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Addition of ion mobility information #109

Closed michaelwitting closed 4 years ago

michaelwitting commented 4 years ago

How can ion mobility data be added to MassBank records?

Discussion with @sneumann, @tsufz, @schymane in Dagstuhl January 2020?

schymane commented 4 years ago

Yes, this is definitely needed, good idea to discuss at Dagstuhl.

michaelwitting commented 4 years ago

Good... I will collect few ideas for discussion. See you there...

schymane commented 4 years ago

If you want to post ideas here in the meantime, please do - I have some other colleagues we could add to the discussion in advance if needed (e.g. UJI in Castellon)

michaelwitting commented 4 years ago

Idea for Tags and Subtags AC$ION_MOBILITY

One of the main question is how to collect instrument parameters, e.g. drift field etc. This is very different for the different instruments. This review might help with finding the best answers: https://onlinelibrary.wiley.com/doi/full/10.1002/mas.21585

bijlsma-l commented 4 years ago

Dear all, I am Lubertus (aka Robert) from UJI Castellon. Emma asked us to participate and I hope can add valuable thoughts to this discussion. I also discussed this with my colleague Juanvi Sancho and we agree with the tags suggested by Michael i.e. drift gas, instrument type, drift time and CCS. These are most important. In the future you might have to consider including resolution. It is probably not yet the case, because this should also be defined, but I can imagine that this becomes more important. Waters for example is developing a cyclic IMS with higher resolution than the TWIMS, because with the TWIMS they are a bit behind with the others (TIMS). Manufacturers will probably continue with this development like with HRMS.

michaelwitting commented 4 years ago

Bruker instrument deliver the inverse reduced mobility. Naming? INVERSE_REDUCED_ION_MOBILITY

see https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1002815

michaelwitting commented 4 years ago

Example for Agilent 6560:

AC$ION_MOBILITY INSTRUMENT_TYPE DT AC$ION_MOBILITY DRIFT_GAS N2 AC$ION_MOBILITY CCS 182.56

tsufz commented 4 years ago

@michaelwitting, are you volunteering to update the record format?

michaelwitting commented 4 years ago

@tsufz I have written the inital documentation in the dev branch. Can you give me access to push the changes?

sneumann commented 4 years ago

Can you do a pull request instead?

Gruß Steffen

I blame Android for the brevity and typos

---- Michael Witting schrieb ----

@tsufzhttps://github.com/tsufz I have written the inital documentation in the dev branch. Can you give me access to push the changes?

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michaelwitting commented 4 years ago

No problem... on it's way soon!

tsufz commented 4 years ago

Close with fd6902c5d2e521cac34c3f40deb2ff590f11d8f7.