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 #191)

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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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[prvst]

Yes, I think this can be done