New term: Affinity complex

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Formally, affinity complexes, isolated in eg TAP experiments, do not have to represent physical complexes but only a collection of physical complexes sharing the common bait. Thus annotation of the raw TAP purifications as 'physical complex' (which implies all the listed participants are present within the same physical complex) is misleading - the list of participants might corresponds to members of two or more physical complexes sharing the same bait. For example proteins Tap-A, B, C, D, E identified as present in a particular TAP purification might correspond to a pair of physical complexes sharing the same TAP-A protein (eg comlex 1: TAP-A, B,C; complex 2: TAP-A, C, D,E) whereas using 'physical interaction' term implies all the listed proteins are present in a single complex.

Applying the proposed 'affinity complex' term here would remove this ambiguity.

Reported by: lukasz99

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• summary: NEW term: Affinity complex --> New term: Affinity complex

Original comment by: lukasz99

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I disagree, the interaction detection method should be enough to label the 'kind' of complex. Having 'affinity complex' would then mean we also need to add 'xray complex' etc.. moreover in which CV this complex type should be in interactor type?

Original comment by: luisa_montecchi

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>I disagree, the interaction detection method should > be enough to label the 'kind' of complex. Having ^^^^^^^^^^^^^^^^^

well, the way I see it, there are two possiblilities:

A) if we're are indeed dealing with 'a new kind of complex' the terms within interaction type hierarchy should be able to describe it without resorting to any other part of CV.

personally, I'd be quite reluctant to say affinity complexes are complexes at all, but a large number of people do use the term so it only seems reasonable to follow the community

B) one can claim affinity complexes are not complexes at all and thus shouldn't be reported as such. if that's the case, only binary interactions between baits and preys should be reported (either as direct as only physical, depending on the possibility of bridging by 3 protein). the problem here is, that the community consensus (as can be inferred from the appearance of papers analysing affinity complexes) seems to be that listing all the members of affinity purification is useful and common practice. creating a cv term addressing this need seems to be in place.

> 'affinity complex' would then mean we also need > to add 'xray complex' etc...

not really. 'xray complex' have the same property as 'gel filtration complex', 'native gel complex' etc - namely that all the participants there are a part of a single, physical complex.

'affinity complexes', on the other hand, list participants that are not necessarily a part of the same physical complex but only of one or more complexes that share a common bait.

personally i see it as a fundamental difference in what the list of participants represents, not how we came to identify one particular list. it happens that at this very moment a list of proteins within 'affinity complex' can be determined only by affinity methods (and thus, for the lack of a better term, 'affinity' is used) but who knows what other methods experimental people will come up with ?

> moreover in which CV this complex type should be > in interactor type?

I'd say it should be a direct descendant of the 'interaction type', ie a sibling of physical and others...

when and if to create a corresponding term within 'interactor type' could probably wait until someone will use an affinity complex in an experiment that will have to be annotated...

lukasz

Original comment by: lukasz99

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for now as an annotation topic

Original comment by: luisa_montecchi

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Rejected at the PSI Washington meeting as considered the term 'physical interaction' encompass this situation.

Original comment by: luisa_montecchi

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• status: open --> closed

Original comment by: luisa_montecchi