Re: Targeted MS2 data

[Brendan MacLean]

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