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Retention time filtering

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Retention time filtering chloe baldreki  2025-01-08 07:08
 

Hi Skyline team,
I have a discovery DIA dataset, searched through Spectronaut, and I'm currently trying to compare the identifications of a protein of interest between two sample groups, which were run alongside a recombinant expression of this protein.
I was hoping to use Skyline to look more into the data, and to provide some additional filtering.
Some of what I wanted to achieve has been possible through Refine>Advanced and setting thresholds here but I was also hoping to filter based on retention time. Is there a way I can set a peptides retention time using a sample I am confident in and then use this as a basis for filtering in other samples?
Thanks for your help!
 
 
Brian Pratt responded:  2025-01-08 11:39

Hi Chloe,

Do I understand correctly that you'd like to be able to eliminate things from the Skyline document that fall outside (or inside?) a specific RT range?

Possibly you could do this manually using the Document grid, sorting on RT then deleting as needed?

Thanks for using the Skyline support board,

Brian Pratt
 
Nick Shulman responded:  2025-01-08 13:06
Skyline's peak picking algorithms have the limitation that they do not take advantage of between-run information.
That is, even when a peptide was very easily detected in some of the runs, Skyline is unable to use that information to make better choices about where to choose peaks in the other runs where the peptide could not so easily be found.
We really hope to have a solution to this scenario soon, maybe in a few weeks.

If there is one replicate for which the correct peak has been chosen for all of the peptides, you can select all of the peptides in the Targets tree and then choose "Edit > Integration > Apply Peak to All".
However, if the best replicate is different for each peptide, then that solution will not work very well for you.
-- Nick