Issue 498: Theoretical peptide z ion does not match

Assigned To:Guest
Opened:2017-02-28 by plloziuk
Changed:2017-08-31 by Brendan MacLean
Resolved:2017-02-28 by Brendan MacLean
Closed:2017-08-31 by Brendan MacLean
2017-02-28 plloziuk
Title»Theoretical peptide z ion does not match
Assigned To»Brendan MacLean
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:

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
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

2017-08-31 Brendan MacLean
Assigned ToBrendan MacLean»Guest