search

pFindStudio / pGlyco3

Apache License 2.0
13 stars 4 forks source link

O- and N- searches #4

Closed ValentinaRangelAngarita closed 4 months ago

ValentinaRangelAngarita commented 3 years ago

Hi! Is there any way I can do a search for N- and O- glycan simulatenously? (I am looking at a raw file that has both N- and O-). Should I just create a new database with both N- and O- and run it in either mode? or would the 138/144 ratio affect the search? Thank you!

jalew188 commented 3 years ago

We are working on this. By using pGlycoSite with combined N- and O- GDB, we can always obtain localized glycans at N- and O-sites, but the problem is the accuracy validation.

We do not check 138/144 intensity ratio or other oxonium ion ratios to classify N/O-glycans when identification and localization, so it is not a problem.

Creating N+O GDB is a bit tricky, but I can share the GDB onto github if you want. Searching for N+O-glycans is not straightforward as well, you can only use command line with some special parameters.

jalew188 commented 3 years ago

Hi @ValentinaRangelAngarita , another problem for combined N- and O-GDB is that, pGlycoSite will check if a localized glycan is in the glycan GDB. N-glycan should be checked by N-GDB, and O-glycan should be checked by O-GDB. pGlycoSite cannot do this checking in the current version if combined GDB is used.