SnIP: sequential non-denaturing immunoprecipitation

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As described in PMID:16623599 Basically, a combination of two consecutive IPs. It is distinct from TAP and likes in that two distinct baits are used. Shall we use a new term (serial affinity purification or simlar ?) as a child of MI:0004 or just stay with (in this case) coIP while listing the relevant proteins as both baits and preys and adding the relevant tags as needed ?

lukasz

Reported by: lukasz99

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Reading quickly the paper you mention it looks like the is one protein (DAP10) carrying simultanously 2 tags, I did not manage to find out wheather the 2 tags are linked or cloned in different termini. I am not against having a generic 'sequencial chromatography' term but I fear graph explosion as any of the chromatophy can be part of a sequence of purification, and using such term we loose the information about the type of chromatography carried out. moreover how would we record the sequence of chromatophies? Any suggestion is wellcome but for now I would suggest you just use coIP.

Original comment by: luisa_montecchi

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not exactly. they've got simultaneously 2 constructs of DAP10 - each with a different tag. a series of 2 coIPs is performed and only then bound proteins are identified. I'd say that if if TAP got it's own term why not this one ? or, at least the sequenitial chromatography term, as you suggest, sitting between affinity chromatography and TAP ?

l

Original comment by: lukasz99

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From Susan More:

• I understand your concern re: graph explosion but I think this really is a different technique and should be recognized as such. Moreover for reasons given below, it can’t really be treated just as a simple combination of existing terms – I think that the intermediate step needs to be specified.

- Maybe as previously suggested, have an upper level term “sequential affinity chromatography”, with “TAP” as a child term, “Sequential IP” as another child term.

- Sequential IP would then need “Sequential non denaturing IP” and “Sequential denaturing IP” as child terms because some people DO denature their IPs, let them renature, and then do the second round of immunoprecipitation (vs. eg eluting with peptide and then doing the second round).

- Eg PMID 9271411 figure 4 - “After the first immunoprecipitates were boiled in the presence of SDS, a second round of immunoprecipitations was performed…”

- Then maybe have as a curation rule that only the first round of IP will be specified with description of bait construct, etc – otherwise it really starts to get impossibly complicated to describe the experiment, for little or no benefit?

Original comment by: luisa_montecchi

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Original comment by: luisa_montecchi