Premium Feature — Available with a Panorama Premium Edition of LabKey Server or when using PanoramaWeb. Learn more or contact LabKey.

The Panorama QC folder is designed to help labs perform QC of their instruments and reagents over time.

Panorama Dashboard

The Panorama QC Overview dashboard offers a consolidated way to view good summaries of system suitability and quality control information. Information from the current folder and immediate subfolders are displayed in a tiled format. For example, subfolders might each represent a specific machine, so you can see instrument conditions at a glance.

The Panorama Dashboard tab shows the QC Summary and QC Plots web parts.

QC Summary

On the Panorama Dashboard, the QC Summary section shows a tile for the current folder and each immediate subfolder the user can access. Typically a folder (tile) would represent an individual instrument, and the dashboard gives an operator an easy way to immediately scan all the machines for status. Each tile includes a visual indicator of AutoQC status.

The count of the number of Skyline documents (targetedms.runs) and sample files (targetedms.samplefile) are scoped to the tile's container. Each tile lists the number of files that have been uploaded, the number of precursors that are being tracked, and summary details for the last 3 sample files uploaded, including their acquired date and any outliers that were identified. Each tile includes a link to View all ## samples and utilization calendar .

The web part menu provides links to:


The TargetedMS module uses the AutoQC tool to ping the server to check if a given container exists, evaluate LC MS/MS performance over time, and quickly identify potential issues.

Learn more about AutoQC on PanoramaWeb here: Quality control with AutoQC

AutoQC Downloads

If you are running Skyline on your instrument computer install AutoQC Loader from this location:

If you are running Skyline-daily, install AutoQC Loader-daily from this location: To learn more about AutoQC, review this documentation: Using AutoQC Results

The QC Summary web part displays a color indicator:

  • Gray ring - AutoQC has never pinged.
  • Red circle - AutoQC has pinged, but not recently.
  • Green check - AutoQC has pinged recently. The default timeout for "recently" is 15 minutes.
Hover over the icon for the time of the last ping.

AutoQC also facilitates the ongoing collection of data in a Panorama QC folder. Each sample is uploaded incrementally and automatically by AutoQC. AutoQC adds new samples to an existing Skyline document, rotating out and archiving old data to prevent the active file from getting too large. As new files are received, they are automatically coalesced to prevent storing redundant copies across multiple files. Whenever a PanoramaQC file receives a new file to import, by the end of that import we have the most recent copy of the data for each sample contained in the file, even if it had been previously imported.

Outlier Indicators

When outliers are present, the type of outlier determines which indicator is used to represent the severity of the issue. If a file contains more than one type of error, the 'highest' indicator is shown.

  • Error: A Levey-Jennings outlier
  • Warning: A Moving Range outlier
  • Info: A CUSUM outlier
  • : No outliers
  • : File excluded

Sample File Details

The display tile shows the acquired date/time for the latest 3 sample files along with indicators of which QC metrics have outliers in the Levey-Jennings report, if any. Hover over the icon for a sample file in the QC Summary web part to see popover details about that file.

The hover details for a sample file with outliers show the per-metric "out of guide set range" information with links to view the Levey-Jennings plot for that container and metric.

Delete a Sample File

To delete an unwanted sample file, such as one you imported accidentally, click the link showing the number of sample files in the folder to open a grid, select the relevant row, and click Delete. The data from that sample file will be removed from the plot.

QC Plots

The QC Plots web part shows one graph per precursor for a selected metric and date range. Choose from a variety of different available Plot Types, picking a Date Range, Scale, and other options. For more details, see Panorama QC Plots.

Example Plots with guide sets and annotations:

Configure Included and Excluded Precursors

The precursors, whether peptides or small molecules, can be divided into two groups for mass spectrometry analysis:

  • Included group: The precursors driving the plots and AutoQC assessments.
  • Excluded group: Those you want to exclude from AutoQC assessments and from plots (unless you check the box to "Show Excluded Precursors").
From the QC Summary or QC Plost web part, choose Configure Included and Excluded Precursors from the menu.

You'll see a grid of the precursors available in the files, with some summary data. By default, all are marked as "Included". Select one or more precursors using the checkboxes, then move them between the two groups by clicking either Mark as Included or Mark as Excluded.

In the QC Plots web part, the Show Excluded Precursors checkbox controls whether to show those marked as being in the "Excluded group".

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