Batch import separate negative and positive polarity files into same replicate

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Batch import separate negative and positive polarity files into same replicate matthias schittmayer  2022-03-01
 

Dear Skyline team,

I am looking for a way to automatically import two separate measurements of the same lipidomics sample (positive and negative polarity acquired on a Bruker timsTOF) into the same replicate in Skyline. I can do so by e.g. importing all positive results and then adding one by one negative polarity files using "Add files to an existing replicate" or using the "Add one new replicate" and selecting the two matching positive and negative data files, but I have to do this manually for each sample which would get quite laborious with larger sample sets. Is there a way of organizing the data or script importing it so positive and negative files are automatically added to the same replicate?

Best,
Matthias

 
 
Nick Shulman responded:  2022-03-01
When you do "File > Import > Results", one of the options is "Add multi-injection replicates in directories".

You should put each of your pairs of positive/negative runs into a separate folder. Then, point Skyline at the parent folder of all of those folders.
-- Nick
 
Brian Pratt responded:  2022-03-01
If that's not convenient, this should also be scriptable using the SkylineRunner program.

SkylineRunner is self-documenting, just run it without any arguments and it emits an extensive help message.

- Brian