Error Loading Bruker .d File in FragPipe

[elena-atanasoska]

log_2025-01-03_21-37-47.txt

While attempting to load the Bruker .d file (20240925_TMA3_H239-WK8.d) in FragPipe, the following error occurred:

Could not load file C:\Users\elena\MS\20240925_TMA3_H239-WK8.d. The file may be corrupted.
java.lang.IllegalArgumentException: Not a valid pathDir for Bruker data directory
at umich.ms.fileio.filetypes.bruker.BrukerTdfFile.(BrukerTdfFile.java:70)
at umich.ms.fileio.filetypes.bruker.BrukerTdfFileBase.(BrukerTdfFileBase.java:70)
...
Caused by: java.lang.IllegalArgumentException: Bruker data dir must contain an analysis.tdf file
at umich.ms.fileio.filetypes.bruker.BrukerTdfFile.(BrukerTdfFile.java:66)

I have attached a picture of the contents of my .d file.

Thanks!

[fcyu]

There is no analysis.tdf file in your .d folder. Is that from ddaPASEF or the traditional mass spectrometry without ion mobility separation? If it is from the traditional mass spectrometry, you need to convert it to the mzML format using msconvert.

Best,

Fengchao

[elena-atanasoska]

This is the folder i am trying to convert

but nothing is shown

[fcyu]

I think your .d folder was corrupted so that there are no MS data.

Best,

Fengchao

[anesvi]

I frequently find that .d folders downloaded from ProteomeXchange are corrupted. Maybe FragPipe can give a better error message if the file is corrupted