Charge reduced loss fragment

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Charge reduced loss fragment Christopher Lößner  2014-06-13 02:32
 
I am interested in a fragment that is originating from a chemical modification and resulting in charge reduction as well as a partial mass loss of this tag. E.g. I have a m/z 500 3+ ion (peptide plus tag) that is resulting in a m/z 700 2+ fragment (peptide minus a part of the tag, as well as reduced charge state). I have tried for some while to come to a solution but wasn't successful yet.
Has somebody an idea how I can annotate and by this quantify these ions?

Best regards,

Christopher
 
 
Brendan MacLean responded:  2014-06-20 21:11
Hi Christopher,
Are you saying that it is essentially the precursor minus a loss and charge? If so, yeah, I don't think that is anything I have yet made possible in Skyline. You are the first to request it in nearly 6 years of doing this.

Makes perfect sense, but currently, you can only have the precursor minus a neutral loss, which obviously results in the same charge state.

All other ions but the precursor allow any charge state you put in the "Ion charges" field in the Transition Settings - Filter tab.

Please confirm that this is indeed what you are asking for, and I will think of how to implement this, and at least put it into our issues list as a TODO for sometime after our next release. I am sure that is not as much help to you as you were hoping, but it is the best I can do right now.

Thanks for posting your feedback.

--Brendan
 
Christopher Lößner responded:  2014-06-23 00:00
Hi Brendan,

thanks you for your reply. You got it perfectly right what I was asking for.
It seems to be then a rather seldom case. Anyway, I am happy that you will put it onto the TODO list.

Thanks a lot and best regards,

Christopher
 
aaron o bailey responded:  2014-11-16 03:48
I am a new Skyline user trying to accomplish a similar task. I am also interested in creating a method which identifies charged loss transitions. It would be helpful to have the option to assign a neutral MI/avg mass and/or a chemical formula as well as a loss delta charge state.

Cheers,
Aaron