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Preparation of spectral libraries with the Astral Analyser

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Preparation of spectral libraries with the Astral Analyser n dasilva  2024-04-24 01:55
 

At the moment, we are currently attempting to create a spectral library using Skyline for a PRM experiment; using DDA data of the full proteome and of heavily labelled peptides, acquired using the Astral equipment.

It is possible to import the raw files, although a message saying that there is " no matching instrument configuration for the analyser type" appears.
Also when setting the MS/MS filtering acquisition method, as it is not possible to find the Astral mass analyser as an option, what would be recommended to use in this particular case?

I appreciate all the attention given,
Best regards,
Nádia
 
 
Mike MacCoss responded:  2024-04-24 10:09

Hi Nádia
It is possible to directly search the DDA data in Skyline using MSFragger, MSAmanda, or MSGF+. There is a tutorial on it at: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search There is also a good tutorial if you just want to build a spectrum library from your own search results obtained outside of Skyline. https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit
Both of these tutorials are good places to start.

Also, if you are using the Orbitrap Astral, I would recommend doing DIA first to pick your targets for doing PRM. This is the strategy that our lab uses. There is a webinar on this topic at:
https://skyline.ms/project/home/software/Skyline/events/2023 Webinars/Webinar 22/begin.view?

I hope this helps,
Mike