Dear Skyline Team,

I'm encountering a bug while importing precursor lists using Skyline CMD - could you help me finding a solution?

I'm using the following command:

"D:\Software\Skyline\SkylineRunner.exe" ^
    --in="test.sky" ^
    --import-pep-list="seq_for_sky.txt" ^
    --out="test.sky"

This gives me the error: "Object reference not set to an instance of an object.".

The imported list looks the following:
C[+57]L[+7]ADVVVK[+8]I++
EL[+7]C[+57]SQP[+6]AE+
AL[+7]HPALP[+6]TA+
K[+8]M[+16]M[+16]DAKEK[+8]V++
EC[+57]GP[+6]QILLL[+7]++
SLR[+10]EEA[+4]TV++
LLLG[+3]DHP[+6]EAA++
SL[+7]WPV[+6]ISATWEA++
THL[+7]AAM[+16]DA[+4]+

Interestingly, when I remove the entries EC[+57]GP[+6]QILLL[+7]++ and THL[+7]AAM[+16]DA[+4]+ (which have the label at the last position), it works. Similarly, removing only the label at the last position also works.

Also just pasting the content of the txt file into a Skyline document produces the same error with this description:
Skyline (64-bit) 24.1.0.199 (6a0775ef83)

System.Reflection.TargetInvocationException: Object reference not set to an instance of an object. ---> System.NullReferenceException: Object reference not set to an instance of an object.
   at pwiz.Skyline.Model.PeptideGroupBuilder.AppendSequence(String seqMod) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Import.cs:line 3007
   at pwiz.Skyline.Model.FastaImporter.Import(TextReader reader, IProgressMonitor progressMonitor, Int64 lineCount) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Import.cs:line 178
   at pwiz.Skyline.Model.SrmDocument.ImportFasta(TextReader reader, IProgressMonitor progressMonitor, Int64 lines, ModificationMatcher matcher, IdentityPath to, IdentityPath& firstAdded, IdentityPath& nextAdded, Int32& emptiesIgnored) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1431
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass814_0.<ImportFasta>b__2(IProgressMonitor longWaitBroker) in C:\proj\skyline_24_1\pwiz_tools\Skyline\SkylineFiles.cs:line 1792
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_24_1\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\skyline_24_1\pwiz_tools\Skyline\Util\Util.cs:line 1926
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.SkylineWindow.ImportFasta(TextReader reader, Int64 lineCount, Boolean peptideList, String description, ImportFastaInfo importInfo) in C:\proj\skyline_24_1\pwiz_tools\Skyline\SkylineFiles.cs:line 1794
   at pwiz.Skyline.Menus.EditMenu.Paste(String text) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Menus\EditMenu.cs:line 535
   at pwiz.Skyline.Menus.EditMenu.Paste() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Menus\EditMenu.cs:line 345

So I suspect there is a bug with the combination of labeling at the last position & defined precursor charge state. As suggested in other posts in the support, I tried different separators between the peptide sequence/label and the charge state, but unfortunately none of them worked.

I attached the txt as well as my (blank) Skyline document for reproducibility and would be super grateful for a solution!

Thanks for your always amazing support! Cheers
Jonas