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


METHODS
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).


BACKGROUND
frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca


BACKGROUND
Supplementary data are available at Bioinformatics online.
Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
Frédéric
F
Fournier
Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
Charles
C
Joly Beauparlant
Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
René
R
Paradis
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.
Arnaud
A
Droit
D000465:Algorithms; D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface