Premium Panorama features add additional functionality to help users focus on the metrics that are most meaningful to them. 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 New Metrics
An administrator can create their own 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 the Add New 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 checkboxes.
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.