This topic describes how Panorama folder administrators can customize metrics, enable or disable them, and define new metrics of their own.
Enable and Disable Metrics
An administrator can control which QC metrics
are available for quality control plots on a folder-by-folder basis. Disabling metrics may be practical for a variety of reasons, including if they produce many outliers without being diagnostic of real problems. For each metric, you can select:
- Enabled: Always show the metric in this folder.
- Auto: (Default) Show the metric when relevant data is present. For custom metrics, you provide your own query to control when to enable the metric.
- Disabled: Never show the metric in this folder.
The configuration menu is available on the QC Plots
- In the upper right of the QC Plots web part, open the (triangle) pulldown menu.
- Select Configure QC Metrics.
- Use the pulldowns to select Enabled/Auto/Disabled as desired.
- The Type column indicates whether a metric is scoped to a single molecule (precursor) or to a run as a whole.
Disabled metrics are hidden from the main QC plot page, QC summary web part, and pareto plot.
Define Custom Metrics
An administrator can create their own custom metric by first defining a query, typically in the targetedms
schema, with the following columns:
|MetricValue||NUMERIC||The value to be plotted|| |
|SampleFileId||INT||Value of the related Id in targetedms.SampleFile|| |
|PrecursorChromInfoId||INT||Value of the related Id in targetedms.PrecursorChromInfo. May be NULL, in which case there will be click handler for the point.|
|SeriesLabel||VARCHAR||The peptide sequence, custom ion name, etc|| |
|DataType||VARCHAR||How to label the series in the overall list (typically either “Peptide”, “Fragment”, etc)|| |
|PrecursorId||INT||Value of the related Id in the targetedms.Precursor or targetedms.MoleculePrecursor table.|| |
|mz||NUMERIC||mass to charge ratio|| |
The fields PrecursorChromInfold must be included in a query for run-scoped metrics but should return NULL.
The fields SeriesLabel, DataType, PrecursorId, and mz are optional. They will be automatically calculated if they are missing, but you can use them to customize the display.
Once your query is defined, reopen the Configure QC Metrics
page from the web part menu and click Add New Custom Metric
In the popup:
- Enter a Name
- Select the Schema and Query for Series 1.
- Give provide an Axis Label.
- If you would like a second Y-axis tracking a different schema and query, specify those in Series 2.
- Select the Metric Type:
- Precursor: This metric varies for each individual molecule.
- Run: This metric will have a single value per run, such as a maximum value of a pressure trace during a run.
- If you would like to be able to use the Auto option to enable your metric based on the presence of data, supply the following:
- Enabled Schema: Schema in which to find the "Enabled" query.
- Enabled Query: Query to determine when to enable the metric.
- Click Save.
The new metric will appear on the metric configuration list as a clickable link. Click to see the definition. You can edit and save or delete if if necessary. As with predefined metrics, you can enable or disable your custom metric using the same menu in the Status
When enabled, your new metric will also be available in the QC Plots pulldown menu for plotting. If you created a molecule-scoped metric, each series will be titled with the value of the "SeriesLabel" column from the backing query.
Example: Peptide ID Count
A real world example of adding a custom metric is to track the peptide ID counts in runs imported into the Skyline document in the folder. You can find an example of the steps used to create this metric, as well as an example data folder on PanoramaWeb:
Define Pressure Trace Metrics
Pressure traces, total ion current, and other chromatograms help monitor the performance of the mass spectrometry equipment. For example, a higher than normal value in system back pressure during the acquisition probably indicates the system is overpressure or starting to leak. Skyline will automatically extract pressure traces and other sample-scoped chromatograms from the raw files. When they're present, you can can monitor this at specific time points by configuring a metric to pull the pressure trace within the chromatogram at specific points in time, or track the time that a specified pressure value is reached.
There are two options for these metrics:
- Track trace value at user defined time (in minutes)
- Track time of user defined trace value
Open the Configure QC Metrics
page from the web part menu and click Add New Trace Metric
. In the popup, specify:
Use trace value when time is greater than or equal to
- Metric Name: You can use the name to give users details about the metric.
- Use Trace: Select the trace to use. If this box reads "No trace can be found", you will not be able to create a trace metric.
- Y Axis Label: You can use this label to give information about units (PSI, etc) as needed.
- Select the type of trace with the radio buttons:
: Enter the number of minutes in the box.Use time when the trace first reaches a value greater than or equal to
: Enter the desired value in the box.
- Click Save to add the new metric.
- Use the Status dropdown to set it to Enabled/Auto/Disabled.
- Click Save to return to the QC Plots dashboard.
You can now view your new metric(s) in QC plots, outlier calculations, and automated emails.