DIA\Panorama

support
DIA\Panorama brown459  2018-08-23 12:05
 

I am trying to set up a skyline method that I can use to port data to panorama so that I can share data with a collaborator.

I should describe what I am attempting to do.

I have a collaborator that has some samples and a control. I am trying to generate a DIA project that I can quantify the peptides found in my previous DDA searches (Using DIA to increase my coverage). Then I want to be able to share this data with my collaborator. She is interested in the relative abundances of the different proteins/peptides in the different samples.

I have so far made a skyline document that has the concatenated DDA runs (from all files) and am in the process of acquiring the DIA data from those same samples. I am of the opinion that the DIA will give me better confidence and quantification overlap.

I am not sure if I am setting my skyline document up wrong/or my panorama page up wrong— I would love any help!

I have attached the method that I was planning on using. And am in the process of running the DIA experiment.

I have already reached out to Vagisha and she mentioned that I should also post here.
Thanks,

CJB

 
 
Nick Shulman responded:  2018-08-23 12:15
Can you send us a .sky.zip file? That file would contain the .sky file that you already attached, plus supporting files including your spectral library and extracted chromatograms.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.

If that .zip file is less than 50MB, then you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick
 
brown459 responded:  2018-08-23 13:44
I uploaded what I believe to be the correct .zip you requested here. I don't have the DIA files yet, but I have the files from the DDA analysis exported there. Those files were the ones that I used to build the peptide spectral library which I hope to use for the DIA analysis.

Is my end goal something that I could foreseeable do with panorama?

Thanks,

CJB
 
Nick Shulman responded:  2018-08-23 14:00
Thanks for sending us your files.

You should probably take a look at the DIA tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dia

I believe it describes your exact scenario where you have DDA peptide search results, and you want to use those results to help Skyline with choosing transitions and retention times.