Search peptidomics diaPASEF data with fasta generated library

Describe the issue or question:

I am currently using the DIA_SpecLib_Quant workflow with diaPASEF data. Since my sample is comprised of endogenous peptides, I have set enzyems to null in MSFragger. My goal is to create a spectral library from the fasta file and use this in-silico spectral library to quantify my results in DIA-NN. However, FragPipe will not let me proceed without specifying a spectral library even though the interface says it is optional. Is what I am trying to do even possible in FragPipe?

[https://github.com/Nesvilab/FragPipe/issues/1022] In a previous post, chris-discopharma said inputting "" for the optional spectral library can bypass the issue but I got an error.

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

java.nio.file.InvalidPathException: Illegal char <"> at index 0: "" at java.base/sun.nio.fs.WindowsPathParser.normalize(Unknown Source) at java.base/sun.nio.fs.WindowsPathParser.parse(Unknown Source) at java.base/sun.nio.fs.WindowsPathParser.parse(Unknown Source) at java.base/sun.nio.fs.WindowsPath.parse(Unknown Source) at java.base/sun.nio.fs.WindowsFileSystem.getPath(Unknown Source) at java.base/java.nio.file.Path.of(Unknown Source) at java.base/java.nio.file.Paths.get(Unknown Source) at com.dmtavt.fragpipe.cmd.CmdDiann.configure(CmdDiann.java:247) at com.dmtavt.fragpipe.FragpipeRun.lambda$configureTaskGraph$68(FragpipeRun.java:1851) at com.dmtavt.fragpipe.FragpipeRun.configureTaskGraph(FragpipeRun.java:1974) at com.dmtavt.fragpipe.FragpipeRun.run(FragpipeRun.java:313) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:179) at jdk.internal.reflect.GeneratedMethodAccessor39.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:517) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:511) at org.greenrobot.eventbus.AsyncPoster.run(AsyncPoster.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

Nesvilab / FragPipe

Search peptidomics diaPASEF data with fasta generated library #1442