Issue 722: How can I put z+1 ions in the fragments list for ETD?

Assigned To:ritach
Opened:2020-03-27 by an.staes
Changed:2022-01-14 by Brendan MacLean
2020-03-27 an.staes
Title»How can I put z+1 ions in the fragments list for ETD?
Assigned ToGuest»Brendan MacLean

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,

2020-03-30 Brendan MacLean
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.

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.


2021-03-06 Brendan MacLean
Notify»Birgit Schilling
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.

2021-05-13 Brendan MacLean
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.

2022-01-08 Brendan MacLean
Assigned ToBrendan MacLean»ritach
NotifyBirgit Schilling»Birgit Schilling;Nick Shulman
We need to do this soon. Rita, please make it your next top priority when you finish up what you are working on now.

2022-01-14 Brendan MacLean
Birgit, can we get some of the EAD files you were showing me last week to give Rita something to test with?