Real-time transfer of data to Skyline

Real-time transfer of data to Skyline benoit fatou  2019-10-18

Hi Skyline Support,

I was wondering if there is a possible way to perform an automatic transfer of data to Skyline just after the acquisition.
That would be very helpful especially for large number of samples.

Thank you very much for your help,

Benoit FATOU

Brendan MacLean responded:  2019-10-18

We have developed a tool called AutoQC Loader that does this:

It was designed with a focus around automatically importing and uploading to Panorama system suitability runs to an AutoQC folder, where runs are aggregated and displayed longitudinally in Systems Process Control plots for tracking mass spec system suitability and flagging when a mass spec is out of control on expected variables like Peak Area, Retention Time, etc.

However, you can turn off the upload to the Panorama AutoQC folder and configure it to just recognize new files acquired on a mass spec and load them into a Skyline document on your instrument PC, or people have even configured AutoQC Loader to monitor a shared drive that their mass spectrometers post to.

It has become very flexible over time.

At base, however, the tool itself is just monitoring for new mass spec files and then using the Skyline command-line interface (SkylineRunner or SkylineCmd) to do everything else (import data into a Skyline document, upload a Skyline document to Panorama, etc.) You can read more about the command-line interface in Help > Documentation > Command-Line. Others have written their own automated data processing pipelines using just the command-line interface.

Here is a presentation at our 2017 Skyline User Group Meeting from Amerys where they build a pipeline they say processes thousands of samples per week. User Group Meeting at ASMS/page.view?name=zhang

Good luck with your own automated Skyline data processing pipeline.


Hope this helps

benoit fatou responded:  2019-10-18

Thank you very much Brendan for your help!

I will definitely look into that and get back to you if I have any question.