Issue loading Fragpipe results into PDV

[etetruck]

Hello, I am trying to load previous Fragpipe results into the standalone PDV viewer. I add the psm.tsv and mzml files generated by diatracer (these are timsTOF data). I get the error "failed to parse MSfrage result,please check your file".
Any idea what the issue could be please?

I could open these in the FP-PDV, but it freezes after a few seconds so I cannot really browse the results.

[KaiLiCn]

Hi,

The PDV has been integrated into FragPipe and it supports the visualization in FragPipe after searching. Here is the tutorial: https://github.com/Nesvilab/FragPipe-PDV/blob/master/FragPipe-PDV%20tutorial.pdf

Kai

[etetruck]

Hi Kai,

Thank you for answering. My issue with the integrated PDV is that it always completely freezes after a few second of opening the results from Fragpipe so I cannot do anything (cannot select proteins, cannot close, etc). This is why I wanted to try the standalone to see if that could potentially help. Any advice as to how to open the results with the standalone?
Many thanks!

[KaiLiCn]

I am not sure if the standalone version can still handle the result from the newer version of FragPipe.

Can you tell me which version of FragPipe you are using right now? If FragPipe-PDV is frozen, you can close the main FragPipe. Then there might be an error dialog showing up. There is a thread-confict if some thing is wrong in your result folder.

You can also share your FragPipe log file with me.

Kai