Unassigned spectra

Unassigned spectra akhilabrai  2024-04-05 22:23

Hi team,

Can we export the unassigned spectra from our DIA data in skyline? Is there any option available?

Thank you.

Nick Shulman responded:  2024-04-05 22:33
I do not understand your question.
I think I know what an unassigned spectrum is in DDA data, but that definition doesn't really apply to DIA spectra.

If you want to export lists of numbers from Skyline, the way to do that is by creating a custom report which you can learn about in the Custom Reports tutorial:

However, custom reports cannot be used to export spectra.

Can you clarify what you are asking?
-- Nick
akhilabrai responded:  2024-04-05 23:22
We usually filter unassigned spectra from DDA data in Proteome Discoverer by applying PSM ambiguity is not equal to unambiguous.

So does that mean all the spectra from DIA get assigned to a protein in Skyline?
Mike MacCoss responded:  2024-04-07 13:56
Hi Akhila,
Our DIA analyses use a peptide-centric instead of a spectrum-centric strategy (see... https://www.mcponline.org/article/S1535-9476(20)32639-6/fulltext). So we do analyze spectra. Simplisticly we take peptides, generate XICs, and score those chromatograms.

Most DIA based spectrum-centric methods use the covariance with time to generate deconvoluted pseudo-spectra to search. So those aren't really spectra that exist in the data file.

Hope this helps,