Question: isobar and iTRAQ data
0
gravatar for queso012
4.3 years ago by
queso0120
United States
queso0120 wrote:

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             

 

 

 

 

 

 

ADD COMMENTlink written 4.3 years ago by queso0120

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.

ADD REPLYlink written 3.8 years ago by Dario Strbenac1.4k
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