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adding lanthanide element as modification
(5 responses) lvyayao90 2018-11-06

Dear support team

I tried to edit a new modification using two lanthanide elements, but i was noticed that "only H O N C S P Se Li F Na S Cl K Ca Fe Ni Cu Zn Br Mo Ag I Au Hg B As Cd Cr Co Mn Mg Si are compatible". I wonder if you can please add lanthanide elements as compatible elements in the list, for our team think lanthanide elements are very useful tags in quantitative proteomics.

I'd be grateful for any help.

Thanks,

Lv yayao

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MSe Data from Waters PLGS software
wkray 2015-04-30
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()
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