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Creating Library from Stellar GPF-DIA Fragpipe analysis Fails

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Creating Library from Stellar GPF-DIA Fragpipe analysis Fails maithreyan kuppusamy  2025-08-28 04:57
 

Hi,

I analyzed Stellar GPF-DIA runs in fragpipe. When I tried to create the library from the Fragpipe search results it failed. I have attached the error.

One more thing I noticed - Fragpie search of GPF-DIA with and without adaptiveRT results in very different ID numbers - I do not know why.

Thanks,
Maithy
 
 
Nick Shulman responded:  2025-08-28 16:13
I see that you are getting the error:
Mismatch between spectrum id format of the spectrum file (scan=13) and the spectrum id (controllerType=0 controllerNumber=1 scan=4249)

Another user was getting a similar error.
They were able to work around this problem by copying their .raw file to the name:
250827_MKU02_AC_MCF7_Test_200ng_GPF_900_1000_uncalibrated.raw

I am not sure, but they might also have needed to delete the file "250827_MKU02_AC_MCF7_Test_200ng_GPF_900_1000_uncalibrated.mzML".

You can see the other support request here:
https://skyline.ms/announcements/home/support/thread.view?rowId=71210

Let us know whether putting the raw file "250827_MKU02_AC_MCF7_Test_200ng_GPF_900_1000.raw" in there fixes the problem, or whether you need to rename it to "250827_MKU02_AC_MCF7_Test_200ng_GPF_900_1000_uncalibrated.raw".
-- Nick