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Topics - Ondrej

MS-DIAL / GitHub platform for MS-DIAL discussions

July 23, 2023, 10:39:05 PM

Hello everyone,
There is a new platform to discuss features, ask questions, give feedback and report a bug:

https://github.com/systemsomicslab/MsdialWorkbench/issues

https://github.com/systemsomicslab/MsdialWorkbench/discussions

https://github.com/systemsomicslab/MsdialWorkbench

Ondrej

MS-DIAL / gap filling problem

March 23, 2023, 07:04:47 AM

Hi,
I am testing MS-DIAL v 5.1.230222 and I found a problem with "Gap filling by compulsion" option.

Quote

Gap filling by compulsion: If you check this, the peak recognition is performed by the average peak width of samples having the metabolite feature even though no local maximum is observed in the chromatogram. This is validated by default.

I do not want it, I switched it OFF.
However, there is peak intensity and peak area value even in case of BLANK, where there is no peak / data at all (see attached image).
It should not be there.
O.

MS-DIAL / benchmark ver 4.9.221218 vs 5.1.230222

March 23, 2023, 05:25:00 AM

Hi,
I processed an identical set of metabolomics data using identical parameters either in ver 4.9.221218 or ver 5.1.230222.

MS-DIAL 4.9.221218 processed 164 files in 7 minutes (from the first "dcl" file to last) and saved the alignment file in next 6 minutes.
Total 13 minutes.

MS-DIAL 5.1.230222 processed 164 files in 20 minutes (from the first to the last) and I canceled the alignment after 60 minutes (CPU at constant ~6.6% and slowly increasing allocated memory ~14.2 GB).
Total 20 + 60...

Update, after fresh restart:
MS-DIAL 5.1.230222 processed 164 files in 19 minutes (from the first to the last) and finished the alignment in 2 hours and 11 minutes.
Total 2 h 20 min.
O.

MS-DIAL / MS-DIAL (ver.5.1.230222) uses only up to 8 threads

March 23, 2023, 03:49:12 AM

Hi,
The computer has 8 CPU cores, thus 16 threads are available.
MS-DIAL 4.92 is fine and uses 16 threads.
MS-DIAL 5.1.230222 uses max 8 threads.
Why there is this limitation?
Thanks,
O.

MS-DIAL / Nomenclature of oxidized lipids (LipidBlast)

September 08, 2022, 04:42:00 AM

Dear Hiroshi,
could you please unify the LipidBlast nomenclature with the recommended format?
(DOI 10.1194/jlr.S120001025, Liebisch et al. JLR, 2020)

I am using MS-DIAL v4.90 (Windows) and the main problem is with the reported oxygens. Using LM notation the 'position' should be before the "O" and the number of oxygens after the "O".

MS-DIAL name is: PI 17:0_18:2;2O
The normalized name at this level should be: PI 17:0_18:2;O2

MS-DIAL: SM 42:2;2O
LipidMaps: SM 42:2;O2

MS-DIAL: ST 29:2;O;S
LipidMaps: ST 29:0;O

Thank you,
Ondrej

MS-DIAL / MrmprobsConsoleApp parameters

November 19, 2021, 08:00:19 AM

Hi Hiroshi,
would it be possible to add a command line option to export the raw matrix data file?
Thank you.
Ondrej

Code: [Select]

Mrmprobs Console App requires the following args:
                                                MrmprobsConsoleApp.exe <analysisType> -i <input folder> -o <output folder> -m <parameter file> -r <reference library file> -d <dia dictionary file (required in abfdia)>
                                                Where: <analysisType>   is one of abfmrm, mzmlmrm, mzmlscan, abfscan, abfdia    (required)
                                                           <input folder>       is the folder containing the files to be processed      (required)
                                                           <output folder>      is the folder to save results   (required)
                                                           <method file>        is a file holding processing properties (required)
                               <reference library file>           is a file containing rt/transition/ratio/range information at tab-delimited text.
                               <dia dictionary file>    is required in DIA-data process containing SCAN/DIA ScanID MzBegin MzEnd information as tab-delimited text

MS-DIAL / MRMPROBS 2.60 view/edit data export problem

November 05, 2020, 08:21:28 AM

Hi Hiroshi,
I found a possible bug. I have one peak close to my analyte RT. When my analyte is not present, MRMPROBS selects the wrong peak nearby. As expected.

Now I want to manually remove the wrong peak.
If I do it in the "View" mode using left and/or right mouse button, raw data matrix shows the value or N.D. Fine.

If I do it in the "Edit" mode and I select no peak, raw data matrix still shows the previous (last) value. And it should be N.D. as above.
Best,
Ondrej

MS-DIAL / MRMPROBS 2.50 max integer problem

October 16, 2020, 02:17:07 AM

Hi Hiroshi,
I found a problem in MRMPROBS 2.50 when the peak is very high.
With some peaks, we reach the limit of 32-bit integer (ranges from -2,147,483,648 to +2,147,483,647).
I see the peak height well, but when I change the info to peak area, I get a negative value.
Thus, when exported as raw matrix, I get zero values.
Could you please change it to 64 bit integer? Thank you.
Ondrej

MS-DIAL / Show ion table

October 09, 2020, 06:41:35 AM

Hi Hiroshi,
I have a problem with "Show ion table" function.
I am not able to use it in some projects. Let's say I have ~800 peaks spots (Blank+, MS2 acquired+, Suggested+) that I need to review.
When I click on the icon, the progress bar "Progress of preparing alignment spot table viewer" stops at random position and never reaches the end. Sometimes is freezes at ~20%, sometimes at ~80%. I can use the X to close the bar and try again.
HW resources are available.
If I completely rebuild the project, it helps sometimes, but sometimes it freezes again. True for multiple versions of MS-DIAL.
Could you please suggest how to find what is wrong?
Thank you,
O.

MS-DIAL / MRMPROBS project cant be reloaded

September 09, 2020, 12:06:53 PM

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

MS-DIAL / carnitine annotation

June 23, 2020, 02:21:49 AM

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 ID	Average Rt(min)	Average Mz	Metabolite name	Adduct type	Post curation result	Fill %	MS/MS assigned	Reference RT	Reference m/z	Formula	Ontology	INCHIKEY	SMILES
1874	0.818	426.35803	CAR 18:1	[M]+	similar chromatogram in higher mz_2018	1	TRUE	3.18	426.35779	C25H48NO4	CAR	HOAMADDCQBUDDY-KHPPLWFENA-O	CCCCCC\C=C/CCCCCCCCCC(=O)OC(CC(O)=O)C[N+](C)(C)C

MS-DIAL / MRMPROBS 2.50 crashes with multiple files and compounds

June 12, 2020, 09:42:37 AM

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()