Documentation
Untargeted metabolomics
Set parameters

Set parameters

Download the default parameters. Make sure to check and adjust the following three key parameters:

ion_mode

Set to “positive” or “negative”.

ms1_abs_int_tol

You may use 30000 for Orbitrap data, and 1000 for TOF data.

ms2_library_path

The absolute path to the MS/MS database file (e.g. D:/databases/ms2_library.mzML).

Key parameters

Here we summarized six most important parameters in masscube for untargeted metabolomics data processing:

  1. mz_tol_ms1: the mass tolerance for MS1 feature detection. 0.005-0.01 Da is recommended.
  2. ms1_abs_int_tol: the intensity tolerance for MS signals. 1000 is recommended for TOF data, and 30000 is recommended for Orbitrap data.
  3. mz_tol_alignment: the mass tolerance for feature alignment. 0.01-0.015 Da is recommended.
  4. rt_tol_alignment: the RT tolerance for feature alignment. 0.1-0.3 min is recommended.
  5. ms2_sim_tol: the threshold for MS/MS similarity score. 0.7-0.8 is recommended.
  6. ms2_library_path: the MS/MS library for MS/MS annotation.

More about parameters

Explanation of the commonly used parameters for the untargeted-metabolomics workflow can be found here.

For more tunable parameters, please refer to the API documentation or the source code in the params module.

Make a sample tableAbout MS/MS database