Curve fitting


Curve fitting

After generating a sensorgram, the next step is fitting the curves. The first and only model to use is the 1:1 Langmuir interaction describing the single exponential of the data. With the first attempt, leave the bulk contribution and drift on zeor and do not fit. Start by providing the initial fitting values and press “fit” to see the result. If the sensorgram consists of nice curves the fit will be ready in seconds; the fitted line follows the curves and will procide well defined values with small errors.

Fitting curves
1:1 interaction fitting
Fitted values
Fitted values

More realistic, optimization of the initial values and adjusting the fitting ranges may be necessary. This is normal and it is a good idea to fit the sensorgram with several initial values that differ a magnitude in scale. If, after fitting with different initial values, the results converge to the same values, it can be assumed that the values are well defined and robust. After the initial fittings, bulk contribution and/or drift can be fitted when necessary. Both bulk concribution and drift should be small compared to the curve response and proportional to the analyte concentration.

The next step is to critically compare the fitting with the measured curves. Does the fitting follow the curves? Are the calculated buffer jump values in line with the curves? Are the values of the parameters (Rmax, ka, kd) possible? Some instruments provide a quality control on the fitted parameters, however, always inspect the parameter values and the curves yourself.

Large RI jumps
1:1 fitting with large RI jumps

In the figure ‘1:1 fit with large RI jumps‘, the fit is not following the curves during the dissociation phase. By adding a larger buffer jump the program attempts to make the fit better. One other thing immediately apparent is that the overall response is too high. A way to solve this is to immobilize less ligand and repeat the experiment.

Other small problems, like small buffer jumps or low baseline drift can be solved with subtracting reference channels and blank (buffer only) injections (double referencing).

To validate further the interaction, several more steps are necessary. For instance, reverse the ligand and analyte and perform the experiments again. If you used the kinetic protocol, try an equilibrium experiment. Repeat the experiment with different batches of the same reagents to identify batch-to-batch variation. In all cases, a same value for kinetic constants is expected.

Read more

Read more about data fitting at the Data fitting introduction page.

Comments  

# sazzbazz 2018-02-01 04:48
If there is an RI jump during dissociation, does it also suggest a two state fit, where the first and the second order dissociation are not identical? A differential slope during association is also observed in such cases.
For small molecules a bulk is often visible. Increasing the Flow rate or changing the immobilization level does not impact the observed bulk.Why?
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# Arnoud1 2018-02-01 08:38
The RI-jump during dissociation is added by the fitting algorithm to make the fit 'better'. The algorithm has no clue to what it is fitting. Therefore, I would not say the adding of a RI-jump is a clue for a two state interaction. A two-state or heterogeneous model will always fit better because it has more parameters.
The bulk jump is the result of concentration and composition differences between the flow buffer and sample. Thus changing the flow rate will not solve this. A higher or lower immobilization level can have some impact due to the excluded volume (https://www.sprpages.nl/experiments/data-processing) by the immobilized ligand.
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# Lei 2016-03-16 07:29
How could I do the fit by adding a larger buffer jump? Thank you.
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# Arnoud1 2016-03-16 19:28
You can set the RI in the fitting model to a constant value.
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# Omar 2016-01-18 12:33
Please, what can I if I have mass transfer curve [I have like calibration curve]
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# Arnoud1 2016-01-18 19:14
You can incorporate a mass transfer term in the fitting.
Look at http://www.sprpages.nl/data-fitting/models/mass-transfer

Better is to avoid mass-transfer by immobilizing less ligand
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# ahsaab1976 2015-11-18 02:02
Hi Arnoud,

When I run the fitting in BiaEvaluation I always get sharp lines, I mean the lines don't go smoothly with the curve, always go with right angles around the curve without any curvature, do you why and how can I resolve this
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# Arnoud1 2015-11-18 11:06
You can try to change the initial values of the fitting. And start by fixing the RI in zero.

You can also post a question at the forum and include a sensorgram for clarification
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# Vivian Huerta 2013-10-15 21:32
Hi Arnoud:
What if the Rmax value is the one that does not seem possible? For example if it looks way too high? I am facing this problem in my experiments, I have tried to use a constant Rmax in the fitting which I have estimated experimentally and the KD varies in from 10e-09 to 10e-10
thanks in advance for your comments
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# Arnoud 2013-10-15 21:33
Did you try to fit the curves individually to get an idea what can cause this strange behaviour?
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# Jon Ashley 2012-11-19 20:34
Does this apply to concentration assays? I think a distinction has to be made between the quailty of kinetic based assays and concentration based assays somewhere.
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# Arnoud 2012-11-19 20:35
The focus of this page is on the kinetics.
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# Madhurima Mitra 2017-09-12 13:05
If the reaction is not 1:1, then the binding cant be analysed with SPR?Is some other model available? please reply
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# Arnoud1 2017-09-12 19:37
You can analyse other reactions than 1:1 with SPR but as with all experiments that use modelling you should have an other way of confirmation of the used model.
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