singjust/mobidik repository overview

Refer to Mobi-DIK documentation⁠ at openswath.org⁠ for full documentation and information.

⁠MOBI-DIK Data Conversion

For the Mobi-DIK workflow, the generated .tdf files from diaPASEF runs can be converted to standard formats (mzML) with diapysef. Make sure diapysef is installed before you proceed.

Using the script convertTDFtoMzML.py can convert the .tdf file to a single mzML file. It allows merging of frames for the same precursors, filtering of range of frames, splitting of files by overlapping window settings, and compression of data with PyMSNumpress.

⁠Inputs

• -a: Analysis directory of the raw data (.d) (Required)
• -o: Output filename (Required)
• -m: Number of frames for merging
• -overlap: Number of overlapping windows
• -r: Range of frames to convert

For detailed options and descriptions, simply type:

   convertTDFtoMzML.py --help

⁠Example

   data_dir=diaPasef_run.d
   output_file='diaPasef_run.mzML'

   convertTDFtoMzML.py -a=$data_dir -o=$output_file

The converted mzML files can be processed with the assay library in OpenSwathWorkflow.

⁠Example Data Conversion

docker run -it --rm -v `pwd`:/data/ singjust/mobidik:latest convertTDFtoMzML -a /data/diaPasef_run.d -o /data/diaPasef_run.mzML --overlap=2