MSDial_Lipid_Treatment

MSDial_Lipid_Treatment is an open-source tool designed for lipid biomarker detection and annotation following Orbitrap LC-MS/MS DDA analysis. The tool processes mzML format data and identifies biomarkers for two diseases (T and H), as well as common metabolites between them. Additionally, it provides statistical visualizations.

Note: Currently, the code is tailored to work only with the specific metadata conditions of this project. Future updates will support more general metadata and conditions.

Installation

1. Clone the repository or download the ZIP file.
2. Prepare your dataset:
   • Convert raw data to mzML format using MSConvert:
     • Install ProteoWizard: ProteoWizard
     • Convert MS1 data and save the output in:
       • 01.0-MS1mzmlThermo-POS for positive mode (POS) data.
       • 01.0-MS1mzmlThermo-NEG for negative mode (NEG) data.
     • Convert MS2 data and save the output in:
       • 02.0-MS2mzmlThermo-POS for positive mode (POS) data.
       • 02.0-MS2mzmlThermo-NEG for negative mode (NEG) data.
   • Prepare metadata:
     • Create a CSV file (use ; as the delimiter) for each data mode (POS and NEG).
     • Save the files in the 02-Nico_metadata directory.
   • Install MSDIAL:
     • Download and install MSDIAL ver.4.9.221218 Windowsx64: MSDIAL
     • Place the MSDIAL installation in the bin directory and ensure the PATH is set correctly for execution in batch (.bat) files.
   • Prepare the annotation databases:
     • Download the MSP database for NEG and POS from MSDIAL and save it in the 01-mzmlThermo directory.
     • Generate the in-house database for POS and NEG data is in the correct format (TXT).

Parameters and Execution

1. Configure parameters for feature extraction and annotation:

   • Adjust parameters for feature extraction in NEG mode:
     01-mzmlThermo\01.0-MS1mzmlThermo-NEG\NEGparametre.txt
   • Adjust parameters for feature extraction in POS mode:
     01-mzmlThermo\01.0-MS1mzmlThermo-POS\POSparametre.txt
   • Adjust parameters for feature annotation in NEG mode:
     01-mzmlThermo\02.0-MS2mzmlThermo-NEG\M2parametreNEG.txt
   • Adjust parameters for feature annotation in POS mode:
     01-mzmlThermo\02.0-MS2mzmlThermo-POS\M2parametrePOS.txt

2. Run analysis and annotation scripts:

   • Execute MSDial.bat for feature extraction and statistical analysis.
     Note: Both NEG and POS datasets must be ready before running this step.
   • Execute Annotation-MSDial-NEG.bat for annotating NEG features extracted and selected after running MSDial.bat.
   • Execute Annotation-MSDial-POS.bat for annotating POS features extracted and selected after running MSDial.bat.

3. Output:

   • All statistical results and CSV files will be generated in the 04-codeOutput directory.