Feature request for HLA analysis

[fazeliniah]

Dear MSFragger developing team,
Thank you again for this amazing software. We are making good progress with using the none-specific HLA workflow in MSFragger.
Our collaborator is interested to do cleavage signature analysis for some the identified peptide. For this purpose, we need the amino acids in the protein sequence that are located at either up or downstream of detected peptides (3 AA either side). Please see the example in Figure 4: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7008090/
I hope you can add this feature and look forward to testing it.
Thanks

[fcyu]

Thanks for your kind words and suggestions.

It sounds like something that downstream analysis tools should do. But we will discuss internally and keep you posted.

Best,

Fengchao

[anesvi]

We should move this to philosopher requests Felipe: can we add a column in PSM.tsv (and maybe ion and peptide.tsv) showing more AAs on each side E.g. 6 on each side in the following format for peptide KLNGFTYPR MQLTSQ.KLNGFTYPR.DSWERL Thanks Alexey From: fazeliniah ***@***.***> Sent: Friday, November 5, 2021 3:14 PM To: Nesvilab/MSFragger ***@***.***> Cc: Subscribed ***@***.***> Subject: [Nesvilab/MSFragger] Feature request for HLA analysis (Issue Nesvilab/FragPipe#1034) External Email - Use Caution Dear MSFragger developing team, Thank you again for this amazing software. We are making good progress with using the none-specific HLA workflow in MSFragger. Our collaborator is interested to do cleavage signature analysis for some the identified peptide. For this purpose, we need the amino acids in the protein sequence that are located at either up or downstream of detected peptides (3 AA either side). Please see the example in Figure 4: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7008090/ I hope you can add this feature and look forward to testing it. Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#1034>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM6YR35H3OQN2NM2NSHTUKQ3HXANCNFSM5HOQUUQQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[prvst]

Yes, I think this can be done

[ulrich-eckhard]

Is there any update on this feature? I would be also highly interested in getting something like 6 residues (or more) on each site then I may could used the peptide outputs directly for cleavage specificity analysis after an unspecific search.

[prvst]

I'm including this request for the next release

[ulrich-eckhard]

That would be amazing! Big big thanks already!

[ulrich-eckhard]

Hey Felipe! Is there any time estimate when this feature may will be available? Big thanks in advance already,
Ulrich

[prvst]

I'm aiming for the upcoming release 5.0, in the following weeks

[ulrich-eckhard]

great to hear! :-)

[fcyu]

Implemented in version 5.0.

[fazeliniah]

Hi, I am not sure if I see this new feature in version 5.0. Maybe I am missing something.

[ulrich-eckhard]

Hey Felip! Didn't find time yet to test it actually. Swamped with student assignments but I hope to find time in July to play with these data again! Big thanks already! u

[ulrich-eckhard]

Hi, I am not sure if I see this new feature in version 5.0. Maybe I am missing something.

Hey Fazeliniah!
probably you found it already, but just stumbled about the thread again. i think it is only implemented at the PSM level and not the peptide level. there is now a columns called "Extended Peptide", which has the 8 preceding and the 8 succeeding amino acids (separated from the identified peptide by a dot. so xxxxxxxx.peptide.xxxxxxxx).
cheers,
u

[ulrich-eckhard]

Hey MSFragger/FragPipe Team!
Just noticed something odd with the "extended peptide" column: when checking for a specific cleavage site, I realized that the "extended peptide" column didn't have the correct amino acid sequence and instead, two positions that are leucines in the database were indicated as isoleucine. So I checked quickly the amino acid occurrence within the left extended region, and indeed, I only got 0.22% occurrence for leucine, while 12.85% for isoleucine. In the "right" extended peptide region it is not as dramatic but still 2.09 vs 12.54% occurrence, so also likely something going wrong here. Any idea what could be happening?
Big thanks already!
u

[fcyu]

Thanks for the feedback. I think it is due to this bug in Philosopher: Nesvilab/philosopher#430 . Hopefully, we will have a chance to work on this again.

Best,

Fengchao

[ulrich-eckhard]

it sounds similar indeed. but surprised that the same problem is in the bioinformatically-inferred/extended peptide regions. Big thanks already for looking into it!
u