parsing data to prm and dda mass filters

parsing data to prm and dda mass filters tara chouinard  2023-08-10 09:24

The prm/dda setting will not parse orbitrap data for separate peak integration for shared transitions despite the NCE being unique (22% v. 30%). Is there a way to parse data in skyline similar to mass filter parsed data for methods with both DDA and targeted experiments?

Nick Shulman responded:  2023-08-10 09:33
I do not understand your question.
It might be easier to understand what you are asking if you send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

It would be helpful if you would send us that .zip file as well as one or more of your .raw files.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:
-- Nick
tara chouinard responded:  2023-08-10 10:30
Hi Nick,

I just uploaded the relevant zip file with supporting files. My ask is that I only want to quantitate on the tMS data but Skyline is either integrating tMS and DDA data with the same transitions or it is defaulting to the DDA data. I can send a raw file example to let you see the mass filters if that helps.
Nick Shulman responded:  2023-08-10 10:42
Yes, it would be helpful if you could send us your .raw file.

It sounds like you would benefit from a new feature that we added to Skyline-daily.
In Skyline-daily, you can right-click on something in the Targets tree and use the menu item "Edit Spectrum Filter" to specify that extracted chromatograms should only use a subset of the matching spectra.

There is a little bit of information about how this new feature works here:

Let me know if you have any questions about this new feature and I will update the documentation to be more clear.
-- Nick
tara chouinard responded:  2023-08-10 10:59
That sounds like exactly what I am looking for. Thanks! Is that feature available in the beta version? I can send you a zip file with a couple of raw files. I am not using a tribrid instrument with an LT just an exploris 240.

Thanks so much for your help!
Nick Shulman responded:  2023-08-10 13:30
Yes, Skyline-daily is our beta release.
You can install it by clicking on the "Skyline-daily (beta)" button on the main Skyline web page:

Unfortunately, I just discovered that this Spectrum Filter feature does not work at all with small molecule documents. I will figure out a fix for this and I will probably be able to give you a URL where you can download a special build of Skyline-daily where this feature does work with small molecules.
-- Nick
Nick Shulman responded:  2023-08-10 20:35
You can download a special build of Skyline-daily which has this fix in it here:
The bug fix will also be present in the next update of the official Skyline-daily which will probably be released in a few days.
-- Nick