I and L still occasionally mixed up

[hollenstein]

Dear Fengchao,

I've already commented on the relevant and still open issue in the philosopher repository. But since I didn't get a reply yet I wasn't sure if you have also seen it. I just wanted to let you know that the wrong reporting of L and I still exists in FragPipe/Philosopher (5.1.1).

In case you don't remember what it was about. This time found a peptide in the combined_peptide.tsv table with I in its sequence that didn't exist in the reported protein, the actual sequence in the protein was the same but with an L instead of the I. We then checked the FASTA file and found the reported sequence in a decoy protein.

Best,
David

[fcyu]

Hi David,

Thanks for the reminding. I am aware of that. Philosopher is the program that I am not familiar with because it was developed by Felipe and in Go.

There are several bugs that have been bothering the users and us for a long time. We are discussing internally how to deal with that.

Best,

Fengchao

[hollenstein]

Hi Fengchao,

thanks for the update. I might have an idea how to fix this particular issue in philosopher. At least if I am guessing correctly that you use the filter command from philosopher in the FragPipe pipeline for updating your output files.

But this seems to be the case because in the ".workflow" files I found the following line pretty close to the end of the pipeline.
phi-report.filter=--sequential --picked --prot 0.01

Let me know if you want me to help.

Best,

David

[fcyu]

Hi David,

Sound great! Yes, the filter and report command are what FragPipe is using to get the peptide to protein mapping and generate the tsv tables.

A pull request to https://github.com/Nesvilab/philosopher is more than welcome.

Best,

Fengchao