Questions on masscube

[Ivy-ops]

Hi Developer,

Thank you for creating this excellent software — it’s impressively fast!

After reviewing the tutorial, I have a few questions:

(1) I have positive- and negative-mode data, with each mode containing three batches. How should I prepare the sample_table.csv? Should I process each batch in each mode separately or together?

(2) How many ms_type options does MassCube support? I see the template includes "orbitrap", "qtof", "tripletof", and "others". What does “others” include? How about qtrap?

(3) I tried the "untargeted-metabolomics" option in the quick start, where some steps are skipped. How can I configure this function so that the skipped steps are included?
Step 5: MS signal drift normalization is skipped.
Step 6: Sample normalization is skipped.
Step 7: Statistical analysis is skipped.

(4) Which databases does MassCube cover?

Thank you for your time and support.
-Ivy

[huaxuyu]

Dear Ivy,

Thanks for using MassCube! For your questions:

(1) I have positive- and negative-mode data, with each mode containing three batches. How should I prepare the sample_table.csv? Should I process each batch in each mode separately or together?

You can processed them together if they were acquired using the same analytical method (e.g. same LC gradient, same MS...). In this case, you may prepare a long sample_table to include the samples from all three batches, and then MassCube will automatically recognized batches and apply normalization. Just make sure to enable "signal normalization" in the parameter file.

(2) How many ms_type options does MassCube support? I see the template includes "orbitrap", "qtof", "tripletof", and "others". What does “others” include? How about qtrap?

It should support qtrap data. Now ms_type is not a required parameter (please obtain the latest parameter file here: https://huaxuyu.github.io/masscube_parameters/). Let me know if you have any issues for qtrap data processing.

(3) I tried the "untargeted-metabolomics" option in the quick start, where some steps are skipped. How can I configure this function so that the skipped steps are included?
Step 5: MS signal drift normalization is skipped.
Step 6: Sample normalization is skipped.
Step 7: Statistical analysis is skipped.

Yes, you will need to enable those functions in the parameter.csv file. For example, to run signal normalization, you may set "signal_normalization" to yes and provide enough QC samples (more than 3).

(4) Which databases does MassCube cover?

Now it includes MassBank, GNPS, MS-DIAL and MassBank EU (see this page for more details: https://huaxuyu.github.io/masscubedocs/docs/workflows/database/)

Hope you enjoy using MassCube.

Best,
Huaxu

[Ivy-ops]

Fantastic! Thank you Huaxu! I will try them out!

-Ivy