauparlant¹, René Paradis¹, Arnaud Droit²

Affiliations

¹ Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
² Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, CanadaProteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.

PMID: 24700319
DOI: 10.1093/bioinformatics/btu178

Abstract

Summary: rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor.

Availability and implementation: rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0).

Contact: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computer Graphics
Databases, Protein
Internet
Proteomics / methods*
Software*
Tandem Mass Spectrometry*
User-Computer Interface*