I am a temple university graduate student. I was writing a simple
script to batch process my mass spectrometry imaging data. I've tried
several applications like proteowizard, pymzML, pyOpenMS. But none of
them have solved my problems so far. Now I turned to mzR for help. I
had a question of how to export .mzML files using mzR or any other
The main function of this script is to import, analyze and export
.mzML data files. The work flow is described below:
1. A Bruker run (say test.d) file is converted to test.mzML file by
msconvert using proteowizard
2. The test.mzml file is imported to R
3. Two spectra are extracted first by aveaging part of the test.mzml
scans. For example, one spectra (a) equals (scan2+scan3)/2, the other
(b) equals (scan6+scan7)/2. This can be done easily by calulating the
peaks count in the scans.
4. b minus a to get the final target spectrum
5. The target spectrum will be saved as target.mzML. This is the step
I have problem now that I couldn't find any functions to use.
Thanks for your help.
-- output of sessionInfo():
R version 3.0.3 (2014-03-06)
Platform: i386-w64-mingw32/i386 (32-bit)
 LC_COLLATE=English_United States.1252
 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252
 LC_TIME=English_United States.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
Sent via the guest posting facility at bioconductor.org.