Isotope Detection deimos.slice(): What are the correct values to use?

[jessieolough]

Hi Sean,

Hope you are keeping well?

I am trying to create plots for high-intensity features similar to how you have done at the bottom of the Isotope Detection documentation. However, my plots are not coming out correct and I suspect that I am not using the correct values in the low = [] and high = [] parts of the feature = deimos.slice() function.

From the example provided, I can see that 758.570374 in the function corresponds to the m/z values for the feature with index 382. Unfortunately, I cannot see where the 0.5, 34.4, 0.75, 5.116775, 36.5, and 2 values come from in this data or in the method. Would you be able to explain where these come from, please?

The whole function for reference:

feature = deimos.slice(ms1, by=['mz', 'drift_time', 'retention_time'],
                       low=[758.570374 - 0.5, 34.4, 0.75],
                       high=[758.570374 + 5.116775, 36.5, 2])

Any help would be much appreciated.

Kind regards,
Jessica

[smcolby]

So the by keyword signals what dimensions we're slicing by. Accordingly, low represents the lower bound for each dimension, and high the upper bound. In the above, we are thus slicing the data between ~758 and ~767 in m/z, between 34.4 and 36.5 ms in drift time, and between 0.75 and 2 minutes in retention time.

In the example, these values were selected based on inspecting the data: this particular feature spans these ranges in each dimension. Hope that helps!

[jessieolough]

Hi Sean,

Thanks so much for your explanation, it helps a lot. Between that, as well as the example code for the Peak Detection steps where the equivalent graphics are also made, this issue seems to be fixed now.

All the best,
Jess