Table of Contents

 guest
2024-04-24
Webinar #11 Panorama Public and Panorama AutoQC
Questions and Answers
Registration

Webinar #11 Panorama Public and Panorama AutoQC


Interest in Panorama is clearly growing as Webinar #11: Panorama AutoQC and Panorama Public drew 100 attendees -- the most we have ever had for a Panorama webinar.  We certainly encourage Skyline users to explore Panorama and take advantage of its collaborative capabilities. 

In this webinar Vagisha Sharma, Panorama lead developer, gave an introduction to Panorama, PanoramaWeb and presented a tutorial on publishing supplementary data for manuscripts to Panorama Public. This was followed by an overview and tutorial from Josh Eckels, Panorama lead at LabKey Software, on Panorama AutoQC and the new quality control features in Panorama.

We've uploaded the presentation files and supporting data set as well as the recording of Webinar 11.  Additionally, we've provided written answers to the questions posed in our Q&A period at the end of the Webinar. 

Vagisha Sharma
(Lead Developer
- Panorama)

     Presentation Slides

Tutorial Files
(58 M)
    

Josh Eckels
(Lead Panorama
Developer - LabKey)

       

Presentation Slides		    
Publish to Panorama Public (24 pages)
[tutorial]

Review Webinar 10

Working with Modifications in Skyline
See video, presentation slides, and other files presented at the webinar.


Review Webinar 12

Isotope Labeled Standards in Skyline
See video, presentation slides, and other files presented at the webinar.


Panorama Resources

For more information on Panorama visit the following links:



Questions and Answers


Dear Skyline Users,

Our eleventh Skyline Tutorial Webinar took on topic of Panorama Public and Panorama AutoQC and had questions during the Q&A portion - here are the answers:

Q: Is it possible to use regex to watch QC runs in a folder?

Ans: Not in the current version. But it will be available in the next release.

Q: Can AutoQC be run for metabolite QC - small molecules?

Ans: Since AutoQC, under the hood, relies on Skyline to import raw files into the document it will be able to import small molecule data. However, Panorama does not yet fully support small molecule data contained in Skyline documents, so you will not be able to view those results in Panorama. But, once small molecule support has been completed in Panorama it will be possible to use the Panorama QC workflow for small molecules as well.

Q:Does AutoQC supports monitoring/importing multi-sample wiff files from Sciex instruments?

Ans:Since AutoQC delegates to Skyline to import raw files, it should support importing multi-sample wiff files. This has not yet been tested, though.

Q: Is the panorama DB scheme available?

Ans:Panorama is part of LabKey Server, which is an open-source biomedical data management platform. You can get the source code here: https://www.labkey.org/wiki/home/Documentation/page.view?name=sourceCode and look at the schema SQL. A graphical database design can be made available upon request. If you have your own Panorama server or are an administrator of a project on PanoramaWeb, you can explore the schema in a web-browser through the schema browser interface - accessible via the Admin > Developer Links > Schema Browser menu. Select "targetedms" from the list of available schemas to look at the tables in the Panorama database.

Q:Will AutoQC become part of chorus?

Ans: There are no plans currently to build Chorus support in AutoQC. We expect that AutoQC will mostly be used on instrument computers before the raw files are uploaded to Chorus.



Registration


Dear Skyline Users,

The Skyline Tutorial Webinar Series rolled on last month with over 230 users registering to attend Working with Modifications in Skyline.  For anyone who would like to review what was presented, a recording of the webinar, presentation slides and data files have been posted to the site, with added content that did not fit into the webinar session.

We are very excited to announce our next webinar in the series:

Webinar #11: Panorama Public and Panorama AutoQC

[registration closed]

When:  Tuesday, Oct. 20, 8am(Pacific Time)
- plan for 1 hour presentation + 1/2 hour Q&A
  • Publish Skyline documents to Panorama Public as supplementary data for manuscripts
  • Track mass spectrometer performance over time with new Panorama quality control (QC) features
  • Identify and visualize instrument performance issues

In this webinar Vagisha Sharma, Panorama lead developer, will present a brief tutorial on publishing supplementary data for manuscripts to Panorama Public, followed by an introduction and tutorial from Josh Eckels, Panorama lead at LabKey Software, on Panorama AutoQC and the new quality control features in Panorama.

Join us, learn and help us to better meet your targeted proteomics research needs.

--Skyline Team

Presenters

Vagisha Sharma
(Lead Developer - Panorama)

Josh Eckels
(Lead Panorama Developer - LabKey)

Review Webinar 10

Working with Modifications in Skyline
See video, presentation slides, and other files presented at the webinar.


Week-Long Course at
ETH, Zurich

Register by November 15th for this week-long targeted proteomics course and learn about SRM, PRM and DIA and how to set up acquisition and analyze resulting data with Skyline.