Hi all, 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 bioconductor packages. 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. Best regards, Jian -- output of sessionInfo(): R version 3.0.3 (2014-03-06) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.