Closed rugenni closed 2 months ago
@KaiLiCn , could you take a look when you get a chance?
Note that it is a DDA+ search with the ddaPASEF data. PDV was supposed to look at the *_uncalibrated.mzML
files, and there were multiple ranks per scan.
Best,
Fengchao
Hi Nils,
Could you also share the Fragpipe.workflow
file inside your result folder with me?
Kai
Hi Nils,
I fixed the bug. Could you try the latest version of FragPipe-PDV? You could find it here: https://github.com/Nesvilab/FragPipe-PDV/tree/V1.2.2 . There is a README
showing how to update it mannually inside FragPipe. We also update a tutorial file. You could find everything there.
Let me know if you have any iusse when you update it.
Kai
Hi Kai and Fengchao,
thank you very much for your quick help, everything is working now.
Best, Nils
log_2024-07-01_16-12-19.zip
Hi,
I processed three timsTOF .d files with FragPipe 22 using the LFQ-phospho workflow. When I try to open Fragpipe-PDV I get the error message "Invalid spectrum file path, please check it". All files are located within the same folder, I did not move any file. I noticed some warnings during PTMProphet like "chmod 664 interact-Steffi_A_rank5.mod.pep.xml" failed: Operation not permitted". Is this a known problem? (I ran FragPipe on a Windows 10 PC as Administrator).
Many thanks, Nils