overlap DIA

overlap DIA Tobi  2019-08-28

Dear Skyline team,

could you please give out some information regarding overlap DIA? You recommended to use MSConvert to demultiplex DIA data with overlap. However, MSConvert usually results in an error message:

Failed - System.Exception: SpectrumToIndices() Number of demultiplexing windows changed. Minimum window size or window boundary tolerance may be set too low.
at pwiz.CLI.msdata.MSDataFile.write(MSData msd, String filename, WriteConfig config, IterationListenerRegistry iterationListenerRegistry)
at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map2 usedOutputFilenames) at MSConvertGUI.MainLogic.Go(Config config, Map2 usedOutputFilenames)

Is this because of acquiring the DIA with overlap and with margins? I also noticed when having overlap DIA with margins that those margin sizes can slightly differ in size after window placement optimization, could that be another potential issue?

I know that potential debugging MSConvert is not your job, but can you please tell me which variants of overlap SWATH you tested and what sould be working (margins, optimized placement...).

If you are interested please find the uploaded raw file for you to read the DIA scheme.

Best regards,

Tobi responded:  2019-08-28

*Add bug report,

when having acquired thermo raw files with overlap, skyline occasionally fails to fully import/read the acquisition scheme. It is most likely not a big deal and correctable by hand, if you know that you have to check for this.

Mike MacCoss responded:  2019-08-28

Hi Tobi,
Great to hear you are using the overlap DIA. We never intended someone to collect overlap DIA with margins. I'm not entirely sure how that would be used. That said, we should probably add better error messages to MSConvert when it encounters these types of files and also we should make sure that the method generating capabilities of Skyline warns a user too. That said, lots of people use Skyline to generate methods in ways we never imagined so we wouldn't want to prevent this.

Here is some documentation that has been developed for performing these sorts of overlapping experiments.

We will try and improve the error messages and also we will do better to make sure that all of the documentation is available and easier to find on the http://skyline.ms site.

Thanks for you support board post and let us know if you have any other questions,

Tobi responded:  2019-08-28

Dear Mike,

thank you very much for all the collected material, it really makes my day. I also agree that overlap DIA with margins and optimized placement sounds exotic, but it might have an advantage not listed in the paper. Looking forward to the continuous development. It would always be nice to have new tricks compatible with old ones.

Highest regards,