interaction detection: mass spectrometry

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it looks like we need a generic mass spectrometry term for interaction detection in order to annotate experiments that do identify interactions but in a way different than the current definition of 'mass spectrometry studies of complexes' (MI:0069) - these might include studies bases on deuterium exchange (eg PMID:18184591). I would suggest adding a generic 'mass spectrometry term' as a parent of MI:0069 so that the meaning of MI:0069 stays the same but methods other than ESI/TOF of complexes can be annotated with this generic term

lukasz

Reported by: lukasz99

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reading quickly the paper 18184591, I understand that DXMS is used to characterized the most exposed amide groups on a monomer of a multimer complex: TCP peptides that demonstrated rapid hydrogen/deuterium exchange lie on the filament surface whereas those that exchanged slowly are buried, either by the protein fold or by subunit-subunit interactions.

It does not seam to me MS is the interaction detection but possibly a feature detection, in case we have had a feature type 'buried aa' and 'surface aa'. The aggregation of the various mutant is then visualized by transmission electron microscopy and previously known by Xray.

I am afraid it could be quite missleading to have a term mass spectrometry in CV interaction detection as many person not from the ppi field may think the high trought put complex analysis are done by 'mass spectrometry'. However we can consider changing MI:0069 to be more generic and vague enough to include such structural studies by deuterium exchange.

Original comment by: luisa_montecchi

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well, if you're saying mass spec is not the way interaction was detected, what else then ? which of the current terms is to be used ?

lukasz

Original comment by: lukasz99

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I agree that mass spec is the participant ID not the interaction detection. Label exchange appears to be the interaction detection method, which would require a new term. It is conceptually similar to footprinting - in that the interaction prevents access by an outside agent. Perhaps we need a new parent "accessing study" with children footprinting and new term radio-isotopic exchange. I'm open to a better descriptor than "accessing study". Accessing study - the interaction between two partners prevents access to the molecules by an external agent which would otherwise modify one or both of the participants. Radio-isotope exchange - Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchage.

Sandra

Original comment by: orchard

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From the description and what I could find from the Web the deuterium labeling is prior to the column seperation and fragmentation before carrying out the MS. This would be similar to SILAC where labeling is done prior to seperation of the proteins and MS. Do we really need individual techniques for the different methods folks use for labeling the proteins or peptide fragments. ICAT would also be under consideration particularly since it too can be done in vivo in cell lines.

Participant identification is really still the final method of MS and Interaction detection is whatever was used to pull out the complexes in the first place.

You could possibly consider putting these as tags on molecules and Can protein footprinting then be used?

Original comment by: jyotikhadake

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>Can protein footprinting then be used?

The definition of footprinting states that this is protection from degradative enzymes. I think a separate term would be better.

Sandra

Original comment by: orchard

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I agree on the footprinting solution: why not modifying the current term footprinting MI:0417 to 'enzymatic footprinting' and add a general parent footprinting/accessibility study with a new child Radio-isotope exchange footprinting.

Lukasz would it be ok for you?

http://www.ebi.ac.uk/ontology-lookup/?termId=MI%3A0417

Original comment by: luisa_montecchi

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new suggestion:

current status is: footprinting : -protease accessibility laddering -dna footprinting --chemical footprinting ---dimethylsulphate footprinting ---potassium permanganate footprinting --enzymatic footprinting ---DNase I footprinting

we could obsolete DNA footprinting (also to avoid the correspondance with interactor type) and create a new term isotope label footprinting and arrange the hierarchy as following

footprinting : -chemical footprinting --dimethylsulphate footprinting --potassium permanganate footprinting --isotope label footprinting **** new -enzymatic footprinting --DNase I footprinting --protease accessibility laddering

Original comment by: luisa_montecchi

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Yes - makes sense. Sandra

Original comment by: orchard

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agreed.. except that isotope label footprinting can be done with either mass spec or NMR which asks for something like NMR footprinting & MS footprinting as children of isotope label footprinting but also as children of a generic NMR and (yet to be added) generic massspec terms, respectively

lukasz

Original comment by: lukasz99

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other footprinting could be followed by MS (for instance protease accessibility laddering) but as we can hardly represent multiple technology methods, I would rather not create the 2 children terms of isotope label (also to avoid graph explosion) but only mention in the definition both MS ans NMR can detect the deuterium exchange.

Original comment by: luisa_montecchi

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Isn't the vocabulary supposed to provide the means of accurately describing the experiment ? MS vs NMR can potentially provide quite different information (different timescales, different region resolution) and thus it seems to be valid to have separate terms. There seems to be many cases within cv of providing terms at similar level of detail (monoclonal/polyclonal antibodies for westerns, different versions of phage display, etc) so distinguishing between different methods of tracing isotope exchange doesn't seem to be too excessive. Especially that the distinction her is most likely to be made by the data authors and thus quite easy to trace...

Original comment by: lukasz99

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Lukasz if you consider the method most important step being the NMR or MS step you can use the existing terms. I will create a isotope label footprinting I prefer to differ the discussion of having terms that are combinations of methods like NMR+isotope footprinting or MS+isotope footprinting to the Toledo meeting.

luisa

Original comment by: luisa_montecchi

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see MI:0901 in next release

Original comment by: luisa_montecchi

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I'm sorry but the current changes does not cut it:

- hydrogen exchange is NOT enzymatic

• current MS term is still narrowed down to _entire_complexes being characterized; when looking for hydrogen exchange no complex of any sort is identifies - only change of mass of individual interactor(s) are followed...

l

Original comment by: lukasz99

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MI:0069 definition relaxed

Original comment by: luisa_montecchi

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• status: open --> closed

Original comment by: luisa_montecchi