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Unique peptides column limit

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Unique peptides column limit Max Karlsson  2017-10-03 07:19
 

Hi,

Hope all is well with you guys. I tried to use the unique peptides tool (probably on far too many peptides) and got the following error:

Skyline version: 3.6.0.10493 (64-bit)
Installation ID: d044130d-6124-49e5-88d3-36c1bbddf29a
Exception type: InvalidOperationException
Error message: Sum of the columns' FillWeight values cannot exceed 65535.

--------------------

Stack trace:

   at System.Windows.Forms.DataGridView.OnAddingColumn(DataGridViewColumn dataGridViewColumn)
   at System.Windows.Forms.DataGridViewColumnCollection.Add(DataGridViewColumn dataGridViewColumn)
   at pwiz.Skyline.EditUI.UniquePeptidesDlg.LaunchPeptideProteinsQuery() in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\EditUI\UniquePeptidesDlg.cs:line 220
   at pwiz.Skyline.EditUI.UniquePeptidesDlg.OnShown(EventArgs e) in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\EditUI\UniquePeptidesDlg.cs:line 186
   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()

Exception caught at:
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   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.ShowUniquePeptidesDlg() in c:\proj\skyline_3_6_x64\pwiz_tools\Skyline\Skyline.cs:line 2200
   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_6_x64\pwiz_tools\Skyline\Program.cs:line 299


Does the unique peptide tool work as well if I do it on subsets of the peptides one at a time, or is there some workaround?

Thanks,
Max
 
 
Nick Shulman responded:  2017-10-03 11:06
Thank you for contacting us about this. Several people have run into this error before, but no one gave us their email address, so we did not actually have a repro case.

The limit is going to be raised in the next update of Skyline-Daily.

It would be very helpful if I could take a look at your Skyline document, so that I can make sure that we handle this scenario correctly.

In Skyline, you can use the menu item:
File > Share > (Complete)
to create a .zip file containing your Skyline document and supporting files including the background proteome.

You can upload that .zip file here:
https://skyline.ms/files.url

By the way, it looks like you are using Skyline 3.6. You might want to upgrade to the latest released version (3.7). All versions of Skyline have this bug in them but the Skyline-Daily that is coming out in a few weeks will have a higher limit.
 
Max Karlsson responded:  2017-10-04 05:39

Hi,

Uploaded "Max mock library.sky.zip" too the repository.

Cheers,

Max