Reporting results


Reporting results

Equal important to the method you have used in the experiments, is what you report afterwards in your publication. You already know that it is very hard to repeat a published experiment. This is mainly because the author is not writing down all the experimental conditions. This shortcoming is recognised and David Myszka proposed the TBMRFAADOBE (The Bare Minimum Requirements For An Article Describing Optical Biosensor Experiments) (1).

  • instrument used in analysis
  • identity, source, molecular weight of ligand and analyte
  • surface type
  • immobilization condition
  • ligand density
  • experimental buffers
  • experimental temperatures
  • analyte concentrations
  • regeneration condition
  • figure of binding responses with fit
  • overlay of replicate analyses
  • model used to fit the data
  • binding constants with standard errors

As an example, here is a possible text for the methods part of your publication


The surface plasmon resonance experiments were performed using a BIACORE 2000 (GE Healthcare) equipped with a research-grade CM5 sensor chip. The ligand (60 kDa, >90% pure based on SDS–PAGE) was immobilized using amine-coupling chemistry. The surfaces of flow cells one and two were activated for 7 min with a 1:1 mixture of 0.1 M NHS (N-hydroxysuccinimide) and 0.1 M EDC (3-(N,N-dimethylamino) propyl-N-ethylcarbodiimide) at a flow rate of 5 μl/min. The ligand at a concentration of 5 μg/ml in 10 mM sodium acetate, pH 5.0, was immobilized at a density of 200 RU on flow cell 2 and flow cell 1 was left blank to serve as a reference surface. Both surfaces were blocked with a 7 min injection of 1 M ethanolamine, pH 8.0. To collect kinetic binding data, the analyte (34 kDa, >95% pure based on SDS–PAGE) in 10 mM HEPES, 150 mM NaCl, 0.005% P20, pH 7.4, was injected over the two flow cells at concentrations of 90, 30, 10, 3.3 and 1.1 nM at a flow rate of 60 μl/min and at a temperature of 25°C. The complex was allowed to associate and dissociate for 90 and 300 s, respectively. The surfaces were regenerated with a 5 s injection of 10 mM H3PO4. Triplicate injections (in random order) of each sample and a buffer blank were flowed over the two surfaces. Data were collected at a rate of 1 Hz. The data were fit to a simple 1:1 interaction model using the global data analysis option available within BiaEvaluation 3.1 software.


As an additional service to your readers, you can incorporate a figure depicting the layout of your interaction.

Proteininteraction
Protein interaction
Captureinteraction
Capture and interaction
Flow cells
Flow cells

References

(1)Rich, R. L. and Myszka, D. G. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J.Mol.Recognit. 23: 1-64; (2010). Goto reference