Fengchao

Thanks. Then, I will let Felipe @prvst take a look. Best, Fengchao

Hi Ben, To be honest, I am not sure. We are working on other modules in FragPipe to add some new functionalities. If I have time, I will add a...

Hi Ben, Thanks for your kind words! We will keep you posted. Best, Fengchao

You can find it from combined_peptide.tsv, combined_modified_peptide.tsv, or combined_ion.tsv. Best, Fengchao

Hi David, Thanks for your feedback. I think it is also related to the issue https://github.com/Nesvilab/philosopher/issues/430 . We will see what we can do. Best, Fengchao

Hi Patrick, It is a known issue. Can you try the msbooster-1.0.zip from https://github.com/Nesvilab/FragPipe/issues/533#issuecomment-973283953 ? You need to replace the one in the `fragpipe/tools` folder. Best, Fengchao

Hi Patrick, It looks like something was wrong with Philosopher. Can you try the latest Philosopher (4.1.1)? If the latest version still gives the error, can you try using PeptideProphet...

MSBooster needs Percolator. MSBooster cannot work with PeptideProphet. Percolator or PeptideProphet can work alone without MSBooster. It is not about Philosopher, actually. But sine your error is from Philosopher filter...

Hi Patrick, Can you confirm that PeptideProphet with the Philosopher 4.1.1 can work, but MSBooster+Percolator cannot? What I cannot understand is why PeptideProphet or MSBooster+Percolator makes any difference for Philosopher...

Hi Patrick, Can you send me the log from the one with PeptideProphet? Thanks, Fengchao