search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
184 stars 37 forks source link

Invalid Spectrum File Path #1777

Closed Rachitha17 closed 4 days ago

Rachitha17 commented 1 week ago

- Upload your log file log_2024-09-09_11-51-34.txt

I keep getting an error " Invalid Spectrum File Path", kindly help! Below is the screenshot Screenshot 2024-09-09 115504 Screenshot 2024-09-09 115646

KaiLiCn commented 1 week ago

Hi,

Looks like you didn't finish the search correctly. Can you check your searching parameters and run FragPipe again? FragPipe-PDV only works on completed search result. If you are new to the FragPipe, please follow our tutorial. https://fragpipe.nesvilab.org/

Kai

Rachitha17 commented 1 week ago

Thank you so much I shall try again

Rachitha17 commented 1 week ago

I would like to know if Fragpipe supports Bruker .d files, or do you recommend converting to mzmL format

fcyu commented 1 week ago

It support .d files, but we don't recommend converting .d to mzML format.

Best,

Fengchao

Rachitha17 commented 1 week ago

The bruker instrument used is not ddaPASEF, it was mentioned in the tutorial that other .d files need to converted to mzmM files, any guidance on this!

Thank you, Rachitha

fcyu commented 1 week ago

Oh, if it is neither ddaPASEF nor diaPASEF, which means no ion mobility separation, then you need to convert it to mzML.

Best,

Fengchao

Rachitha17 commented 1 week ago

Thank you so much