Species determination of Culicoides biting midges via peptide profiling using matrix-assisted laser desorption ionization mass spectrometry

Introduction

This repository contains the complete R scripts to reproduce the analysis described in:

K. R. Uhlmann, S.Gibb, S. Kalkhof, U. Arroyo-Abad, C. Schulz, B. Hoffmann, F. Stubbins, S. Carpenter, M. Beer, M. von Bergen, R. Feltens. 2013. Species determination of Culicoides biting midges via peptide profiling using matrix-assisted laser desorption ionization mass spectrometry. https://doi.org/10.1186/1756-3305-7-392

Please find the dataset at http://dx.doi.org/10.6084/m9.figshare.801878
(The dataset is downloaded by the setup.R script automatically.)

Install

• You have to install R (>= 3.0.0) for your operation system: http://cran.r-project.org/
• Download the R scripts: https://github.com/sgibb/Culicoides/archive/master.zip
• Start R and run the setup.R script (this is needed only for the first use):

source("setup.R")

Run the analysis

After installing R and the needed packages by running the setup.R script you could start the analysis by calling:

source("analysis.R")

(use source("figure7") to create the IPP vs SMM plot (figure 7) and source("digest_drosophila_melanogaster.R") to perform the in-silico digestion of the Drosophila melanogaster reference proteome)

Contact

You are welcome to:

• submit suggestions and bug-reports at: https://github.com/sgibb/Culicoides/issues
• compose an e-mail to: mail@sebastiangibb.de