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The current behaviour of LipidCreator when transitions lists that contain CEs for a subset of transitions only, setting the remaining ones to -1, is not well defined. It may be necessary to not export the CE column at all, once transitions are included that have no CE set. See #15 for more details on the discussion. Exporting -1 values as of now may cause vendor-dependent interpretation of what that value actually means. We should carefully check that this does not have unwanted side-effects. Unfortunately, we may not be able to avoid this issue completely, since users may export and transfer multiple transitions lists from LipidCreator to Skyline, thereby mixing transitions with proper CEs and ones without any CE.

Manually editing collision energies in the final transition review table is possible but extremely tedious beyond ten or so transitions.

Since the CEs could be transitively assigned on the Lipid Precursor Level, we could think about adding an additional column to allow manual assignment of CEs.
Alternatively, the final "Lipid Transitions Review" dialog could add a filter box for e.g. precursor names and copy / paste functionality for the "Explicit" column to easier set the same value for all transitions.

I used the ‘isotope suffix’ +[2]H5 for the FA1 chain

I want to use the same ‘isotope suffix’ +[2]H5 for the FA2 chain,
Given that the tracer FA 16:0(+[2]H5) can be converted in vivo to FA 18:0(+[2]H5).
But I cannot (without a workaround).

I suppose the same bug exists for TAGs and CLs… where it could be likely to have 2-3-4 labelled FA chains in an intact molecule.

What about PC 16:0-d5/16:0-d5… would probably happen in lung tissue?

Skyline 21.1 with LipidCreator 1.2.0.772 throws the following exception when I try to send a transition list to Skyline.

2021-06-09 16:30:51,855 [1] INFO  LipidCreator.LipidCreator - LipidCreator is connected to Skyline file: ''
2021-06-09 16:30:51,869 [1] INFO  LipidCreator.LipidCreator - Running LipidCreator version 1.2.0.772 in skyline tool mode on Win32NT
2021-06-09 16:30:51,869 [1] INFO  LipidCreator.LipidCreator - Using C:\Users\Nils Hoffmann\AppData\Local\Apps\2.0\MPQT09M7.MR0\O893NBD3.RW2\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\LipidCreator as base directory for relative resource lookup. Resolved executing assembly location: C:\Users\Nils Hoffmann\AppData\Local\Apps\2.0\MPQT09M7.MR0\O893NBD3.RW2\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\LipidCreator\LipidCreator.exe
2021-06-09 16:30:51,870 [4] INFO  LipidCreator.LipidCreator - Opening connection to Skyline through pipe f909f6a6-06db-4e86-a1ea-2f81d9529f3c
2021-06-09 16:30:51,878 [4] INFO  LipidCreator.LipidCreator - Connected to Skyline through pipe f909f6a6-06db-4e86-a1ea-2f81d9529f3c
2021-06-09 16:31:05,296 [1] ERROR LipidCreator.LipidCreator - An error occured, data could not be sent to Skyline, please check if your Skyline parameters allow precursor masses up to 1464.8057Da.
System.Reflection.TargetInvocationException: Ein Aufrufziel hat einen Ausnahmefehler verursacht. ---> System.Reflection.TargetInvocationException: Ein Aufrufziel hat einen Ausnahmefehler verursacht. ---> System.IO.IOException: Data columns not found in first line.
   bei System.Windows.Forms.Control.MarshaledInvoke(Control caller, Delegate method, Object[] args, Boolean synchronous)
   bei System.Windows.Forms.Control.Invoke(Delegate method, Object[] args)
   --- Ende der internen Ausnahmestapel�berwachung ---
   bei System.RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)
   bei System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)
   bei System.Reflection.RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)
   bei SkylineTool.RemoteService.ProcessClientThread(Object streamArg) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\SkylineTool\RemoteService.cs:Zeile 95.
   --- Ende der internen Ausnahmestapel�berwachung ---
   bei SkylineTool.RemoteClient.RemoteCallName(String methodName, Object[] arguments)
   bei LipidCreator.LipidCreator.sendToSkyline(DataTable dt, String blibName, String blibFile)
2021-06-09 16:31:18,122 [1] INFO  LipidCreator.CreatorGUI - Closing LipidCreator!
2021-06-09 16:31:18,123 [1] INFO  LipidCreator.LipidCreator - Disposing SkylineToolClient!

If I add a custom isotope group for SM, .e.g SM 18:1;2/18:1(d9) with [M+H]1+ and filters (precursor only, only heavy) to the lipid list, it does not not display the "+ heavy isotopes" string under "Options". When I proceed, it is clearly visible in the Lipid Precursor Review dialog.

Every time when a project file is open / saved, the dialog starts with a default directory. It should remember the latest directory that was used before.

In order to be able to cross-check packages containing LipidCreator, the binary should also output its full version information and Git commit hash on the command line with the -v or --version switch.

Fragment m/z 361 and 375 missing…?
Are other low abundant fragment m/z values between 239 and 511 calculated correctly?
Fragment ion nomenclature is also somewhat misleading/incorrect.

Hi, I have a problem with generating spectral library from lipids other than Lipid Mediators. When I try to export the spectral library of for example SMs and send it to skyline / or even export and import manually, it's either empty or half empty.

In general, I need only precursor peaks (m, m+1 and m+2) and I managed to generate a library with these ions (through error messages) but when I import any raw file, it crashes with a report that the library is empty (although I see that these three ions are present).
I got this errors :

FIRST ERROR

Skyline version: 22.2.0.351-28f9b9301 (64-bit)
Installation ID: 65ccb65e-31f1-4508-aef5-8a24be1c7ce4
Exception type: Exception
Error message: Failed loading library 'C:\Users\admin\AppData\Local\Apps\2.0\54Y9TB26.H5C\JKRJ99XD.B21\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\Tools\LipidCreator..\Temp\test.blib'.
Specified cast is not valid.
Format: BiblioSpec
FileRevision: 0
SchemaVersion: 0
FilePath: Generated By LipidCreator

System.Exception: Failed loading library 'C:\Users\admin\AppData\Local\Apps\2.0\54Y9TB26.H5C\JKRJ99XD.B21\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\Tools\LipidCreator..\Temp\test.blib'.
Specified cast is not valid.
Format: BiblioSpec
FileRevision: 0
SchemaVersion: 0
FilePath: Generated By LipidCreator ---> System.InvalidCastException: Specified cast is not valid.
at System.Data.SQLite.SQLiteDataReader.VerifyType(Int32 i, DbType typ)
at System.Data.SQLite.SQLiteDataReader.GetInt32(Int32 i)
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.CreateCache(ILoadMonitor loader, IProgressStatus status, Int32 percent) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 624
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(ILoadMonitor loader, IProgressStatus status, Boolean cached) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 1034
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(ILoadMonitor loader, IProgressStatus status, Boolean cached) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 1200
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(ILoadMonitor loader) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 995
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(BiblioSpecLiteSpec spec, ILoadMonitor loader) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 150
at pwiz.Skyline.Model.Lib.LibraryManager.LoadLibrary(LibrarySpec spec, Func`1 getMonitor) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\Library.cs:line 298
at pwiz.Skyline.Model.Lib.LibraryManager.LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\Library.cs:line 123
at pwiz.Skyline.Model.BackgroundLoader.OnLoadBackground(IDocumentContainer container, SrmDocument document) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\BackgroundLoader.cs:line 130
Exception caught at:
at pwiz.Skyline.Model.BackgroundLoader.OnLoadBackground(IDocumentContainer container, SrmDocument document) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\BackgroundLoader.cs:line 130
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.Threading.ThreadHelper.ThreadStart()

SECOND ERROR

Skyline

An error occurred attempting to import the test library.
Failed loading library 'C:\Users\admin\AppData\Local\Apps\2.0\54Y9TB26.H5C\JKRJ99XD.B21\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\Tools\LipidCreator..\Temp\test.blib'.
Specified cast is not valid.
Format: BiblioSpec
FileRevision: 0
SchemaVersion: 0
FilePath: Generated By LipidCreator

I looked for solution everywhere and could not find help.

I contacted Skyline support, they told me that problem is that .blib file is empty.
They wrote me this :
I see that the value in the "NumSpectra" column is NULL, which causes problems for Skyline. I should probably contact the Lipid Creator programmers and tell them to fix this. The .blib file does not contain any spectra, so, even if you were able to get it to work with Skyline, it would not be useful because it is empty. It might be that there is a different problem going on which is causing that .blib file to be empty.

Let me know if you could help me with this.
Otherwise, this is a great and useful piece of software ! Thank you :)
Dominika

When I run the latest LipidCreator build (https://github.com/lifs-tools/lipidcreator/actions/runs/767101082) or a locally built version and start an interactive Tutorial, e.g. the PRM Tutorial, LipidCreator crashes after I click on "Continue":

2021-04-20 14:32:06,947 [1] INFO  LipidCreator.LipidCreator - Running LipidCreator version 1.1.2.769 in standalone mode on Unix
2021-04-20 14:32:06,955 [1] INFO  LipidCreator.LipidCreator - Using /home/nilshoffmann/Downloads/LipidCreator(1)/LipidCreator as base directory for relative resource lookup. Resolved executing assembly location: /home/nilshoffmann/Downloads/LipidCreator(1)/LipidCreator/LipidCreator.exe
System.ArgumentException: A null reference or invalid value was found [GDI+ status: InvalidParameter]
  at System.Drawing.GDIPlus.CheckStatus (System.Drawing.Status status) [0x00098] in <345861cc94284a0bb0f2f2528d6cd247>:0 
  at System.Drawing.Graphics.DrawImage (System.Drawing.Image image, System.Int32 x, System.Int32 y, System.Int32 width, System.Int32 height) [0x00025] in <345861cc94284a0bb0f2f2528d6cd247>:0 
  at System.Drawing.Graphics.DrawImage (System.Drawing.Image image, System.Drawing.Rectangle rect) [0x0002c] in <345861cc94284a0bb0f2f2528d6cd247>:0 
  at (wrapper remoting-invoke-with-check) System.Drawing.Graphics.DrawImage(System.Drawing.Image,System.Drawing.Rectangle)
  at System.Windows.Forms.Control.DrawToBitmap (System.Drawing.Bitmap bitmap, System.Drawing.Rectangle targetBounds) [0x000f4] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at (wrapper remoting-invoke-with-check) System.Windows.Forms.Control.DrawToBitmap(System.Drawing.Bitmap,System.Drawing.Rectangle)
  at System.Windows.Forms.Control.DrawToBitmap (System.Drawing.Bitmap bitmap, System.Drawing.Rectangle targetBounds) [0x000c2] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at (wrapper remoting-invoke-with-check) System.Windows.Forms.Control.DrawToBitmap(System.Drawing.Bitmap,System.Drawing.Rectangle)
  at LipidCreator.Overlay.update (System.Drawing.Point location, System.String dir) [0x00106] in <3e436ff1f24d4c638595dddbede6f7c3>:0 
  at (wrapper remoting-invoke-with-check) LipidCreator.Overlay.update(System.Drawing.Point,string)
  at LipidCreator.Tutorial.TutorialSRMStep () [0x00287] in <3e436ff1f24d4c638595dddbede6f7c3>:0 
  at LipidCreator.Tutorial.nextTutorialStep (System.Boolean forward) [0x00039] in <3e436ff1f24d4c638595dddbede6f7c3>:0 
  at LipidCreator.TutorialWindow.nextTutorialWindow (System.Object sender, System.EventArgs e) [0x0000d] in <3e436ff1f24d4c638595dddbede6f7c3>:0 
  at System.Windows.Forms.Control.OnClick (System.EventArgs e) [0x00019] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Button.OnClick (System.EventArgs e) [0x00011] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.ButtonBase.OnMouseUp (System.Windows.Forms.MouseEventArgs mevent) [0x00069] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Button.OnMouseUp (System.Windows.Forms.MouseEventArgs mevent) [0x00000] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Control.WmLButtonUp (System.Windows.Forms.Message& m) [0x00078] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Control.WndProc (System.Windows.Forms.Message& m) [0x001b4] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.ButtonBase.WndProc (System.Windows.Forms.Message& m) [0x00037] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Button.WndProc (System.Windows.Forms.Message& m) [0x00000] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Control+ControlWindowTarget.OnMessage (System.Windows.Forms.Message& m) [0x00000] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.Control+ControlNativeWindow.WndProc (System.Windows.Forms.Message& m) [0x0000b] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
  at System.Windows.Forms.NativeWindow.WndProc (System.IntPtr hWnd, System.Windows.Forms.Msg msg, System.IntPtr wParam, System.IntPtr lParam) [0x00085] in <6d635ac3dc1c4424ad385ded79f1e868>:0 
2021-04-20 14:32:26,169 [1] INFO  LipidCreator.CreatorGUI - Closing LipidCreator!

This happens on Ubuntu 20.04 with the latest Mono version:

Mono JIT compiler version 6.12.0.122 (tarball Mon Feb 22 17:33:28 UTC 2021)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
	TLS:           __thread
	SIGSEGV:       altstack
	Notifications: epoll
	Architecture:  amd64
	Disabled:      none
	Misc:          softdebug 
	Interpreter:   yes
	LLVM:          yes(610)
	Suspend:       hybrid
	GC:            sgen (concurrent by default)

I was surprised that my ‘search settings’ were not saved automatically!

Incl my recent ‘manage heavy isotopes’ for a particular lipid class…

When adding plasmalogens, e.g. PC O-a or -p, only one FA chain is added to the Lipid list.

While Skyline users will receive a visual cue that an updated version of LipidCreator is available from the ToolStore, users of the standalone version will not receive any notification at the moment.
It would be great if we could either check GitHub's releases API

Using a GET request with the HTTP Header Accept=application/json, the endpoint https://github.com/lifs-tools/lipidcreator/releases/latest returns

{
  "id": 48720087,
  "tag_name": "787",
  "update_url": "/lifs-tools/lipidcreator/releases/tag/787",
  "update_authenticity_token": "JLhrOeswHJxqD5oNBOh5bdu7UsoLtb7Z35M3Rdi5QFozpBeToO0UdC2PDeYHEYPTV59Onp8TEJvJNo3gzOqI4Q==",
  "delete_url": "/lifs-tools/lipidcreator/releases/tag/787",
  "delete_authenticity_token": "l6icnoZAaE83n8Km2Ka71vJPT2veQjT+KxbMSfoi5GU9qlmN5zgj/KOUWNBHt6aSNq78Dcl/OVBPwPSqhkn0KQ==",
  "edit_url": "/lifs-tools/lipidcreator/releases/edit/787"
}

Since our build numbers are strictly increasing, this can be checked against LipidCreator's internal build number. If the latest release number is greater, an update is available.

This happens for the LipidMapsTest.cs:

The file 'test/lipidmaps.csv' in line '31322' could not be read:
The given key 'Ch' was not present in the dictionary.

This error should either be caught if it is expected, or it should lead to a non-zero exit code of the testsuite.

In order to allow for an easier customization of LipidCreator, an additional "Custom" tab could be added that allows the user to define new lipid classes with a defined headgroup (sum formula) + FA / LCB and corresponding fragment templates.

This would make it easier for users to also provide new lipid classes and fragments for proper inclusion and attribution in LipidCreator. Potentially, allowing to add these as SMILES would make it easier to use as well.

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