Hi Patrick,

Skyline does not currently have the option of exporting chromatogram images as part of a report. Do you need a physical document with all the images, or would it suffice to have an online report, with links to chromatograms, that you can share with collaborators?

If you do not need a physical document, you might be able to use our web-application, Panorama, to create reports with all the information you need, and share them with your collaborators. If you are not familiar with Panorama, you can get more information on https://panoramaweb.org. In short, Panorama is a repository for organizing your Skyline documents that also lets you view results (e.g. chromatograms) contained in Skyline documents in a web-browser. You can then provide links to the data to your collaborators. You would not need to send them Skyline documents or custom reports.

Here is an example report I created for a Skyline document uploaded to our Panorama server. It contains, amongst other pieces of information, the precursor peak areas measured in each replicate. If you click on the area ("Total Area" column) you will see the chromatogram image. Clicking on the "Details" link in a row will also bring up the chromatogram image.
https://daily.panoramaweb.org/labkey/query/MacCoss/vsharma/CPTAC/ResponseCurve/executeQuery.view?schemaName=targetedms&query.queryName=precursorchrominfo&query.viewName=WithChromLinks

You can view results contained in the source Skyline document, uploaded to Panorama, here:
https://daily.panoramaweb.org/labkey/targetedms/MacCoss/vsharma/CPTAC/ResponseCurve/showPrecursorList.view?id=720. Click on the protein, peptides or precursors in the table on this page to view other details and graphs.

If you think an online report like this will meet your needs, then feel free to request a project on our public server PanoramaWeb (
https://panoramaweb.org/labkey/wiki/home/support/page.view?name=hosted-project-signup-form). Uploading a document from Skyline to Panorama is easy, and I can help you set up a custom report ,like the one linked above, that you can share with your collaborators.

Panorama also allows programmatic access, in various programming languages, to the uploaded data. So, you could, for example, write your own web-application that extracts data in an automated way from Panorama for display in custom HTML pages. An example of this kind of usage is the CPTAC Assay Portal that uses Panorama to store Skyline files. On this page (https://assays.cancer.gov/CPTAC-287) you will see Panorama listed as the "Data Source" for a lot of the sections, including chromatograms.

If you think putting your Skyline documents in Panorama, and providing online reports will work for you, then please go ahead and request a project on PanoramaWeb. The tutorials on the homepage should help you get started.

Thanks!
-Vagisha

Hi Vagisha,
Thanks so much for the detailed response. Panaroma does sound like it might work in certain circumstances for us. Unfortuately, in this particular case there are some confidentiality issues which would preclude its use I think. We are also looking at alternative ways to report data which would obviate the need for chromatogram images - for example reporting start/end times for integrated peaks - and of course Skyline can do this very easily and in an automated way. I will let you know if I end up using Panorama in the future.
Thanks again for your help.
Patrick

Hi Patrick,

Good to hear that you may find use for Panorama in certain cases!

Just a note about secure data sharing in Panorama, since confidentiality is important in your workflow. Panorama is built into LabKey Server (https://labkey.org) that implements a comprehensive access control model that lets you keep your data completely private, share it with a select group of collaborators, or make it public. In fact, LabKey Server is being used in organizations to manage clinical data. Every user gets an account on Panorama, and you can configure which users have access permissions on a folder so that only the right people can see your data.

On PanoramaWeb, the server we host at the University of Washington, Brendan and I as site administrators have access to all the projects and folders. If that is an issue, you could install Panorama on your own server as some other labs and pharma companies have done.

I hope that you will eventually give Panorama a try!

Best regards,
Vagisha

Hi Patrick,
If you are interested in running your own Panorama instance, you may want to look at the Panorama Partners Program:

https://panoramaweb.org/labkey/wiki/home/page.view?name=panoramaPartnersProgram

If confidentiality is enough of a priority that you cannot allow us as administrators of PanoramaWeb access to your data, then managing your own server may be the way to go. As Vagisha notes, some very large pharma companies are already doing this.

Thanks for using Skyline and providing feedback on your needs.

--Brendan