This documentation is for an older version of AutoQC Loader. Please refer to the latest documentation here.

AutoQC Loader

AutoQC Loader automates the process of importing results files into a Skyline document and uploading the document to a folder on a Panorama server. It uses SkylineRunner to launch Skyline without showing the Skyline window. Command-line arguments are passed to this invisible instance of Skyline to import results files to a Skyline document and upload the document to the Panorama server specified in the settings.
Install AutoQC Loader for Skyline 3.5 or later, or Skyline-daily ( or later)

When AutoQC Loader starts up for the very first time, it will check for existing Skyline or Skyline-daily installations in the following order:

  • C:\Program Files\Skyline
  • C:\Program Files\Skyline-daily
  • Web installation (ClickOnce) of Skyline
  • Web installation (ClickOnce) of Skyline-daily
If an existing installation is found it is used for all future invocations of the program. The first two locations in the list above are the default locations for the Administrator Install of Skyline and Skyline-daily. Most users do not need an administrator install of Skyline, and install Skyline via the web-installer instead. The installation of Skyline or Skyline-daily that should be used by AutoQC Loader can also be configured in the Settings tab of the program window. Click the Apply button after making changes to the Skyline settings.

To start monitoring a local folder for QC results, create a new configuration in AutoQC Loader by clicking on the Create a new configuration button in the Configurations tab. Each configuration is a combination of settings that include the location of the template Skyline document, the local folder where QC results will be written, and the folder on a Panorama server where the results will be uploaded. Multiple configurations can be enabled allowing users to monitor more than one QC data folder at the same time. Configurations are saved so that instrument operators can enable a previously created configuration if they are acquiring data for an ongoing project with intermittent breaks in data acquisition.

Configuration Settings

In the AutoQC Configuration form enter the appropriate settings in the Settings tab.

Configuration name: This can be the name of the project or study for which data is being acquired.
Skyline file path: This is the path to the template Skyline document into which QC results files will be imported. Please note that the Integrate all setting (Settings > Integrate all) must be checked for Skyline documents that contain QC results. This setting forces Skyline to calculate areas for all fragment ions between the integration boundaries and gives better quantitative results.
Folder to watch: This is the folder that AutoQC Loader will monitor for new QC results files. Any new results files added to the folder will automatically be imported into the given template Skyline document. When a configuration is enabled or started, all existing results files in this folder that are newer than the last imported result in the Skyline document will get imported. If the document does not have any imported results, AutoQC Loader will import all the results files in the folder.
File filter: One of the options in this combo-box can be used to apply a filter on the QC files that will be imported to the Skyline document. Only files with names that match the selected option will be imported. The default option (All) will import all results files added to the QC folder without applying any filters.

Results time window: The results time window determines how long imported results will be retained in the Skyline document. This is a rolling window and only results acquired within the last ā€˜nā€™ days, where ā€˜nā€™ is the width of this window in days, will be retained in the document. When a new run is imported into the document any results that no longer fall within this time window, ending on that day, will be removed from the document. The default (and minimum) width of the window is 31 days. Please note that AutoQC Loader does NOT delete any results files on the computer. Only results imported into the document that are older than the current time window are removed from the document. This is done to keep the active Skyline document from getting too large.
Instrument type: The instrument type setting tells AutoQC Loader the type of files (e.g. *.raw for Thermo instruments, *.wiff for SCIEX instruments etc.) to look for in the folder that it is monitoring.
Expected acquisition duration: The expected acquisition duration determines how long AutoQC Loader will wait before attempting to import a new results file. Most instruments write directly to the output results file during acquisition, and an error occurs if an attempt is made to read the file before acquisition is complete. When AutoQC Loader detects a new results file in the QC folder, it will wait for the duration specified in this setting before attempting to import the file. The default value for this setting is 75 minutes (10 min. trapping time + 60 min. gradient + 5 min. extra).

Panorama Settings For a Configuration

To upload the Skyline document containing QC results to a Panorama server, check the Publish to Panorama checkbox in the Panorama Settings tab. Enter the URL of the Panorama server, your email and password on the server along with the path to the folder on the server where the document should be uploaded. AutoQC Loader will upload the document to the Panorama server each time a new results file is imported into the document.

The Panorama server manages redundant results files included in multiple, successive Skyline documents uploaded to a QC folder by keeping only the most recent copy of the results.

Starting or Stopping a Configuration

In the main AutoQC Loader window, under the Configurations check the box next to the configuration name to start the configuration. AutoQC Loader will start the monitoring the local folder specified in the configuration for new results files. Uncheck the box to stop the configuration.

AutoQC Loader Settings

If you want AutoQC Loader to keep running continuously on your computer, and start-up automatically after the computer restarts check the Keep AutoQC Loader running checkbox in the Settings tab. This will place a shortcut to AutoQCStarter.exe in the Windows Startup folder. AutoQCStarter.exe checks every few minutes to see if AutoQC Loader is running, and starts it if it is not running. Any configurations that were running when AutoQC Loader was last running are also started.

Check the Minimize program to Windows System Tray to minimize the AutoQC Loader window to the Windows System Tray instead of the Task Bar.


AutoQC Loader writes to a log file (AutoQC.log) in the directory that contains the template Skyline document. Please provide this log file to the developers if you run into any issues with AutoQC Loader.

Data Archival

AutoQC Loader creates a monthly archive (* of the Skyline document. Archive creation is triggered when the first run is imported into the document in a given month. For example, when the first run is imported into the Skyline document,, in the month of August 2015, an archive file,, is created in the same directory as