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topdownproteomics / ProteoformNomenclatureStandard

ProForma, a Proteoform Notation Standard
https://topdownproteomics.github.io/ProteoformNomenclatureStandard/
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Does the order of prefix tags and N terminal modifications matter? #28

Open rfellers opened 6 years ago

rfellers commented 6 years ago

I know that this is valid from the manuscript: [Unimod]+[1]-S[21]GRGK...

Is this also valid ProForma? [1]-[Unimod]+S[21]GRGK...

veitveit commented 6 years ago

I would say no. Definition of the key type should always come first.

On Wed, 21 Mar 2018, 22:12 Ryan Fellers, notifications@github.com wrote:

I know that this is valid from the manuscript: [Unimod]+[1]-S[21]GRGK...

Is this also valid ProForma? [1]-[Unimod]+S[21]GRGK...

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acesnik commented 6 years ago

Good question! I agree with @veitveit. It's valid syntax (computer readable), but for human readability, I think we should always have the key definition to be first, since it pertains to the N-terminal modification tag.

rleduc42 commented 6 years ago

I agree with veitveit and acesnik.

rfellers commented 6 years ago

Excellent, sounds like everyone is in agreement. I guess that means it is adopted? Is there a living standard document that will incorporate this clarification? Either way, I can now continue with the parser development, thanks!

acesnik commented 6 years ago

Yes, I think we should adopt this as an addition to Rule 6, the one that talks about prefix tags. Here is the living document. Our first change after publishing the initial standard!