Dear All,
I have .raw files from iTRAQ and I'm a trying use the isobar bioconductor package. The input file formats for this package is csv and mgf formats. I was able to convert my .raw files to mgf format (using Proteowizard/msconverter) and .raw to mzXML format. Does anyone have any suggestions on what tools to use and how to convert my files to csv format? I am new to proteomics data, so any insight will be appreciated. Thanks! Below is my session info:
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] isobar_1.10.0 plyr_1.8.1 Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.3
loaded via a namespace (and not attached):
[1] distr_2.5.3 Rcpp_0.11.3 sfsmisc_1.0-26 startupmsg_0.9 SweaveListingUtils_0.6.2
[6] tools_3.1.0
There isn't any utility provided by the developer of
isobar
. You have to export the data and write your own tool to format it into the required columns.