Magnus Arntzen

Hi, this was analyzed using Fragpipe v15.0 on Windows with Philosopher 3.4.13. Please see the attached file. [210831 FP mismatch.zip](https://github.com/Nesvilab/FragPipe/files/7088759/210831.FP.mismatch.zip) An example protein present in reprint.int and not in combined_protein.tsv...

Allright, I'll upgrade for next time around but I won't have time to rerun the data with the new version now - it takes 4.5 days of analysis at a...

Is it possible to run only parts of the pipeline, like in MaxQuant partial run? Please let me know how to do that.

Hi again, I reran the data as suggested with filtering, reporting and quant using Fragpipe v16 with Philosopher 4. The output is better, I think, with clear differences to previous...

Thank you for your help - I will filter as instructed for now! Best regards!!