Method and system for interaction analysis

• US 20050131650A1
• Filed: 09/20/2004
• Published: 06/16/2005
• Est. Priority Date: 09/24/2003
• Status: Abandoned Application

• Current Assignee: GE Healthcare Bio-Sciences AB (GE Healthcare Technologies, Inc.)
• Original Assignee: Biacore AB (General Electric Company)
• Inventors: Onell, Annica, Andersson, Karl, Borg, Peter
• Application Number:
  US10/945,567
• Publication Number:
  US 20050131650A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G01N 2021/212 Arrangement with total internal reflection
• CPC Class Codes: G01N 2021/458 using interferential sensor, e.g. sensor fibre, possibly on optical waveguide
• CPC Class Codes: G01N 21/21 Polarisation-affecting properties G01N21/19 takes precedence
• CPC Class Codes: G01N 21/272 for following a reaction, e.g. for determining photometrically a reaction rate (photometric cinetic analysis)
• CPC Class Codes: G01N 21/45 using interferometric methods; using Schlieren methods
• CPC Class Codes: G01N 21/553 and using surface plasmons fluorescence excitation G01N21/648; enhanced Raman G01N21/658
• CPC Class Codes: G01N 21/658 enhancement Raman, e.g. surface plasmons

Abstract

The invention relates to a computer-implemented method for determining at least one kinetic parameter for the interaction of an analyte in solution with an immobilized ligand from a data set comprising a plurality of different binding curves, each of which represents the progress of the interaction of the analyte with the ligand with time, comprising the steps of: a) performing at least one fit of the whole data set or subsets thereof to a predetermined kinetic model for the interaction; b) based on the result of the fit or fits performed in step a), identifying and excluding binding curves of unacceptable quality; c) performing a final fit to the remaining data set; and d) obtaining therefrom the kinetic parameter or parameters. The invention also relates to an analytical system for carrying out the method, as well as a computer program, computer program product and computer system for performing the method.

Claims

1. A computer-implemented method of determining at least one kinetic parameter for the interaction of an analyte in solution with an immobilized ligand from a data set comprising a plurality of different binding curves, each of which represents the progress of the interaction of the analyte with the ligand with time, which method comprises the steps of:

a) performing at least one fit of the whole data set or subsets thereof to a predetermined kinetic model for the interaction;

b) based on the result of the fit or fits performed in step a), identifying and excluding binding curves of unacceptable quality;

c) performing a final fit to the remaining data set; and

d) obtaining therefrom the kinetic parameter or parameters.

2. The method according to claim 1, wherein step c) is omitted and step d) is applied to the result of step a) when the remaining data set in step c) is identical to a data set to which a fit has been made in step a).

3. The method according to claim 2, wherein a fit is made to the whole data set in step a) of claim 1 and no binding curves are excluded in step b) of claim 1.

4. The method according to step 2, wherein fits are made to subsets of the whole data set in step a) of claim 1 and the remaining data set after exclusion of a binding curve or curves in step b) of claim 1 is identical to a data subset to which a fit has been made in step a) of claim 1.

5. The method according to claim 1, wherein a batch of data sets are processed, and wherein at least one kinetic parameter for each data set is determined.

6. The method according to claim 1, wherein step d) comprises presenting the results of the final fit sorted with regard to at least one quality parameter.

7. The method according to claim 6, wherein the quality parameter comprises goodness of the fit.

8. The method according to claim 1, wherein the exclusion of binding curves in step b) at least partly is based on residual analysis.

9. The method according to claim 1, wherein the exclusion of binding curves in step b) at least partly is based on cross-validation.

10. The method according to claim 9, wherein binding curves of unacceptable quality are identified by residual analysis.

11. The method according to claim 1, wherein at least one fit is made to the whole data set and the quality of the fit with respect to each binding curve is determined by residual analysis to identify binding curves of unacceptable quality.

12. The method according to claim 1, wherein the data set is divided into a plurality of subsets, a separate fit to the kinetic model is made for each subset, and the fits for the different subsets are compared with each other to determine if the data set contains binding curves of unacceptable quality.

13. The method according to claim 1, wherein steps a) and b) are repeated at least once before proceeding to step c).

14. The method according to claim 1, wherein step a) is preceded by a quality control to exclude binding curves which do not satisfy at least one predetermined curve quality criterion.

15. The method according to claim 1, wherein the kinetic model in step a) is a differential equation or a system of differential equations representing one to one binding with mass transfer.

16. The method according to claim 1, wherein the at least one kinetic parameter to be determined is selected from the association rate constant and the dissociation rate constant.

17. The method according to claim 1, wherein the plurality of binding curves included in each data set comprises binding curves representing different analyte concentrations.

18. The method according to claim 1, wherein the analyte-ligand interaction data of each data set is determined by a biosensor.

19. The method according to claim 18, wherein the biosensor is based on evanescent wave sensing.

20. The method according to claim 19, wherein the biosensor is based on surface plasmon resonance (SPR).

21. An analytical system for detecting molecular binding interactions, comprising:

(i) a sensor device comprising at least one sensing surface, detection means for detecting molecular interactions at the at least one sensing surface, and means for producing detection data representing binding curves which represent the progress of each interaction with time, and

(ii) data processing means for performing steps a) to d) of claim 1.

22. A computer program comprising program code means for performing the kinetic parameter determination of claim 1 when the program is run on a computer.

23. A computer program product comprising program code means stored on a computer readable medium or carried on an electrical or optical signal for performing the kinetic parameter determination of claim 1 when the program is run on a computer.

24. A computer system containing a program for performing the kinetic parameter determination of claim 1.