Fengchao

Thanks for the issue report. It seems that DIA-NN 1.9 changed the speclib file name? ```shell [2024/06/13 17:36:39] Creating spectral library from files: [2024/06/13 17:36:39] library.tsv.skyline.speclib Process java.lang.ProcessBuilder@34f7cfd9 returned non...

Thanks for the prompt reply. It seems that FragPipe got a new speclib file name that we/Skyline don't expect: `--import-search-file=E:\FragPipe-v22-test\proteome_anotherattempt\library.tsv.skyline.speclib`. I will investigate tomorrow and get back to you ASAP....

It should be fixed in https://github.com/Nesvilab/FragPipe/releases/tag/23.0 Best, Fengchao

It is due to the version incompatibility. Could you upgrade FragPipe, MSFragger, and IonQuant to the latest version? Thanks, Fengchao

Have you configured Python, installed EasyPQP, and enabled the spectral library building module? Thanks, Fengchao

You probability could disable MSBooster because the labeled peptides won't have good predicted retention time and intensities. But I will let @yangkl96 to take a look to make MSBooster more...

Thank for the bug report. We are aware of this bug. Will fix it soon. Best, Fengchao

This bug has been fixed in https://github.com/Nesvilab/FragPipe/commit/9614455f2a2cea695d195b29b1b2bc2e6684554c If you want to try the pre-released version, please send an email to yufeATumich.edu (replace `AT` with `@`). Thanks, Fengchao

Somehow I couldn't find the issue question on GitHub, so I will just reply to this email. You only run IonQuant with the existing temp files. FragPipe extracts and collects...

Closing the GitHub issue is not the reason for not finding it, because it is still there and replyable. I can see your latest reply by clicking the [view it...