Parameters

masscube provides default parameters for users to start with. Download the default parameters. You only need to change two settings based on your data:

ion_mode

“positive” or “negative”

ms1_abs_int_tol

30000 for Orbitrap data, and 1000 for TOF data.

ms2_library_path

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:

MS1 mass tolerance: the mass tolerance for MS1 feature detection. 0.005-0.01 Da is recommended.
Intensity tolerance: the intensity tolerance for MS signals. 1000 is recommended for TOF data, and 30000 is recommended for Orbitrap data.
Mass tolerance for alignement: the mass tolerance for feature alignment. 0.01-0.015 Da is recommended.
RT tolerance for alignment: the RT tolerance for feature alignment. 0.1-0.3 min is recommended.
MS/MS similarity score threshold: the threshold for MS/MS similarity score. 0.7-0.8 is recommended.
MS/MS library: the MS/MS library for MS/MS annotation.

More about parameters

For advanced programming users, much more parameters in masscube are tunable. Please refer to the API documentation for more details.

Data preparation Database