Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adjust I and L in the psm.tsv, peptide.tsv, and ion.tsv after razor assignment #430

Open
fcyu opened this issue Oct 19, 2021 · 11 comments
Open
Assignees

Comments

@fcyu
Copy link
Member

fcyu commented Oct 19, 2021

The razor assignment might make an alternative protein as the razor protein. Since we don't distinguish I and L in the protein mapping, some peptides might not exist in their razor protein. Need to change some I to L, or L to I after razor assignment, so that the peptides in the tsv files are correct.

Best,

Fengchao

@fcyu
Copy link
Member Author

fcyu commented Dec 12, 2022

@prvst Is it done?

Best,

Fengchao

@prvst
Copy link
Collaborator

prvst commented Dec 12, 2022

done

@fcyu
Copy link
Member Author

fcyu commented Dec 12, 2022

Thanks,

@fcyu fcyu closed this as completed Dec 12, 2022
@fcyu
Copy link
Member Author

fcyu commented Dec 14, 2022

I guess this issue was actually not fixed according to the user's latest feedback: Nesvilab/FragPipe#771 (comment)

Felipe @prvst , can you take a look?

Thanks,

Fengchao

@fcyu fcyu reopened this Dec 14, 2022
@fcyu
Copy link
Member Author

fcyu commented Jan 13, 2023

Felipe told me that it was fixed in Philosopher 4.8.0

Best,

Fengchao

@fcyu fcyu closed this as completed Jan 13, 2023
@hollenstein
Copy link

Dear FragPipe team,

I've reanalyzed my test samples with the new version of FragPipe and Philosopher, and for some peptides I still get wrongly reported "L" when there should be an "I". For example the peptide "ELIEELIAK" is reported as "ELIEELLAK". So it seems that not all "L" are converted to "I". Also the reported peptide sequence "ELIEELLAK" does not occur in the fasta file.

In contrast to the previous issue 771, the reported peptide start and end positions seem to be correct now.

Version info:
FragPipe version 19.1
MSFragger version 3.7
IonQuant version 1.8.10
Philosopher version 4.8.0

Would be great if you could look into this once more.

Best,
David

@fcyu
Copy link
Member Author

fcyu commented Jan 30, 2023

Seems to be the same issue as #409 Need Felipe to fix.

Best,

Fengchao

@fcyu fcyu reopened this Jan 30, 2023
@prvst
Copy link
Collaborator

prvst commented Jan 30, 2023

Please use Philosopher version 4.8.1

@hollenstein
Copy link

I've run it now with Philosopher version 4.8.1, and the issue is still present.

@fcyu fcyu transferred this issue from Nesvilab/FragPipe Apr 5, 2023
@fcyu
Copy link
Member Author

fcyu commented Apr 5, 2023

@prvst Has this bug been fixed after version 4.8.1? If yes, could you share the fixed version with @hollenstein ?

Thanks,

Fengchao

@hollenstein
Copy link

Hi, I've tested it with the FP 19.2-RC and philosopher v5.0.0-RC18 and the I / L issue is still present.

Best,
David

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants