It will be very helpful if I can master some skill for proteomics data. Now, I am focusing on NGS data which is based on DNA and RNA sequences.
Mark the bioconductor package here:
http://www.bioconductor.org/packages/2.12/data/experiment/html/RforProteomics.html
It looks like I have to get familiar with R.....
although I only used limma for some microarray analysis.