Global modifications (modifications for a specific AA over the whole sequence)

[sgibb]

In MS proteomics sometimes iodoacetamide is used to break the disulfide bonds. This yield to iodoacetylated cysteine residues (Unimod:4).

Currently you have to annotated the sequence as follows:

[Unimod]+C[4]SEQUENC[4]EC[4]

That would be difficult and error prone for humans for long sequences (could be done by a computer and regular expressions easily).

It would be nice if there could be a prefix tag for global modifications as well. As basis for discussion I would suggest the > operator:

[Unimod]+C[4]>CSEQUENCEC

Or would something like this destroy the human readability?

[stefanks]

The use of iodoacetamide implies that we are not discussing intact proteoforms as they exist in live cells, but rather the observed ones that may have sample handling artifacts.

I would argue that since this is not an issue for proteoforms in their natural form, there is no need for a special short-hand notation to emphasize "global" modifications.

More thoughts, anyone?