Data preparation
File conversion
Raw LC-MS data need to be converted to mzML or mxXML format for further processing in MassCube.
We recommend to use MSConvert for file conversion.
Download and install MSConvert
Visit the official website to download ProteoWizard.
File conversion using MSConvert
Step 1. Set options
Check the boxes as shown in Fig. 1.
Step 2. Set the Peak Picking filter
Step 3. Add the Peak Picking filter
Step 4. Browse and load files
Step 5. Start conversion
By default, the converted files will be saved in the same directory as the raw files.
Convert files in command line mode
Parameter file
A parameter file (.csv) is used to set parameters for the workflow. A templete is provided here. If not provided, the default parameters will be applied. For MassCube version 1.0 or earlier, please use this template.
Sample table
A sample table (.csv) is used to claim the name of samples and their groups including biological groups, quality control samples, or blank samples. A templete is provided here. For MassCube version 1.0 or earlier, please use this template
For large-scale metabolomics data, it’s not easy to prepare the sample table manually. In MassCube, we provide a function to automatically generate the sample table based on the file names in the data folder, and users can further define the groups.
Automatically generate sample table
In the project folder, open a terminal and run the following command:
generate-sample-tableYour project folder should include a subfolder named data that contains the raw LC-MS data files in mzML or mzXML format.
my_project
├── data
│ ├── sample1.mzML
│ ├── sample2.mzML
| └── ...
|── ...