Issue 482: set negative ion mode for peptides

Assigned To:Guest
Opened:2016-10-13 by an.staes
Changed:2021-12-30 by Brian Pratt
Resolved:2021-12-30 by Brian Pratt
Resolution:Won't Fix
Closed:2021-12-30 by Brian Pratt
2016-10-13 an.staes
Title»set negative ion mode
Assigned To»Brendan MacLean
Is it possible to have the negative transitions (and precursor) of a peptide? We aren't able to detect a phosphopeptide very well, because of its charge (negative). So we want to measure it in negative mode, but therefore we need the negative ions in Skyline...

2016-10-13 Brendan MacLean
Assigned ToBrendan MacLean»bspratt
We have this for small molecules. Not sure how hard it would be to implement for peptides. Never before seriously requested over 8 years of the project. I think we would have to show a "Add Precursor" right-click menu item like we have for small molecules and make choosing negative ion mode in the form this brings up possible. I don't think we want to show negative precursors in the pop-up pick-lists we show when you click the drop arrow to the right of a peptide in the Targets list when you hover over it. That would just add too much distraction, given this being its only request in 8 years.

Brian, can you give this some thought?

2016-10-31 Brian Pratt
I would think that the place to handle this would be the transition list import. Either enable an explicit charge state column, or extend the logic to allow for the idea that m/z is what it is due to deprotonation.

2016-10-31 Brian Pratt
Or, just allow user to request negative charges in the Transition Settings | Filter tab. Again, assuming deprotonation.

2019-06-11 Brian Pratt
Titleset negative ion mode»set negative ion mode for peptides
Added "for peptides" to title.

Question: do we understand peptide fragmentation in negative ion mode?

2021-12-30 Brian Pratt
resolve as Won't Fix
Assigned ToGuest»Brian Pratt
We just don't know enough about peptide fragmentation in negative ions mode to support this (we do know from conversation with Mike that it's different than with protonation).

The workaround for a user who is confident in the expected fragments would be to describe everything as small molecules.

2021-12-30 Brian Pratt
Assigned ToBrian Pratt»Guest