[Feat/aut789] - Walkthrough: Targeted flux analysis with GC-MS SIM Agilent

[ahmedskhalil]

Objective

• Documentation for the tutorials section in RtD
• Walkthrough : Targeted flux analysis with GC-MS SIM Agilent
• Docs can be viewed at : https://smartpeak-.readthedocs.io/en/feat-aut789/guide/tutorials.html

[dmccloskey]

This is looking quite nice.

I forgot to mention this on the other LC_MS/MS method, but I will mention it here: it would be great to have a screenshot of the chromatograms for a complete MDV (i.e., all of the transitions for e.g., lactate or some other comonent_group) to help visualize what an MDV is and how it can be inspected. Also for the HeatMap, I would recommend using the "Peak_apex_int" instead of LogSN.

It looks like there is a mismatch between the TraML file transitions, and the components defined in the quantitation methods and FeatureFilters/QCs.

[ahmedskhalil]

This is looking quite nice.

I forgot to mention this on the other LC_MS/MS method, but I will mention it here: it would be great to have a screenshot of the chromatograms for a complete MDV (i.e., all of the transitions for e.g., lactate or some other comonent_group) to help visualize what an MDV is and how it can be inspected. Also for the HeatMap, I would recommend using the "Peak_apex_int" instead of LogSN.

It looks like there is a mismatch between the TraML file transitions, and the components defined in the quantitation methods and FeatureFilters/QCs.

I have updated the screenshots. Regarding the mismatch, I have compared the file structures in other examples and had an initial thought that the transition_group_id was swapped with the transition_name column so I tried that out and it has caused SmartPeak to crash. Could you please elaborate with an excerpt from both files?

[dmccloskey]

Very nice updated.

The issue is that the compounds between the TraML and FeatureFilter... or FeatureQC... files are not consistent. The names provided in the transition_group_id names in the traML should be provided in the ...ComponentGroups... files and the transition_name names in the traML should be provided in the ...Components... files. Please let me know if that makes sense.

[ahmedskhalil]

The names provided in the transition_group_id names in the traML should be provided in the ...ComponentGroups... files

Very nice updated.

The issue is that the compounds between the TraML and FeatureFilter... or FeatureQC... files are not consistent. The names provided in the transition_group_id names in the traML should be provided in the ...ComponentGroups... files and the transition_name names in the traML should be provided in the ...Components... files. Please let me know if that makes sense.

The transition_group_id in the traML file (i.e. Lactate) is mapped to component_group_name in *ComponentGroups* files, and the transition_name (i.e. Lactate_219) in the traML file is mapped to component_name in the *Components* files.

[dmccloskey]

The transition_group_id in the traML file (i.e. Lactate) is mapped to component_group_name in *ComponentGroups* files, and the transition_name (i.e. Lactate_219) in the traML file is mapped to component_name in the *Components* files.

OK great. Thanks for updating that. I must have just missed it then. Does the workflow run or are you still encountering errors?

[ahmedskhalil]

The transition_group_id in the traML file (i.e. Lactate) is mapped to component_group_name in *ComponentGroups* files, and the transition_name (i.e. Lactate_219) in the traML file is mapped to component_name in the *Components* files.

OK great. Thanks for updating that. I must have just missed it then. Does the workflow run or are you still encountering errors?

I just reran it with the latest version without any issues.