JoFlossy

Many thanks Magnus

Many thanks Fengchao - For future revisions, is there any consideration of having unique, razor+unique or razor only options (like in MaxQuant) when running a workflow in FragPipe?

Thanks Vadim, Please see log file below. I used DIANN 23.1 for both the spectra library generation and the sample analysis. [report.log.txt](https://github.com/user-attachments/files/22262718/report.log.txt)

Sorry didn't get the complementary report log for the above analysis but here is another analysis with both log files with similar problem as above. [report.log.txt](https://github.com/user-attachments/files/22262886/report.log.txt) [report.log.txt](https://github.com/user-attachments/files/22262887/report.log.txt) Thanks, John

Thanks Vadim, Okay, I guess I do not need to check the protein inference when using the spectra library generated from GPF for sample file analysis? Is this correct? Cheers,...