Fengchao

It is because one of the glycan module was enabled accidently. Could you go to the `Glyco` tab and disable everything there? Thanks, Fengchao

Hi @oliver-bernhardt > The FDR algorithm implemented in Spectronaut was developed by John D. Storey from the Department of Biostatistics at the University of Washington, Seattle. It was published in...

Hi @oliver-bernhardt , Thanks for the correction! I guess I don't know DIA tools as good as you do. Strictly speaking, it should be CScore -> p-value -> BH FDR...

Hi Annalisa, I think it was due to the version incompatibility of the Python packages. ```shell C:\ProgramData\Anaconda3\lib\site-packages\pandas\core\computation\expressions.py:21: UserWarning: Pandas requires version '2.8.4' or newer of 'numexpr' (version '2.7.3' currently installed)....

This time, there are no IDs from your data. Please double check your settings and data ```shell *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) |...

In case you don't know, there were also no IDs from the DIA files in your first log file. ```shell 001. F120191219_PF_C1R-B5701_w632_MS_12122019_S1_DIA_Q1.mzML 1.5 s | deisotoping 0.5 s [progress: 4124/4124...

No problem. You could share one DIA file and the fasta file with me to take a look if you want. Best, Fengchao

Could you share your log file (the file with the name starts with "log_2024"). Thanks, Fengchao

Is your data from timeTOF ddaPASEF? If so, please don't convert it to mzML but use the .d Best, Fengchao

Could you share the log file of the other analysis? Also the "final result file" that you were referring to? Thanks, Fengchao