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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Spectral library #556

Open ttessie2 opened 2 years ago

ttessie2 commented 2 years ago

I've been having trouble running my DDA and DIA files in MSFragger using the MSFragger-DIA workflow. The issue seems to be with the mzML DIA files. I've been discussing this on the Fragpipe and openms github, but there really hasn't been a resolution. It's my understanding that MSFragger-DIA is just making a spectral library from the DDA and DIA files and then quantifying that with DIA-NN, but I could be wrong. Since I'm not able to run this workflow in MSFragger is there a work around to make a similar combined library that I can quantify in DIA-NN directly? I'll note that I have no issues with running my DIA files directly in DIA-NN.

vdemichev commented 2 years ago

Yes, you can run lib-free searches in DIA-NN directly