The Panorama Chromatogram Libraries Tutorial shows you how to build a chromatogram library for peptides. The same type of functionality is now available for small molecules.

Chromatogram libraries capture representative chromatograms for a given target in a given set of instrumentation. Users can upload additional documents and then curate which version of a chromatogram is considered the most representative or canonical and should be the one stored in the library. A completed library can be downloaded as a .clib file, which is a SQLite database. That can then be imported into Skyline to inform and score future assays that use the same small molecules, peptides, or proteins.

Highlights and attributes for small molecules include ion-mobility types of data like cross-sectional profiles and mobility, collision energy, and more.

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Upload small molecule documents to a chromatogram library folder

Obtain your small molecule data Skyline file. Within Skyline, you will publish to Panorama, creating the required file. You can find a few examples in the LabKey test data on github if you want to demo these tools before you have your own data. In this walkthrough, we start with the "SmMolLibA.sky.zip" and later import the "SmMolLibB.sky.zip" file to show how to resolve conflicts.

Follow the steps in the Panorama Chromatogram Libraries Tutorial to create a place to work.
  • Create a new folder of type Panorama, selecting Chromatogram library.
  • Click the Data Pipeline tab.
  • Click Process and Import Data.
  • Drop your Skyline file(s) into the target area to upload them.
  • Select the desired file, then click Import Data.
  • In the popup, confirm that Import Skyline Results is selected, then click Import.
  • You will see import progress in the pipeline. When complete, continue.

See summary data for both protein and small molecule content

Click the Panorama Dashboard tab to see the overview of the data available in this library. Note the Molecules tab on the right.

Note that if you checked the box to "Rank peptides within proteins by peak area" you will see a different dashboard combining information about proteins and peptides with your small molecule data. If you see the tabs Peptides and Proteins, you may want to recreate the folder without that box checked to work with small molecule data.

Tour page layouts and folder tabs

As shown above, there are three web parts:

  • Chromatogram Library Download: Summary information, statistics, and a button to download this revision.
  • Mass Spec Search: Search for proteins, peptide sequences, or peptides with specific modifications.
  • Targeted MS Runs: This panel lists the Skyline files you have imported, with the counts of molecule lists, small molecules, precursors, transitions, and replicates.
Click the Molecules tab for lists of molecules and precursors.

Click the name of a molecule in the Molecules webpart, Molecule column (shown here "C4H9NO3" for a summary, listing of precursors, chromatograms, and panel for generating summary charts at the bottom of the page.

Resolve conflicts for both protein and small molecule content

If documents are imported with conflicting information, the dashboard will show a message indicating the number of conflicting molecules. You must resolve all conflicts before you can extend this library. Click Resolve Conflicts to do so.

For each conflict, you will see the Newly Imported Data on the left and the Current Library Data on the right. In each row, select the checkbox for the version you want to include in the library. Click Apply Changes when finished.

Download .clib SQLite files that contain both protein and small molecule data

To download the .clib SQLite files, click Download on the Panorama Dashboard.

You can import this .clib SQLite file into Skyline and use it to score future experiments.

Note that if you download the library while there are unresolved conflicts, you will download the latest stable version of the library (i.e. it may be missing more recently added information).

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