FragPipe could not download MSFragger with message error like the image. I manually download MSFragger and put it under Tools folder of FragPipe, but when I browse the folder by FragPipe, I could not see .jar document in MSFragger folder.

Question

FragPipe could not download MSFragger with message error like the image. I manually download MSFragger and put it under Tools folder of FragPipe, but when I browse the folder by FragPipe, I could not see .jar document in MSFragger folder.

Closed this issue a month ago · 4 comments

- FragPipe could not download MSFragger with message error like the image. I manually download MSFragger and put it under Tools folder of FragPipe, but when I browse the folder by FragPipe, I could not see .jar document in MSFragger folder.Describe the issue or question:

Answer 1 · 2024-06-12T20:33:25.000Z

Could you try again?

Thanks,

Fengchao

Answer 2 · 2024-06-12T20:36:10.000Z

Before I received your email, I downloaded MSFragger in FragPipe. But I am unsure how it worked because I also re-installed JAVA JDK and JRE.

Answer 3 · 2024-06-12T20:43:50.000Z

After I downloaded the MSFragger and configured it through browse in FragPipe. I navigated to ..\fragpipe 22-0\fragpipe\tools\MSFragger-4.1 and could not see MSFragger-4.1.jar. However, when I navigated to the same folder on my local disk, I could see the MSFragger-4.1.jar execution file. Sorry for asking so many questions; I am a beginner

Answer 4 · 2024-06-12T21:23:22.000Z

No worries. You just need to specify the folder of the tools, not the path of the jar files, in FragPipe.

Best,

Fengchao