We are trying to determine % incorporation of 15N from MS^E data that has been processed using PLGS 3.0.2. Topograph recognizes the search results (*_final_fragment.csv) but it is having a problem using the mzML files exported from the PLGS software. I was wondering if anyone else has reported a problem like this. What version of mzML and mzXML does Topograph recognize? Do you have any suggestions to remedy this problem?

The error message is below:

4/30/2015 2:33:25 PM    Exception trying to open E:\2015_Cyano_peptide_DB\Ion_Accounting\150423_Cyano_Pep_UHM100_15N_C_IA_final_fragment.mzML    System.Exception: [ChromatogramList_mzML::chromatogram()] Index out of bounds.
   at pwiz.CLI.msdata.ChromatogramList.chromatogram(Int32 index, Boolean getBinaryData)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetScanTimes()
   at pwiz.Topograph.Model.MsDataFileData.Init(MsDataFileImpl msDataFileImpl) in C:\Users\nicksh\svn\topograph_1_1\pwiz\pwiz_tools\Topograph\TopographLib\Model\MsDataFileData.cs:line 51
   at pwiz.Topograph.MsData.MsDataFileUtil.TryInitMsDataFile(Workspace workspace, MsDataFile msDataFile, String& message) in C:\Users\nicksh\svn\topograph_1_1\pwiz\pwiz_tools\Topograph\TopographLib\MsData\MsDataFiles.cs:line 101
Exception caught at:
   at pwiz.Topograph.MsData.MsDataFileUtil.TryInitMsDataFile(Workspace workspace, MsDataFile msDataFile, String& message)
   at pwiz.Topograph.ui.Forms.TurnoverForm.EnsureMsDataFile(MsDataFile msDataFile, Boolean alwaysPrompt)
   at pwiz.Topograph.ui.Forms.TurnoverForm.EnsureMsDataFile(MsDataFile msDataFile)
   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.ScrollableControl.WndProc(Message& m)
   at System.Windows.Forms.Form.WndProc(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.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.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.Application.Run(Form mainForm)
   at pwiz.Topograph.ui.Program.Main()