Hi Nicolas,
You can start with the small molecule tutorials, of which there are now 4 listed on the tutorials page:

http://skyline.ms/tutorials.url

The last "Hi-Res Metabolomics" should be helpful for your case, but you may also want to start more basic.

Hope these help get you started. Thanks for posting to the Skyline support board.

--Brendan

Dear Brendan,

thank you for your fast answer!
ok it seems the tutorial quitte change since i red some of them several months ago. I forgot a simple step (adding p to the transition settings ..., my bad sorry)

So now I'm able to have precursor ion and fragment on the same chromatogramm.
but it seems there still is a problem with data processing.
as you can see on the powerpoint, when only the precursor ion is present the "target" column, the processing of peak and its integration is perfect.
but when the precursor ion and the fragment are presents, the peak is not complete. It's especially annoying for the quantification which is most of time based on the precursor ion.
do you know why? is it due to my data? or wrong setting?
I just red again all the tutorial for small molecules and i don't find the case were precursor and fragment are present at the same time on the target list.
But when i'm working on data from PRM tutorial, everything is perfectly working.

thank you again for your help

Nicolas

Hi Nicolas,
One starter question: Is this really PRM data?

You say, "Datas were acquired in DDA with 5 most abondant ions."

When you specify PRM in the MS/MS extraction settings, we found that just extending MS1 and fragment chromatograms through the entire gradient is most often not what you want, especially when the spectra are acquired with scheduled-PRM.

We are planning on adding a DDA acquisition mode in the MS/MS extraction settings, but we don't have it yet. You may want to try DIA mode and just set a narrow isolation range for your spectra, e.g. you can use 0.05 m/z if you expect your precursor m/z values to be high-accuracy, or you could use 1 m/z if you want to extract fragments from any spectrum that might have contained your ion.

I don't think we do the same MS1 chromatogram truncation for DIA isolation schemes as we do for PRM. Obviously, having an explicit DDA option in this list would be best for users like you. Hopefully, we will get to it in the near future.

Thanks again for your feedback and clear presentation of what you are seeing in Skyline.

--Brendan