isobar and iTRAQ data
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queso012 • 0
@queso012-7191
Last seen 6.8 years ago
United States

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             

 

 

 

 

 

 

iTRAQ file conversion csv files mzxml files .raw files • 1.0k views
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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.

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