Specify ionic species further

[douweschulte]

Ion charges can be represented in the current version of ProForma (section 7.1 - MS Extensions)

EMEVEESPEK/3[+2Na+,+H+]
EMEVEESPEK/-1[+e-]

Given examples in the specification
This does not specify notation for the ionic species. It does state however that quite high complexity options are valid: the removal of a OH-. It does not state how higher charged ionic species are notated, for example on higher charged metal ions like Fe[III].

EMEVEESPEK/7[+2Fe+3,+H+]
EMEVEESPEK/1[-OH-]
EMEVEESPEK/1[+N1H3+]

Potential uses for a higher complexity notation. Note on the last example: the 3+ here indicates that there are 3 H and that the charge of the whole species is +1

To me it seems logical to specify this as using the full modification Formula: notation (with e allowed as well) followed by the total number of charges for that species. But that implies that this field can have paired square brackets [], positive and negative numbers internally, and this might introduce some visual ambiguity on what the final number is doing.

Additionally there is one example that does not use a sign on the number of the ions. While there are also examples where there is only a sign used. Formalising the notation seems warranted to me.

EMEVEESPEK/-2[2I-]

Given example in the specification using only a number as the number of times an ionic species is present

\/([+-]?\d+)(\[((?:(?:[+-]?\d+)|(?:[+-]))((?:\[\d+[A-Z][A-Za-z]?\d+)|(?:[A-Z][A-Za-z]?\d*))+([+-]\d*),)*((?:(?:[+-]?\d+)|(?:[+-]))((?:\[\d+[A-Z][A-Za-z]?\d+)|(?:[A-Z][A-Za-z]?\d*))+([+-]\d*))\])?

Here is a beast of a regular expression for how this format could look (does not check for use of valid elements)
Here it is in regex101 with some example matches

"/" <number> ("[" ( <number_or_sign> <formula> <number_or_sign> ",")+ "]")?

This is the same in a bit of somewhat more readable BNF like notation

For a bit of background I came upon this when implementing my own parser for ProForma. I have no serious need or use for any of the complexity here, but my code internally allows to specify any chemical formula as ionic species so I was looking into this section to look into how to export the internal peptides back to fully valid ProForma.