Change ping (MI:0946) name and broaden definition

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Hi,

The name for interaction detection method PING (MI:0946) is rather uninformative, as it stands just for 'protein interaction network generator'. I think we should either change the name to something more descriptive (chambered PISA?) and keep PING as a synonym or broaden the description so we include the meaning of the acronym and a more detailed description than the one the term features currently.

Here's a brief description of the method given in PMID:19098921: "We developed an in vitro microfluidic platform for high-throughput screening of protein interactions, called protein interaction network generator (PING). PING combines on-chip in vitro protein synthesis with an in situ microfluidic affinity assay. PING uses our previously developed mechanical trapping of molecular interactions (MITOMI), which allows one to measure interactions without prey losses owing to washing, and can thus detect weak or transient interactions17. For PING, a co-spotted DNA microarray containing linear template encoding the proteins is aligned and bonded with the microfluidic device (Fig. 1a, b and Supplementary Fig. 1 online). One can therefore easily express thousands of protein combinations (either binary or complex) on a single device without the need for purification or prior knowledge of protein oligomeric state. The experiment consists of three main stages: (i) we use biotinylated BSA and streptavidin to deposit a biotinylated antibody that recognizes the bait protein on a circular area inside each individual chamber; (ii) we express proteins in vitro by filling each chamber with an E. coli extract that allows transcription and translation of the spotted DNA; (iii) the bait is immobilized on the chamber surface, and we measure any interactions between bait and prey using fluorescently labeled antibodies and MITOMI (Supplementary Methods online). In vitro protein expression prevents complications otherwise caused by cell viability or physiology, and PING enables a direct biophysical measurement of interactions for various proteins. Unlike other self-assembling protein array methods, each reaction occurs in its own unit cell, and there are hence no limitations resulting from cross-contamination or diffusion18 (Fig. 1b, c)."

Cheers,

Pablo.

Reported by: pporras

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• assigned_to: nobody --> orchard

Original comment by: pporras

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An update coming from the authors that put together the method. They would prefer that we do not use the term 'ping' any more (we can keep it as a synonym just in case). They are calling it 'miniaturized immunoprecipitation' now (mIP). We can use that name and make the term a child of both 'pisa' and 'coIP'.

Cheers,

Pablo.

Original comment by: pporras

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On top of that PING is a child of PISA which explicitly claims affinity is through His tag whereas PING used biotin. As far as I can tell it is PISA's definition that should be made more generic by dropping any references to a specific affinity variant (histag, straptavidin, etc) so that it could be used to refer to any affinity method where baits are prepared/coupled in situ; appropriate tags could be then used to distinguish between 6xHis/biotin/etc (it's likely variants of the method will use some sort of affinity tag - the use of specific antibodies would beat the purpose of the approach ?) ; this way there's no need to use PING term at all:

• experiments annotated with PISA (current) would remain annotated as they currently are (assuming his-tag, proper protein source and participant detection terms has been used); updated PISA term could still be used as it would be more generic
• PING experiments would use PISA term (updated) with appropriate terms used to specify tag, source and participant indentification method (identification by antibody MI:0421 ?) specific to PING

Original comment by: lukasz99

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sigh... so they actually did coPI with biotin used to immobilize anti-bait antibody... if that's the case PING (or mPI as preferred by the authors) would be made a child of coPI and a generalized PISA that do not mention any specific affinity method; specific PISA would be then made a child of the generic one and of pulldown ?

lukasz

Original comment by: lukasz99

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• status: open --> closed

Original comment by: orchard