Skyline message boxes have a Copy button in the lower left corner. If you click that button, it will copy the entire text of the message to the Clipboar including whatever would be shown if you were to push the "More Info" button.

Can you push that button and send us the full text of that message? That full text will include the call stack which will tell us exactly where in the Skyline source code that error is coming from.
The error like "Value cannot be null" nearly is always caused by a bug in our code. If we could see the rest of that message text we would know what to fix in Skyline so that it gives you a helpful error message instead. We would probably also be able to tell you how to work around the problem.
-- Nick

Hi Nick,
Sure. Please refer to the detailed message below.
Thanks,
Q

---------------------------

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An error occurred during protein association.
Value cannot be null.
Parameter name: key
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OK More Info
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System.Reflection.TargetInvocationException: Value cannot be null.
Parameter name: key ---> System.ArgumentNullException: Value cannot be null.
Parameter name: key
   at System.ThrowHelper.ThrowArgumentNullException(ExceptionArgument argument)
   at System.Collections.Generic.Dictionary`2.Insert(TKey key, TValue value, Boolean add)
   at pwiz.Skyline.Model.Proteome.ProteinAssociation.FindProteinMatches(IProteinSource proteinSource, Func`2 digestProteinToPeptides, ILongWaitBroker broker) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Proteome\ProteinAssociation.cs:line 220
   at pwiz.Skyline.Model.Proteome.ProteinAssociation.UseFastaFile(String file, Func`2 digestProteinToPeptides, ILongWaitBroker broker) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Proteome\ProteinAssociation.cs:line 114
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz\pwiz_tools\Skyline\Util\Util.cs:line 1926
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.EditUI.AssociateProteinsDlg.UseFastaFile(String file) in C:\proj\pwiz\pwiz_tools\Skyline\EditUI\AssociateProteinsDlg.cs:line 502
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Could you send me your FASTA file?

It looks like that error could be caused by a protein name being blank. I am not sure whether the protein name I'm talking about is coming from your FASTA file, or from somewhere else.

If your FASTA file is less than 50MB you can attach it to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url

It might also be helpful if you could send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.

The particular line of code that the error is happening on is new code that was added to Skyline a few months ago (part of the "Group at gene level" new feature, although this code gets executed regardless of whether you check that option).
-- Nick

I used some data from a non-proprietary molecule to avoid IP issue and was able to reproduce the same error message as reported. I have upload NIST fasta.fasta and the D_NIST.sky file through the link you provided above. I searched some of the previous projects without this error and there was no change made to the format of the fasta files used now. Thanks a lot for your help!

I forgot to mention that I also uploaded the sky file in name D_NIST.sky.zip. Thanks.

The space before the protein name ("> light chain") is the problem. The name should come immediately after the ">". I think we'll fix Skyline's FASTA parser to be tolerant of spaces there, but see if that fixes your problem for now.

Hi Matt,
It did fix the reported error. When I doublechecked, it seems that I have used both forms of fasta w/ and w/o the space to get it to work before but I will remember to not include the space after > in the protein name.
Thanks,
Qing