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Transition with precursor m/z in MS2

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Transition with precursor m/z in MS2 dhabaker  2024-01-23 06:44
 

Hello Skyline Support,

For some of the precursors in my PRM data, the MS2 spectra have the precursor m/z as the base peak. While mentioning the same m/z for product m/z in the transition list, Skyline does not give a separate product ion transition peak for this precursor (shown in the attached snapshot). Is there a way to have a separate product ion transition peak when the precursor and product m/z are similar?
I am using Skyline 23.1.
Please let me know if additional details are required to convey the issue if its unclear.
Thank you.

Regards,
Dhanwin
 
 
Brian Pratt responded:  2024-01-24 07:59

Can you provide the transition list you're using?

Skyline does try to eliminate duplicate entries when reading transition lists, and is probably mistaking an attempt to declare an unfragmented precursor in MS2 as being a redundant declaration of the MS1 precursor.

You can add this by hand with a right-click menu in the Targets window, but that's not a long term solution, of course.

Thanks for using the Skyline support board,

Brian Pratt
 
dhabaker responded:  2024-01-24 08:31

Hello Brian,

Thank you for the prompt feedback. Please find attached transition list with some of the precursors.

I tried adding a transition by hand with a right-click menu in the Targets window in Skyline but it seems to give the same transition peak area as that of the MS1 precursor as far as I got it correctly. So, ain't sure if this is still the best option to extract the similar m/z in MS2 as that of MS1 precursor.

Please let me know if there are any other by-pass tricks in Skyline to this issue.

Thanks a lot for all the support.

Regards,
Dhanwin
 
Brian Pratt responded:  2024-01-24 09:02

Let's have a look at your Skyline documented with the manually added transition. Use Skyline's File>Share menu item, and include one of your mass spec files. You can upload that to http://skyline.ms/files.url, or someplace more private if you prefer.
 
dhabaker responded:  2024-01-25 02:07

Hello Brian,

Apologies for the confusion. But the "manual adding of a transition by hand with a right-click menu in the Targets window in Skyline" seems to work, I just had to re-import the results again after adding the manual transition, which I forgot to do previously. So, this alternate trick is working.

Really appreciate your prompt support on the issue.

Regards,
Dhanwin