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Prepare MS data

Prepare MS data

Convert raw data files

Raw mass spectrometry data need to be converted to centroid mzML or mxXML format for MassCube data processing.

We recommend to use MSConvert for file conversion.

Visit the official website to download ProteoWizard and install MSConvert.

Fig. 1. MSConvert GUI

Step 1. Set options

Check the boxes as shown in Fig. 1.

⚠️
Do NOT check Use zlib compression.

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.

Generate a sample table

In the project folder, open a terminal and run the following command:

generate-sample-table

Your 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
| └── ...
|── ...

Set yes in the ‘is_blank’ column for blank samples, and yes in the ‘is_qc’ column for quality control (QC) samples. You can add more columns to the sample table to claim biological groups or other information. For example, you can add a column named ’treatment’ to claim the treatment of each sample like drug A, drug B, or control. Example:

name is_blank is_qc treatment
sample1 no no drug A
sample2 no no drug B
sample3 no no control
QC1 no yes NA
QC2 no yes NA
blank1 yes no NA
blank2 yes no NA
Set parameters