Hi Anas, You can use ProteoWizard msConvert or msConvertGUI for this: http://proteowizard.sourceforge.net/downloads.shtml
And, if you check the "TPP compatibility" checkbox in msConvertGUI, you will get a MGF file that is compatible with both the TPP and Skyline, if you want to do further quantitative analysis with your targeted MS/MS: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_targeted_msms Good luck with your experiments. --Brendan On Thursday, October 4, 2012 2:52:33 AM UTC-7, Anas wrote: > > Hi, > I have done a targeted MS2 on a Q-Exactive II for confirming the identity > of peak features (metabolomics study), > I am trying to find a tool which will give me a parent ion and its > fragment in a list, similar to MGF, for all the peaks in the file (example > attached), > I used a tool called RAW to MGF and it worked only on data dependent files, > XCMS is reporting only MS1 peaks, > seeMS was the closest but it gives only the base peak for each scan in a > list, if I wanted to get the rest of the fragment I had to do it manually > for each scan, > I wonder if there is any or script which could automate the process, > your help is highly appreciated, > Cheers, > Anas > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/_6ADoTNo0IIJ. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
