Make 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

Convert raw MS data Set parameters