Skyline version: 3.5.0.9319 (64-bit)
Installation ID: cc30bf4a-fa48-4337-927e-602932f2cb83
Exception type: TargetInvocationException
Error message: 

Stack trace:
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Util\Util.cs:line 1591
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115
   at pwiz.Skyline.SkylineWindow.ChangeSettingsMonitored(Control parent, String message, Func`2 changeSettings) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 3006
   at pwiz.Skyline.SettingsUI.TransitionSettingsUI.OkDialog() in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\SettingsUI\TransitionSettingsUI.cs:line 557
   at System.Windows.Forms.Control.OnClick(EventArgs e)
   at System.Windows.Forms.Button.OnClick(EventArgs e)
   at System.Windows.Forms.Button.PerformClick()
   at System.Windows.Forms.Form.ProcessDialogKey(Keys keyData)
   at System.Windows.Forms.TextBoxBase.ProcessDialogKey(Keys keyData)
   at System.Windows.Forms.Control.PreProcessMessage(Message& msg)
   at System.Windows.Forms.Control.PreProcessControlMessageInternal(Control target, Message& msg)
   at System.Windows.Forms.Application.ThreadContext.PreTranslateMessage(MSG& msg)

Inner exceptions:
Exception type: System.Reflection.TargetInvocationException
Error message: 

   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Util\Util.cs:line 1591
   at pwiz.Skyline.Util.ParallelEx.LoopWithExceptionHandling(Action loop, Action`1 catchClause) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Util\Util.cs:line 1726
   at pwiz.Skyline.Model.SrmDocument.ChangeSettingsInternal(SrmSettings settingsNew, SrmSettingsChangeMonitor progressMonitor) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 825
   at pwiz.Skyline.SkylineWindow.ModifyDocument(String description, IUndoState undoState, Func`2 act) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 559
   at pwiz.Skyline.SkylineWindow.ChangeSettings(SrmSettings newSettings, Boolean store, String message, IUndoState undoState, SrmSettingsChangeMonitor monitor) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 3040
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClassc2.<ChangeSettingsMonitored>b__bd(IProgressMonitor progressMonitor) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 3003
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213
---------------------------------------------------------------
Exception type: pwiz.Skyline.Util.AssumptionException
Error message: 

   at pwiz.Skyline.Model.TransitionGroupDocNode.ChangeSettings(SrmSettings settingsNew, PeptideDocNode nodePep, ExplicitMods mods, SrmSettingsDiff diff) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 814
   at pwiz.Skyline.Model.PeptideDocNode.ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff, Boolean recurse) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\PeptideDocNode.cs:line 814
   at pwiz.Skyline.Model.SrmDocument.<>c__DisplayClass34.<ChangeSettingsInternal>b__2c(Int32 i) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 828
   at System.Threading.Tasks.Parallel.<>c__DisplayClass17_0`1.<ForWorker>b__1()
   at System.Threading.Tasks.Task.InnerInvokeWithArg(Task childTask)
   at System.Threading.Tasks.Task.<>c__DisplayClass176_0.<ExecuteSelfReplicating>b__0(Object )
Exception caught at: 
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Application.ThreadContext.PreTranslateMessage(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Form.ShowDialog(IWin32Window owner)
   at pwiz.Skyline.SkylineWindow.ShowTransitionSettingsUI(IWin32Window parent, Nullable`1 tab) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 2844
   at pwiz.Skyline.SkylineWindow.transitionSettingsMenuItem_Click(Object sender, EventArgs e) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Skyline.cs:line 2823
   at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
   at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
   at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ToolStrip.WndProc(Message& m)
   at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Program.cs:line 284