Quality control with AutoQC


Panorama AutoQC

The Panorama AutoQC pipeline enables mass spec laboratories to evaluate LC MS/MS performance over time, and quickly identify potential issues. This pipeline comprises three components: Skyline, a Panorama server and AutoQC Loader, a utility program that automates the processing and uploading of QC results from the instrument computer to the Panorama server. The pipeline is initialized by specifying the following:
  • A template document with target QC peptides into which raw data files should be imported as they are acquired.
  • A local folder where QC results files are written.
  • A folder on the Panorama server where data should be uploaded.
After the Skyline documents containing QC results are uploaded to Panorama, users can examine instrument performance though a variety of charts that track several metrics such as retention time, peak area, FWHM etc. More information on the QC capabilities in Panorama can be found in the documentation links below.

Panorama QC folder documentation:

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
AutoQC Loader Documentation

AutoQC Setup Tutorial

A tutorial describing how to setup a Skyline document for use with AutoQC, and setting up the instrument method: AutoQC Setup