Exporting data from AutoQC janelle hancock  2023-02-13 16:10:24

Hello Everyone,
I would like to export a spreadsheet of performance metrics. I can't seem to find a way to export run statistics from AutoQC. Is this possible? Ultimately I need to set reasonable pass/fail criteria, and modelling based on our existing data seems like the best way to do this.

I have been using the associated skyline file to generate document grids, and am able to model RT variation from this. But the TIC and transition/ precursor area plots in Auto QC doesn't seem to have equivalent statistics in Skyline?

Can anyone let me know how to download these from Panorama, or how to get them in the document grid in Skyline?


Brendan MacLean responded:  2023-02-14 10:47:40

Hi Janelle,
To answer the Skyline side of your question, I believe the TIC value can be found at:

Replicates > Files > Total Ion Current Area

The "Transtion / Precursor Area" is a compound value that can be calculated from a Skyline reports as:

Precursor Results > Total Area Fragment / Total Area MS1

While we have occasionally considered implementing a way to create new columns that are simple calculations applied to existing columns, so far, we have really only done with with aggregate functions and pivots, not combining separate columns.

Hope this is helpful. I know Vagisha is exploring the Panorama side of your question.


Vagisha Sharma responded:  2023-02-14 15:54:26

Hi Janelle,

We don't yet have a link or button that lets you export the metrics. But you can do that yourself with a little bit of work. If you are the administrator of a QC folder on PanoramaWeb, then you can view the underlying database schema and queries used to generate the plots. Here is one way to view a grid with specific metric values:

  1. From the admin menu (gear icon, top right corner) select Page Admin Mode.
  2. Click one of the tabs (e.g. "Panorama Dashboard", "Runs") in your QC folder. You will be adding a grid to this tab. For a cleaner view, I suggest adding a new tab, as described at the end.
  3. From the <Select Web Part> menu at the bottom left of the page choose "Query". Click the Add button.
  4. In the Customize Query form select "targetedms" from the Schema drop-down.
  5. Select the "Show the contents of a specific query and view." option next to Query and View.
  6. In the Query drop-down you will see the names of all the available queries. Look for query names that begin with "QCMetric_" and "QCRunMetric_". There should be one query for each metric. For example, the query for Transition / Precursor Area is called QCMetric_transitionPrecursorRatio, and the one for TIC is called QCRunMetric_ticArea.
  7. Click Submit.

The results from the query will get added as a grid to the selected tab. You will see a column with the names of the sample files, and another column with the value of the metric in each file. Refreshing the page will always show the latest results from the database. You can download the data by clicking the "Export" button (third icon from the left) in the toolbar above the column headers. You will have the option to export the data as Excel / TSV / CSV.

You can add multiple queries to the page by repeating these steps. Each query will get added as a new grid. If you just want to have a single grid with the ability to switch between queries, you can do that by selecting the "Yes" option for Allow user to choose query when you are customizing the query in steps 4 through 6. The resulting grid will have a Query button in the menu bar to let you choose which query results to view.

To add a new tab to the folder:

  1. Make sure you are in the "Page Admin Mode".
  2. Click the "+" icon next to the last tab.
  3. Give a name to the tab and click "OK".

Another way of viewing the same data is by going through the Query Schema Browser (described below). But I prefer adding the query to one of tabs in the folder if I am going to view it frequently.

To view the query from the Query Schema Browser:

  1. Click the admin menu (gear icon in the top right corner) and select Go to Module > Query
  2. In the "Query Schema Browser" expand the "targetedms" node in the left panel.
  3. Query names are listed in the left panel under the "targetedms" node. Click one of the queries to select it. In the right panel you will see the name of the selected query and the columns in the query.
  4. Click the View Data link in the top right corner of the right panel to view the results.

I hope this helps! Please let me know if you have any questions. The steps above will only work if you an administrator in the folder. I am happy to help over a Zoom call, if required.


janelle hancock responded:  2023-02-14 17:48:35

Thankyou Brendan and Vagisha, for your detailed answers. I have Skyline doc grids set up for this now, but going straight from Panorama will be more in line with how we ultimately want to manage our system suitability testing. I'll have a go at following the Panorama instructions today, and let you know if we need more help.