Describe fragment ions

[veitveit]

The nomenclature could also be used to describe fragment ions. Then we might have to consider neutral losses, ...

[stefanks]

Could you elaborate more on this? So far we have no mention of charges anywhere in the standard!

[veitveit]

This is more for a discussion. Complex fragmentation spectra, e.g. containing multiple species of a peptide or multiple peptides, might require a detailed description of the fragment ions including sequence, PTMs, losses, ... On the other side, such a description could open Pandora's box by including too many features. 2017-07-31 15:46 GMT+02:00 stefanks <[email protected]>:

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Could you elaborate more on this? So far we have no mention of charges anywhere in the standard! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APEZhW5j38lHw4GX4ZKhYUhqsAmDK1vhks5sTdrTgaJpZM4Onjhi> .

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[acesnik]

Do you think these would be a common use case of the notation?

Personally, I think the "info" tags would be a good place for charges and neutral losses. They might be necessary to get agreement between the ProForma sequence and the experimental spectrum, but I wouldn't want to present them to a biologist.