Would you tell me how to prepare Skyline document to publish to a library folder on Panorama?

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Would you tell me how to prepare Skyline document to publish to a library folder on Panorama? eisuke miyauchi  2019-03-27
 

Dear PanoramaWeb team,

I couldn't import my library downloaded from Panorama into Skyline for DIA analysis.

Would you tell me how to prepare Skyline document to publish to a library folder on Panorama?

Sincerely,
Eisuke

 
 
vsharma responded:  2019-03-28

Hi Eisuke,

Can you please tell me what error you are seeing when you try to use the chromatogram library in your Skyline document?

There is nothing special that you have to do to a Skyline document to import it into a library folder on Panorama. Your document should contain measurements for the precursors and transitions you want to include in your library.

Thanks,
Vagisha

 
eisuke miyauchi responded:  2019-03-29

Dear Vagisha,

Thank you for your quick reply.

The error message "Failure loading spectrum. Library may be corrupted" appeared.

Sincerely,
Eisuke

 
vsharma responded:  2019-03-29

Hi Eisuke,

Can you please share the Skyline document that you used to build the library? You can upload files at this location: https://panoramaweb.org/files.url. Please let me know for which precursors you are seeing this error message.

Could you also let me know which version of Skyline and LabKey Server you are using.

Thanks,
Vagisha

 
eisuke miyauchi responded:  2019-03-31

Dear Vagisha,

I uploaded my Skyline document, 20190308_NHS_EVISvsPBS_iRT_library.sky.

I am seeing the error message "Failure loading spectrum. Library may be corrupted" for all precursors.

I am using Skyline version 4.2.0.19009.
I do not know LabKey Server version.

Sincerely,
Eisuke

 
vsharma responded:  2019-03-31

Hi Eisuke,

I am going to need more than just the .sky file. You will have to create a .zip file containing your .sky file and other supporting files such as the .skyd file which contains extracted chromatograms. You can use the File > Share > (complete) menu in Skyline to create this .zip file.

Sorry I did not clarify earlier that I need the .zip file from Skyline.

-Vagisha

 
eisuke miyauchi responded:  2019-04-01

Dear Vagisha,

I uploaded 20190308_NHS_EVISvsPBS_iRT_library.zip.
I can not find .skyd file.

Sincerely,
Eisuke

 
vsharma responded:  2019-04-01

Hi Eisuke,

Thanks for uploading the file. I don't think it was created using Skyline's File > Share (complate) menu. Those files have a .sky.zip extension. However, looking at the .zip you uploaded it appears that you compressed the folder that contains your .sky file so it should have everything that would have been included in a .sky.zip file created with Skyline. The folder does not contain a .skyd file. Which means that there are no extracted chromatograms for the peptides in your document. It looks like Panorama built a library from you document and included peptides with no chromatograms. This is a bug and and should be fixed. Peptides that do not have chromatograms should not be included in the library.

You need to have imported results / chromatograms in your Skyline document to build a usable chromatogram library with relative ion abundances and retention times.

Have a look at the Data Independent Acquisition tutorial (https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dia) if you haven't seen it already.

Thanks,
Vagisha