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Update record format #203

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tsufz commented Oct 29, 2019

Updata records format and bump to version 2.4.

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schymane commented Oct 29, 2019

I received an email earlier today with additional field suggestions. They want to add precursor intensity and concentration of the chemical. Do you want to hold off with revising until they have replied? For the record I suggested AC$CONCENTRATION and MS$FOCUSED_ION: PRECURSOR_INT.
I mentioned we were revising it like right now ...

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tsufz commented Oct 29, 2019

In meanwhile some comments came in...

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tsufz commented Oct 30, 2019

@schymane, do you know when they will details on their invention? I would like to release 2.4 soon to get it from the table and to start the work with implementation.

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schymane commented Oct 30, 2019

They wanted concentration information and precursor intensity in the records and my suggestions would be to add new tags:
AC$CONCENTRATION
MS$FOCUSED_ION: PRECURSOR_INT

I don't know if we have to wait for more details - if you want to slightly modify my suggestions let's discuss ... I have not had a response...and think we should finalise ...

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tsufz commented Oct 30, 2019

Well, I will put it in with any description and then finalise 2.4.

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tsufz commented Oct 30, 2019

I think AC$CONCENTRATION does not really fit to any of the existing analytical sections. I will create a new general section for comment tags...

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meier-rene commented Oct 30, 2019

Would "AC$CHROMATOGRAPHY CONCENTRATION" fit?

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schymane commented Oct 30, 2019

I toyed with a few ideas and kept landing on AC$CONCENTRATION

We do not always have chromatography (direct infusion?)
MS$FOCUSED_ION CONCENTRATION is also an alternative but certainly not ideal because this has already been ionised.
CH$ also inappropriate as it's the chemical information not the concentration (which is an analytical condition ... hence AC is the proper home in my opinion...)

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tsufz commented Oct 30, 2019

I added the AC$GENERAL section 2.4.7 for such purposes.

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sneumann commented Oct 30, 2019

Hm. In all publications with analytical chemistry I totally support reporting concentrations.
In our case, what's the difference in a MS/MS spectrum of 0.001 mol/l caffeine solution
vs. an MS/MS of 10.0 mol/l caffeine ? What was the intended use case ? Ionisation efficiency ?
I am hesitant to add too much detail. Similarly, what is the intention behind precursor intensity ?
The Grant lab at UConn looked into that (Ecom50). Would we have enough information if we did target those use cases ? I suggest that if we add information, we also give examples in the docs what this can be actually used for. Yours, Steffen

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schymane commented Oct 30, 2019

The email contact wanted indeed to use this data to predict ionisation efficiency based on information such as concentration and precursor intensity. All other info needed is already available (if provided) in the record format. I understand the unwillingness to add too much detail and these should certainly not be compulsory fields, however this is information that people may have. I am not sure how many people will actually add this information and I would be hesitant to add it to RMB esp with our lack of active programmers on it right now, but I see no harm to add it to the record format to standardize it if people wish to add it (otherwise it will e.g. end up in the COMMENT field...)?

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