Allow `PeakGroup`s to be loaded when the measured compound has no labeled elements

[mneinast]

BUG DESCRIPTION

Inspiration

Tracebase does not load measured compounds which are missing the labeled element in the infusate. For example, adenine does not contain any oxygens, and tracebase will not load the adenine data from an "18O" tracer experiment. Loading these measured compounds is prevented during validation or during loading.

Description

Load Peak Group compounds even if they don't have labeled elements.

Make sure this doesn't cause any problems with any code that assumes labels are present.

Comment

None

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ISSUE OWNER SECTION

Assumptions

1. List of assumptions made WRT the code
2. E.g. We will assume input is correct (explaining why there is no validation)

Limitations

1. A list of things this work will specifically not do
2. E.g. This feature will only handle the most frequent use case X

Affected Components

• change: File path or DB table ...
• add: Environment variable or server setting
• delete: External executable or cron job

Requirements

• [ ] 1. List of numbered conditions to be met for the feature
• [ ] 2. E.g. Every column/row must display a value, i.e. cannot be empty
• [ ] 3. Numbers for reference & checkboxes for progress tracking

DESIGN

GUI Change description

None provided

Code Change Description

None provided

Tests

• [ ] 1. A description of at least one test for each requirement above.
• [ ] 2. E.g. Test for req 2 that there's an exception when display value is ''
• [ ] 3. Numbers for reference & checkboxes for progress tracking

[hepcat72]

Summary of slack discussion on this topic:

We will need to accept compounds like adenine but it’s not a priority right now.

Can I ask what the utility is of loading a peak group that doesn't have any elements that are labeled in the tracers?

Right now, there is code that likely assumes that every measured compound has an element that could be labeled.

Let me venture a guess... the biochemistry that results in a labeled element ending up in another compound has byproducts that may not have any elements that are labeled. Quantitatively measuring those unlabeled byproducts could lead to insights into how the labeled element gets into the resulting (other) measured compound? I.e. one chemical pathway versus another?

If that's the case, that would make sense. I would have to check over the code to see what problems there could be related to measured compounds without labeled elements... could you create an issue that describes this?

So if we're purely focused on measuring the fraction labeled in each compound, there is no utility in loading these compounds which do not have any of the labeled element (ie adenine).

Your idea is essentially correct though. Using adenine as an example, it can be produced from adenosine (pictured). If we gave a mouse a drug that blocks this reaction, and this experiment included 18O as the tracer, we would not see any effect on adenine labeling (because it never gets an 18O)....but we would predict lower total adenine ion counts.

So tracebase is designed to prioritize tracing experiments, where the most important and rubust data is the fraction labeled. But it would be nice to secondarily allow a researcher to check if adenine total ion count changed.