Log iRT error but almost working fully Chris Ashwood  2020-02-05
 

Dear Skyline team,

Thanks to Kaipo for putting the logarithmic iRT feature in Skyline, I think I will use it a lot.

I've attempted to use it but I had two issues in the implementation that might be related (one is a limitation with how it's currently set up to be used and the second is a crash I get). The roadblock (and subsequent workaround) is that the calculator only supports linear calibrations (picture attached) but after tweaking how I edit the calculator, it crashes on the final step.

The procedure that hits a snag is:

  1. Calibrate the iRT calculator in linear space (only option) with my standards (Calibrate iRT Calculator window)
  2. Save the calculator then edit the calculator by changing the iRT values to what they are meant to be (Edit iRT Calculator window)
  3. Set regression type to logarithmic and then add results in the bottom right.
  4. Once i click OK, the results field is populated with correct iRT values but then I get an index out of bounds crash.

The crash can be found below.

Cheers,
Chris

Skyline version: 20.1.1.32-562b680be (64-bit)
Installation ID: 586d68dd-c361-4392-a8c5-ad0df1faa1e9
Exception type: IndexOutOfRangeException
Error message: Index was outside the bounds of the array.


Stack trace:

at pwiz.Common.Collections.ImmutableList`1.SingletonImpl.get_Item(Int32 index) in C:\proj\pwiz_x64\pwiz_tools\Shared\Common\Collections\ImmutableList.cs:line 310
at pwiz.Skyline.Controls.Graphs.RTLinearRegressionGraphPane.GraphData.get_XAxisName() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Graphs\RTLinearRegressionGraphPane.cs:line 1397
at pwiz.Skyline.Controls.Graphs.RTLinearRegressionGraphPane.GraphData.Graph(GraphPane graphPane, PeptideDocNode nodeSelected) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Graphs\RTLinearRegressionGraphPane.cs:line 1132
at pwiz.Skyline.Controls.Graphs.RTLinearRegressionGraphPane.UpdateGraph(Boolean selectionChanged) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Graphs\RTLinearRegressionGraphPane.cs:line 429
at pwiz.Skyline.Controls.Graphs.RTLinearRegressionGraphPane.<>c__DisplayClass65_0.<UpdateAndRefine>b__0() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Graphs\RTLinearRegressionGraphPane.cs:line 593

Exception caught at:
at pwiz.Skyline.Controls.Graphs.RTLinearRegressionGraphPane.<>c__DisplayClass65_0.<UpdateAndRefine>b__0() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Graphs\RTLinearRegressionGraphPane.cs:line 593
at System.RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)
at System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)
at System.Delegate.DynamicInvokeImpl(Object[] args)
at System.Windows.Forms.Control.InvokeMarshaledCallbackDo(ThreadMethodEntry tme)
at System.Windows.Forms.Control.InvokeMarshaledCallbackHelper(Object obj)
at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Windows.Forms.Control.InvokeMarshaledCallback(ThreadMethodEntry tme)
at System.Windows.Forms.Control.InvokeMarshaledCallbacks()
at System.Windows.Forms.Control.WndProc(Message& m)
at System.Windows.Forms.Form.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 System.Windows.Forms.Form.ShowDialog(IWin32Window owner)
at pwiz.Skyline.SkylineWindow.ShowPeptideSettingsUI(IWin32Window parent, Nullable`1 tab) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 3394
at pwiz.Skyline.SkylineWindow.peptideSettingsMenuItem_Click(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 3371
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\pwiz_x64\pwiz_tools\Skyline\Program.cs:line 306

 
 
Kaipo responded:  2020-02-05

Hi Chris,
Would you mind sharing your document via File > Share? You can either email it to me directly (kaipot@uw.edu) or upload to https://skyline.ms/files.url

Thanks,
Kaipo

 
Kaipo responded:  2020-02-05

Hi Chris,
Looks like this error is harmless. We will fix it but you can likely ignore it for now. Was the Skyline document in a functional state after you closed the error?
Regarding your other point - you are correct, I will work on implementing this for the next Skyline-daily release.

Thanks,
Kaipo

 
Chris Ashwood responded:  2020-02-06

Hi Kaipo,

The document is functional but if I try to use the iRT score instead of RT, the Replicate comparison view is blank and the chromatogram view window is still has RT as the y-axis instead of the iRT score.

Great to hear you're implementing it on the next Skyline-daily release!

Cheers,
Chris