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Messages - Ondrej

16
MS-DIAL / MRMPROBS project cant be reloaded
Dear Hiroshi,
I have a problem with MRMPROBS when processing large datasets (30+ samples and 20,000+ MRMs).
Everything works fine until I save the project. Then I can not open it again (quite often).
Code: [Select]
Application: MRMPROBS.exe
Framework Version: v4.0.30319
Description: The process was terminated due to an unhandled exception.
Exception Info: System.Runtime.Serialization.SerializationException
   at System.Runtime.Serialization.ObjectIDGenerator.Rehash()
   at System.Runtime.Serialization.ObjectIDGenerator.GetId(System.Object, Boolean ByRef)
etc.
It is difficult to get the info what is actually wrong. Could you please add a debug console or some other kind of warning or log file to the next version? Thank you.
Best,
Ondrej
17
MS-DIAL / Re: Processing of big datasets
Hi Sergey,
check the "temp" folders. You will find small alignment files being processed during the "limbo time", most probably. I would suggest to explore a small subset of your files to get the real impression what is worth the time, and optimize the parameters. E.g. when I tried a lower threshold (20,000 -> 1,000) with ~700 abf files, the gain was ~24,000 -> 27,000 peak spots for extra 15 hours of calculations (1.5 -> 16.5 h). However, many of the extra peaks were within the noise or didn't pass the subsequent quality check.

You can upload another library and skip the peak picking part, but the alignment and gap filling take the most of the processing time.

MS-DIAL will not recover your partially processed data, so plug in a UPS if you are afraid of the power failure.
Best,
O.

18
MS-DIAL / Re: carnitine annotation
Hi Hiroshi,
thank you. Could you please also add [M]+ as a pre-defined adduct type? And eventually also [M]- for compounds with permanent charge.
Ondrej
19
MS-DIAL / carnitine annotation
Hi,
MS-DIAL 4.24, positive lipidomics workflow.

Oleoylcarnitine (CID 46907933, https://pubchem.ncbi.nlm.nih.gov/compound/46907933) is found as m/z 426.35803.
This should be annotated as [M+H]+, but MS-DIAL shows [M]+ Adduct type, probably because of the SMILES notation(?).
Could this be corrected also for all other carnitines? Thank you.
Ondrej

Alignment IDAverage Rt(min)Average MzMetabolite nameAdduct typePost curation resultFill %MS/MS assignedReference RTReference m/zFormulaOntologyINCHIKEYSMILES
18740.818426.35803CAR 18:1[M]+similar chromatogram in higher mz_20181TRUE3.18426.35779C25H48NO4CARHOAMADDCQBUDDY-KHPPLWFENA-OCCCCCC\C=C/CCCCCCCCCC(=O)OC(CC(O)=O)C[N+](C)(C)C
21
MS-DIAL / MRMPROBS 2.50 crashes with multiple files and compounds
Hello,
I use MRMPROBS 2.50:

1) I need to process 30 abf files using key-index: SCAN. It works with tens of compounds in the library, but it crashes when I use 9700 compounds (log below). Is there a limit I do not know about?

2) When an incorrect library is loaded, and the error message acknowledged, there is an option to load another library. In fact, the original file seems to be still loaded, because I get the original error message although I provided a correct library.

3) Maybe just my problem, but Bitdefender removed all MRMPROBS.exe files from my computer.

Best,
Ondrej

Code: [Select]
Application: MRMPROBS.exe
Framework Version: v4.0.30319
Description: The process was terminated due to an unhandled exception.
Exception Info: System.IO.IOException
   at System.IO.__Error.WinIOError(Int32, System.String)
   at System.IO.FileStream.Init(System.String, System.IO.FileMode, System.IO.FileAccess, Int32, Boolean, System.IO.FileShare, Int32, System.IO.FileOptions, SECURITY_ATTRIBUTES, System.String, Boolean, Boolean, Boolean)
   at System.IO.FileStream..ctor(System.String, System.IO.FileMode, System.IO.FileAccess, System.IO.FileShare, Int32, System.IO.FileOptions, System.String, Boolean, Boolean, Boolean)
   at System.IO.StreamReader..ctor(System.String, System.Text.Encoding, Boolean, Int32, Boolean)
   at System.IO.StreamReader..ctor(System.String)
   at Rfx.Riken.OsakaUniv.NewProjectReferencePropertySettingViewModel.getLibraryProperty(System.String)
   at Rfx.Riken.OsakaUniv.NewProjectReferencePropertySettingViewModel.ReferenceOptionClosing()
   at Rfx.Riken.OsakaUniv.NewProjectReferencePropertySettingViewModel.finishExecuteCommand(System.Object)
   at MS.Internal.Commands.CommandHelpers.CriticalExecuteCommandSource(System.Windows.Input.ICommandSource, Boolean)
   at System.Windows.Controls.Primitives.ButtonBase.OnClick()
   at System.Windows.Controls.Button.OnClick()
   at System.Windows.Controls.Primitives.ButtonBase.OnMouseLeftButtonUp(System.Windows.Input.MouseButtonEventArgs)
   at System.Windows.RoutedEventArgs.InvokeHandler(System.Delegate, System.Object)
   at System.Windows.RoutedEventHandlerInfo.InvokeHandler(System.Object, System.Windows.RoutedEventArgs)
   at System.Windows.EventRoute.InvokeHandlersImpl(System.Object, System.Windows.RoutedEventArgs, Boolean)
   at System.Windows.UIElement.ReRaiseEventAs(System.Windows.DependencyObject, System.Windows.RoutedEventArgs, System.Windows.RoutedEvent)
   at System.Windows.UIElement.OnMouseUpThunk(System.Object, System.Windows.Input.MouseButtonEventArgs)
   at System.Windows.RoutedEventArgs.InvokeHandler(System.Delegate, System.Object)
   at System.Windows.RoutedEventHandlerInfo.InvokeHandler(System.Object, System.Windows.RoutedEventArgs)
   at System.Windows.EventRoute.InvokeHandlersImpl(System.Object, System.Windows.RoutedEventArgs, Boolean)
   at System.Windows.UIElement.RaiseEventImpl(System.Windows.DependencyObject, System.Windows.RoutedEventArgs)
   at System.Windows.UIElement.RaiseTrustedEvent(System.Windows.RoutedEventArgs)
   at System.Windows.Input.InputManager.ProcessStagingArea()
   at System.Windows.Input.InputManager.ProcessInput(System.Windows.Input.InputEventArgs)
   at System.Windows.Input.InputProviderSite.ReportInput(System.Windows.Input.InputReport)
   at System.Windows.Interop.HwndMouseInputProvider.ReportInput(IntPtr, System.Windows.Input.InputMode, Int32, System.Windows.Input.RawMouseActions, Int32, Int32, Int32)
   at System.Windows.Interop.HwndMouseInputProvider.FilterMessage(IntPtr, MS.Internal.Interop.WindowMessage, IntPtr, IntPtr, Boolean ByRef)
   at System.Windows.Interop.HwndSource.InputFilterMessage(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndWrapper.WndProc(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndSubclass.DispatcherCallbackOperation(System.Object)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.Dispatcher.LegacyInvokeImpl(System.Windows.Threading.DispatcherPriority, System.TimeSpan, System.Delegate, System.Object, Int32)
   at MS.Win32.HwndSubclass.SubclassWndProc(IntPtr, Int32, IntPtr, IntPtr)
   at MS.Win32.UnsafeNativeMethods.DispatchMessage(System.Windows.Interop.MSG ByRef)
   at System.Windows.Threading.Dispatcher.PushFrameImpl(System.Windows.Threading.DispatcherFrame)
   at System.Windows.Window.ShowHelper(System.Object)
   at System.Windows.Window.ShowDialog()
   at Rfx.Riken.OsakaUniv.MainWindow.newProjectMenu_Click(System.Object, System.Windows.RoutedEventArgs)
   at System.Windows.EventRoute.InvokeHandlersImpl(System.Object, System.Windows.RoutedEventArgs, Boolean)
   at System.Windows.UIElement.RaiseEventImpl(System.Windows.DependencyObject, System.Windows.RoutedEventArgs)
   at System.Windows.Controls.MenuItem.InvokeClickAfterRender(System.Object)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.DispatcherOperation.InvokeImpl()
   at System.Threading.ExecutionContext.RunInternal(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object)
   at MS.Internal.CulturePreservingExecutionContext.Run(MS.Internal.CulturePreservingExecutionContext, System.Threading.ContextCallback, System.Object)
   at System.Windows.Threading.DispatcherOperation.Invoke()
   at System.Windows.Threading.Dispatcher.ProcessQueue()
   at System.Windows.Threading.Dispatcher.WndProcHook(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndWrapper.WndProc(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndSubclass.DispatcherCallbackOperation(System.Object)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.Dispatcher.LegacyInvokeImpl(System.Windows.Threading.DispatcherPriority, System.TimeSpan, System.Delegate, System.Object, Int32)
   at MS.Win32.HwndSubclass.SubclassWndProc(IntPtr, Int32, IntPtr, IntPtr)
   at MS.Win32.UnsafeNativeMethods.DispatchMessage(System.Windows.Interop.MSG ByRef)
   at System.Windows.Threading.Dispatcher.PushFrameImpl(System.Windows.Threading.DispatcherFrame)
   at System.Windows.Application.RunDispatcher(System.Object)
   at System.Windows.Application.RunInternal(System.Windows.Window)
   at Rfx.Riken.OsakaUniv.App.Main()
22
MS-DIAL / Re: MS-DIAL Wish List for 2020-2021!
Hi Hiroshi,
I was reviewing the latest public MSPs (MSMS-Public-Pos-VS14.msp) to understand the “Ontology” meta- information. I wanted to sort the results into compound classes based on the Ontology parameter, but I was not very successful.

Do you think that it would be possible to unify the Ontology classes according to MeSH classification?
Dinesh Barupal did this (http://chemrich.fiehnlab.ucdavis.edu/) and I think that curated classification would make the libraries much more useful. You already have the INCHIKEYs and SMILEs in the file. Some SMILEs and INCHIKEYs are not the "correct" ones that are registered in outher datagases (PubCHem, HMDB, etc.), but I think that (at least for lipids) it could be improved and converted.

Best,
Ondrej