Dear,

When using ETD a common fragment ion is z+1, which is sometimes more present than the z-ion itself. Would it be possible to have the option to show this ion?
Search engines like Mascot also take this into account in their search. So it would be nice to be able to use this ion series as well!

Thank you for considering this as an option.

Kind regards,
An

Hi An,
Sorry about this, but we have not yet implemented a solution to this. Our original implementation had "z" as a proxy for z+1 until someone told us the calculations were off by 1 and we "fixed" that. Later we learned about z and z+1 as separate options, and as you say sometimes z+1 is more present.

https://skyline.ms/announcements/home/support/thread.view?rowId=38133

So, it seems that we will need to add a way to specify both z and z+1 as ion type choices. Perhaps adding z' or z* or something to our nomenclature for ion types in the Transition Settings - Filter tab.

Any further thoughts you have on the subject would be welcome feedback. We don't get a lot of requests for this, but it has clearly come up a few times in the past few years.

--Brendan

This just came up again, along with z+2 ions.

I now think we should probably just support "z+1" and "z+2" ions from the user perspective, regardless of how we encode it internally, rather than coming up with a special notation like z' or z*.

So, a user might specify Product ion types: "c, z+1" for ETD or "b, y, c, z+1" EThcD. Or even "c, z, z+1" for whatever might produce that.

Nick, can you have a look at this one?

Ideally, I guess, we would add "z+1" and "z+2" as recognized ion types in the Transition Settings - Filter tab. It looks like these would just be z-ions with +H and +2H added respectively. Until 2/28/2017, our "z" was actually the "z+1" when that was reported and I switched it to true z-ions changing the mass delta from massDiffY - NH2 to massDiffY - NH3.

We need to do this soon. Rita, please make it your next top priority when you finish up what you are working on now.

Birgit, can we get some of the EAD files you were showing me last week to give Rita something to test with?

Should we call these ions zh and zhh instead of z+1 and z+2. Since they are actually protonated z ions that would be chemically correct. Avoiding the + sign makes implementation a bit easier and allows to have more compact annotations in the spectra viewer ( zh4 instead of (z+1)4 ).

From Birgit and Christie Hunter:

We would like to suggest a different way to annotate
This is also the nomenclature that Mascot is using (Takashi):

The standard nomenclature of z ion in ExD is following,
z+1 = z•
I suggest to use c’ and z•.
z•• is really z•+H and is called z’…

Hopefully skyline are able to use the “•” and the apostrophe in this way…

The definition of z in many software is for CID.

http://www.matrixscience.com/help/fragmentation_help.html

ExD case, I prefer c’ instead of c.

It sounds like we are going to need to add a menu with the various ion types to the Transition Settings - Filter tab, like we have for the chemical FormulaBox control. Not many users can type in a z• from the keyboard. Otherwise, this seems doable. I am not sure I understand why we would switch to c' from c. If there is no ambiguity, then I think we will continue forward with what we have for c-ions.

Implemented in PR https://github.com/ProteoWizard/pwiz/pull/1967