No. of dynamic modifications

David Domjan

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Nov 29, 2021, 10:09:16 AM11/29/21

to MS Amanda

Hey all,

What could really make yhis program have significant advantages to SequestHT or Mascot would be the possibility to select how many of the same modifications one could have for individual ptms.

For example, I have max 4 mod and max 3 of the same but I am also looking to find C-nitrosylation sites, and since they are rare, i would like to be able to select only max 1 per peptide for this one specifically, whereas for S,T phoshorylation 3 max is not too much at all. This way more modifications can be meaningfully analyzed with the same compuattionall regirenments.

All the best,

David

David Domjan

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Nov 29, 2021, 10:11:38 AM11/29/21

to MS Amanda

Also S,T phoshorylation max 3 of the same but for example for the rarer form of Y phosphorylation I'd like for Amanda to only search for max one per peptide.

David Domjan

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Nov 29, 2021, 1:56:06 PM11/29/21

to MS Amanda

On top of that, some modifications, such as ADP-rybosylation have specific consensus sequences which would shorten the cpu time if accounted for quite significantly in my opinion.

Viktoria Dorfer

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Dec 7, 2021, 10:53:58 AM12/7/21

to MS Amanda

Hi David,

thanks for that great suggestion! We are going to look at that and will implement a first version in the standalone version and will then think of how to get that into PD. Would you be willing to work with the standalone version as well?

Best regards,

Viktoria

David Domjan

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Dec 26, 2021, 7:47:23 AM12/26/21

to MS Amanda

Hey Viktoria,

That is great to hear. Sadly though, I am only using MS Amanda in conjunction with PD. But I am sure other users will be happy to have this option even only in the standalone version.