Issue 498: Theoretical peptide z ion does not match

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:3.7
Opened:2017-02-28 by plloziuk
Changed:2017-08-31 by Brendan MacLean
Resolved:2017-02-28 by Brendan MacLean
Resolution:Fixed
Closed:2017-08-31 by Brendan MacLean
2017-02-28 plloziuk
Title»Theoretical peptide z ion does not match
Assigned To»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»3.6
During SRM analysis of Glutathione with NEM modified cys we noticed our theoretical z2 ion (288.1) of the peptide ECG is off by 1 Da from the experimental (287.1). While this is an atypical peptide due to the gamma linkage, the y2 is correct and we've compared this to a number of other fragment prediction algorithms including UWPR which suggest the z ion is 1 Da lighter than that predicted by Skyline. I'm not sure if this issue has come up but wanted to bring it to your attention.

2017-02-28 Brendan MacLean
One question: Are c ions also off by one or are they calculated correctly, and only z ions are off by one.

Great to see Skyline actually under use for ETD. I implemented c and z ion support to make it theoretically support ETD, but it sounds like the calculation has never been quite right and not noticed until someone put it into real practice.

2017-02-28 Brendan MacLean
The code in Skyline looks like:

            _massDiffZ = _massDiffY - _massCalc.CalculateMassFromFormula("NH2");

But this page on wikipedia:

https://en.wikipedia.org/wiki/Electron-transfer_dissociation

Sure makes it look like the code should be changed to:

            _massDiffZ = _massDiffY - _massCalc.CalculateMassFromFormula("NH");

Which would result in a 1 Da mass difference. Does this seem right to you?

On the N-terminal side, the mass deltas look like:

            _massDiffA = -_massCalc.CalculateMassFromFormula("CO");
            _massDiffB = 0.0;
            _massDiffC = _massCalc.CalculateMassFromFormula("NH3");

This also seems wrong. Shouldn't the c ion delta also be NH? or:

            _massDiffC = _massDiffB + _massCalc.CalculateMassFromFormula("NH");

(where _massDiffB is 0).

2017-02-28 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Fixed in trunk with r10555. This will be out in the next Skyline-daily, hopefully tomorrow, and may come out in 3.6 with a second patch, or in the next major release, if we do not do a second patch. Thanks for reporting and helping to resolve.

2017-03-05 Brendan MacLean
Milestone3.6»3.7

2017-08-31 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest