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Custom glycosites #1262

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dennissv opened this issue Sep 25, 2023 · 2 comments
Open

Custom glycosites #1262

dennissv opened this issue Sep 25, 2023 · 2 comments
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@dpolasky
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@dennissv
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Hello, we're studying organisms that has a general O-glycosylation system that targets a specific three amino acid motif. The regex for this motif would be D[ST][AILVMTSGCF] where it's the S or T that's glycosylated. I'm now wondering what the best approach to add this rule would be? Is it possible to use some sort of regex in FragPipe for glycosites? Thanks in advance!

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Dennis
@dpolasky
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dpolasky commented Oct 2, 2023

Hi Dennis,
There is currently no way to restrict to a specific motif (beyond the glycosite being S/T), but we can certainly add it. It will require changes to both MSFragger and the O-Pair localization tool so it will take some time to implement, but I think it is a good capability to have. I'll let you know when we have it ready.

Best,
Dan

@dennissv
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dennissv commented Oct 3, 2023

Hi Dan, thank you for the update and the effort! Appreciate it and looking forward to seeing this feature in the future.

Best,
Dennis

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