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

[fcyu]

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]

@prvst Is it done?

Best,

Fengchao

[prvst]

done

[fcyu]

Thanks,

[fcyu]

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]

Felipe told me that it was fixed in Philosopher 4.8.0

Best,

Fengchao

[hollenstein]

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]

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

Best,

Fengchao

[prvst]

Please use Philosopher version 4.8.1

[hollenstein]

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

[fcyu]

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

Thanks,

Fengchao

[hollenstein]

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