This topic is under construction for the 22.7 (July 2022) release of LabKey Server. For current documentation of this feature, click here.
The Panorama QC folder is designed to help labs perform QC of their instruments and reagents over time. Runs are uploaded using the data pipeline or directly from Skyline. Panorama QC folders support reviewing and plotting both proteomics (peptide/protein) and small molecule data.
Panorama QC Topics
This page contains details about the dashboard, summary, AutoQC, and plots. More topics related to using the Panorama QC Folder type are:
The Panorama QC Overview dashboard offers a consolidated way to view good summaries of 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
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 would represent an individual instrument, and the dashboard gives an operator an easy way to immediately scan all the machines for status. The count of the number of Skyline documents (targetedms.runs) and sample files (targetedms.samplefile) are scoped to the current 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 whether any outliers were identified. Both proteomics and small molecule data outliers are tracked, and a combined count of outliers is presented. Tiles also include a visual indicator of AutoQC
menu for the web part 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.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.
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.
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, sizes, and other options. For more details, see Panorama QC Plots
Example Plots with guide sets
Include or Exclude Precursors (Peptides/Small Molecules)
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
web part, choose Include or Exclude Precursors
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".