Metabolomics Society Forum

Hi everyone,

Is it possible to run the IBF converter from the command line without the GUI? We'd love to batch convert the timsTOF files as a part of a pipeline.

Thanks!
Wen Yu

I am sorry that I couldn't help you for the command line. but i would like to know more detail. could you please tell me which instrument did you use and what is the data format you have for IBFconverter?

Hi Sukis,

We are using the timsTOF instrument from Bruker. The "*.d" raw files it produces can be converted flawlessly to *.ibf files when we drag-n-drop the file folders onto the IBF converter. We'd just like to run this step in a script from the command line if possible.

Thanks!

many thanks. we are using Waters Vion. data is obtained by UNIFI and it is tricky to convert the data.

Hi WenYu and Sukis,

I quickly made the command line version.
https://briefcase.riken.jp/public/M98cQApnakhAV1c
Try to use this first, please?
Type like:

IbfConverterConsoleApp.exe -i <input folder> -o <output folder> -c <abundance cut off>
                  Where: <input folder>   is the folder containing the files to be processed   (required)
                        <output folder>   is the folder to save results   (option). Result files are exported in the same directory for input folder as default.
                        <abundance cut off>   is an abundance cut off parameter.  (option) Zero is used as default

Thanks,

Hiroshi

good! many thanks.

Thanks so much! I'll give it a try.