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Feature request for HLA analysis #1034
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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 |
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 ***@***.***>
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Subject: [Nesvilab/MSFragger] Feature request for HLA analysis (Issue Nesvilab/FragPipe#1034)
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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
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Yes, I think this can be done |
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. |
I'm including this request for the next release |
That would be amazing! Big big thanks already! |
Hey Felipe! Is there any time estimate when this feature may will be available? Big thanks in advance already, |
I'm aiming for the upcoming release 5.0, in the following weeks |
great to hear! :-) |
Implemented in version 5.0. |
Hi, I am not sure if I see this new feature in version 5.0. Maybe I am missing something. |
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 |
Hey Fazeliniah! |
Hey MSFragger/FragPipe Team! |
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 |
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! |
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
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