AnalyzeEpitopeBinning

classifies antibodies by their interaction with a given antigen using dataObject collected by biolayer interferometry.

AnalyzeEpitopeBinning[protocolObject]⟹object

classifies antibodies by their interaction with a given antigen using data found in protocolObject for ExperimentBioLayerInterferometry.

Details

Cross blocking is quantitated by the maximum bio-layer thickness achieved during the association of the second (competing) antibody. If the change in biolayer thickness during exposure to the secondary (competing) antibody exceeds the specified threshold, the two antibodies are considered to bind distinct epitopes and are placed in different bins. If the change in biolayer thickness does not exceed this threshold, they will be placed in the same bin. There are options to set a low binding threshold for certain species, in the even that some antibody-antigen interactions are sufficiently slow that even with long association times they may not reach a comparable bio-layer thickness to the other measured antibodies.
The success of this experiment and validity of the analysis is highly dependent on verifying the on and off rates of the tested antibody/antigen pairings. Ensure that the initial antibody/antigen pairing does not have an excessively high dissociation rate, which will invalidate the experimental results.
All pairings are reported in the A -> B and B -> A binding format.
Any number of data object can be input to this function, though it is highly recommended that every combination of antibodies is studies for most accurate results. If this is not the case, it is possible that antibodies that bind the same epitope will appear in different bins due to a lack of experimental data.

Given an Object[Protocol,BioLayerInterferometry], AnalyzeEpitopeBinning returns an Analysis Object:

Given a list of Data[Protocol,BioLayerInterferometry], AnalyzeEpitopeBinning returns an Analysis Object:

Specify the type of baseline well used to account for drift or solvent/media based fluctuation in response signal (PreviousWell):

Specify the type of baseline well used to account for drift or solvent/media based fluctuation in response signal (SelfBlocking):

Specify the region of each competition step to average to obtain the response value using time:

Specify the region of each competition step to average to obtain the response value using percent of the total step time:

Specify the type of well used to normalize response - use the initial loading step for a given antibody as the maximum value:

Specify the type of well used to normalize response - use a parallel well in which the antibody loads an unblocked antigen covered surface:

Specify species which exhibit slow binding that results in low response even when it is not blocked by the bound antibody:

Specify a lower threshold for species which exhibit slow binding:

Automatically resolve the Threshold to a raw response (in Nanometer) if the data is not analyzed with a NormalizationMethod:

Automatically resolve the Threshold to a normalized response if the data is analyzed with a NormalizationMethod:

If there is no data element matching the requested BaselineType, an error will be shown:

Given an incomplete list of Data[Protocol,BioLayerInterferometry], AnalyzeEpitopeBinning returns $Failed:

If the SlowBindingThreshold is specified but no SlowBindingSpecies are given, an error will be shown:

If the Threshold is given in raw data form but a NormalizationMethod is specified, and error will be shown:

If the Threshold is lower than SlowBindingThreshold, and error will be shown: