Introduction

Data analysis part of the pipeline for confirming frameshifted protein sequences in Euplotes crassus with bottom-up LC-MS/MS proteomics. This is supplementary Bioconductor/R packages for the manuscript:

"Widespread Abrogation of Triplet Translation Continuity and Stop Codon Function in Euplotes"

https://dx.doi.org/10.1038/nsmb.3330

Alexei V. Lobanov, Stephen M. Heaphy, Anton A. Turanov, Maxim V. Gerashchenko, Sandra Pucciarelli, Raghul R. Devaraj, Fang Xie, Vladislav A. Petyuk, Richard D. Smith, Lawrence A. Klobutcher, John F. Atkins, Cristina Miceli, Dolph L. Hatfield, Pavel V. Baranov, Vadim N. Gladyshev

The proteomics data has been deposited to PRIDE PXD004333. The vignette of this R package reproduces all the data analysis steps after the MS/MS search. In addition it describes and includes the protein sequences FASTA files used for MS/MS spectra searching and parameters for MS/MS spectra preprocessing and identification.

In the future this package will be submitted to Bioconductor as ExperimentData package under ReproducibleResearch category.

Links to the vignette describing the analysis steps

Executable document (vignette) precompiled into pdf file is available here or downloaded from here.

Reproducing the analysis

Prerequisites

Please install the following prerequisites before installing the EuplotesCrassus.proteome package:

R language for statistical computing: R
IDE for R: RStudio
pdflatex for compiling pdf files form LaTeX code. The basic LaTeX installation should be sufficient. Although during the R vignette compilation it may require installation a few extra packages. The packages are installed on the fly after accepting by clicking OK button. To install LaTeX follow these links:
- Windows: MikTex
- Mac OS: MacTex
- Linus: On Linux pdflatex is likely to be present, otherwise use your package manager. e.g. sudo apt-get install texlive-latex-base

Reproducing the analysis and vignette

Copy and paste the following code into R console. However, if you do not intend to re-compile the vignette (and thus reproduce the analysis) set the build_vignettes to FALSE. Note, the vignette recompilation takes about 15 minutes.

# install devtools if necessary
# note, devtools comes in a packages with RStudio
install.packages("devtools")
library("devtools")

# add path to Bioconductor repositories
source("http://bioconductor.org/biocLite.R")
options(repos=biocinstallRepos(character()))

install_github("vladpetyuk/EuplotesCrassus.proteome", build_vignettes=TRUE)

library("EuplotesCrassus.proteome")
vignette("euplotes_frameshifts")

To reproduce the vignette compilation install the package with build_vignettes=TRUE or directly open and recompile euplotes_frameshifts.Rmd from the package source.