Artifical N-terminal modification

[Konrad]

Hello,

I have have a question regarding the fixed modification option in TopPic (using toppic-windows-1.4.13). I want to have an artifical modification set as fixed on all N-terminal proteoforms (including truncated proteoforms). I am now wondering whether TopPic is capable of doing so.

As I understand the annotation in the "fixed modification"-file would look like this:

• name, monoisotopic mass,*,N-Term,-1

I have trouble imaging how exactly the modification is added. Here are three options I can think of:

1. Addition on canonical N-termini (as annotated in fasta file)
2. Addition of modification only if no formylation or acetylation
3. Addition on all N-termini (truncated, acetylated etc.)

Grateful for your input!

Konrad

[Konrad]

Ideally I would be able to simply change the two non acetylated N-terminal forms (NONE and NME) by adding the monoisotopic mass of my modification (Modification is only attached on free amine group).

Now idea whether thats possible :)

Thanks again!

Konrad

[liuxia...@gmail.com]

Hi, Konrad, 

The current version of TopPIC supports N-terminal modifications of whole proteoforms or proteoform prefixes. It does not support fixed N-terminal modifications for truncated proteoforms. You can change the mass shift of an N-terminal form like M_ACETYLATION, but it only modifies whole proteoforms or proteoform prefixes. 

Best, 

Xiaowen