SEA-PHAGES | Mass Spec and Post Translational Modifications

Link to this post \| posted 05 Apr, 2019 13:12
scaruso	Good morning, We have some mass spec data to look at and are being told that it likely is suffering from all sorts of post translational modifications, which make it harder for their system to match up the results to the provided data, it seems. Unless, of course, we tell them which to look for. Oh and each one included adds to the computing time. So best to chose judiciously. OK, so, with that in mind, we have come up with only a couple common one identified in the host bacteria. Strep apparently does a lot of acetylation, adenylylation, and modification with prokaryotic ubiquitin-like protein (Pup). But anyone have some suggestions of the best choices to include for Actinobacteriophages in general? Thanks, Steve

Link to this post | posted 05 Apr, 2019 13:12

Good morning,

We have some mass spec data to look at and are being told that it likely is suffering from all sorts of post translational modifications, which make it harder for their system to match up the results to the provided data, it seems. Unless, of course, we tell them which to look for. Oh and each one included adds to the computing time. So best to chose judiciously.

OK, so, with that in mind, we have come up with only a couple common one identified in the host bacteria. Strep apparently does a lot of acetylation, adenylylation, and modification with prokaryotic ubiquitin-like protein (Pup). But anyone have some suggestions of the best choices to include for Actinobacteriophages in general?

Thanks,

Steve

Link to this post \| posted 05 Apr, 2019 16:10
welkin	Hi Steve, Those are good places to start. I've spent a lot of time trying lots of different combinations of PTMs with our data and haven't felt like I've really improved my protein IDs by any statistically significant amount. It seems like you can always match a few peptides in which the PTMs have come off during the collisions; so as long as you are doing ID and not quantitation, it doesn't seem like it makes much of a difference to me. If you do try to add some PTMs to the search, I wouldn't try to do more than 2-3 at a time; eventually if you add enough possibilities in there you'll find anything! Good luck!

Link to this post | posted 05 Apr, 2019 16:10

welkin

Hi Steve,
Those are good places to start. I've spent a lot of time trying lots of different combinations of PTMs with our data and haven't felt like I've really improved my protein IDs by any statistically significant amount. It seems like you can always match a few peptides in which the PTMs have come off during the collisions; so as long as you are doing ID and not quantitation, it doesn't seem like it makes much of a difference to me.

If you do try to add some PTMs to the search, I wouldn't try to do more than 2-3 at a time; eventually if you add enough possibilities in there you'll find anything!

Good luck!

Recent Activity

Mass Spec and Post Translational Modifications