Method for Predicting the Migration Time of Ionic Compounds by Electrophoretic Measurement

• US 20070256935A1
• Filed: 08/24/2005
• Published: 11/08/2007
• Est. Priority Date: 08/25/2004
• Status: Abandoned Application

• Current Assignee: Human Metabolome Technologies, Inc.
• Original Assignee: Human Metabolome Technologies, Inc.
• Inventors: Sugimoto, Masahiro, Soga, Tomoyoshi, Tomita, Masaru
• Application Number:
  US11/660,676
• Publication Number:
  US 20070256935A1
• Time in Patent Office: Days
• US Class Current: 204/451
• CPC Class Codes: G01N 27/447 using electrophoresis

Abstract

When the migration time of a low molecular weight compound having an unknown migration time in microchip electrophoresis, capillary electrophoresis, or a capillary electrophoresis mass spectrometer is predicted, first, with respect to a substance having a known electrophoretic migration time, characteristic quantities (descriptors) thereof which can be numerically expressed from a structure thereof are computed to predict the relation between the characteristic quantities (descriptors) and the migration time; the migration times of some substances are measured by electrophoresis or an electrophoresis mass spectrometer to learn about the relation; and using the learnt result, the migration time of the substance having an unknown migration time in the electrophoresis or electrophoresis mass spectrometer is predicted from the structure thereof.

Claims

1. A method for predicting a migration time of an ionic compound by electrophoretic measurement, characterized in that, when the migration time of a substance having an unknown migration time in microchip electrophoresis, capillary electrophoresis, or a capillary electrophoresis mass spectrometer is predicted,

first, with respect to a substance having a known electrophoretic migration time, characteristic quantities (descriptors) thereof which can be numerically expressed from a structure thereof are computed to predict relation between the characteristic quantities (descriptors) and the migration time;

the migration times of some substances are measured by electrophoresis or an electrophoresis mass spectrometer to learn about the relation; and

using the learnt result, the migration time of the substance having an unknown migration time in the electrophoresis or electrophoresis mass spectrometer is predicted from the structure thereof.

2. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 1, wherein the characteristic quantities (descriptors) include a descriptor indicative of a molecular feature, the descriptor being calculated from a three-dimensional structure predicted based on a two-dimensional structure of the substance, an ionization exponent calculated from the two-dimensional molecular structure, and a net charge of a compound.

3. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 2, wherein the three-dimensional structure has such a shape as to take the most stable structure as a single compound in terms of energy, assuming that the structure is singly present in a vacuum without being affected by anything else.

4. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 2, wherein that the net charge of the compound is calculated using the following Equations:

$\begin{array}{cc}\text{\hspace{1em}<br><br>}<br><br>{\mathrm{\alpha <br><br>}}^{-}=\frac{{10}^{\left(\mathrm{pKa}-\mathrm{pH}\right)}}{{10}^{\left(\mathrm{pKa}-\mathrm{pH}\right)}+1}-1& \left(1\right)\\ {\mathrm{\alpha <br><br>}}^{+}=\frac{{10}^{\left(\mathrm{pKa}-\mathrm{pH}\right)}}{{10}^{\left(\mathrm{pKa}-\mathrm{pH}\right)}+1}& \left(2\right)\\ q=\underset{i=1}{\overset{n}{\sum <br><br>}}<br><br>\text{\hspace{1em}<br><br>}<br><br>{\mathrm{\alpha <br><br>}}_i^{-}+\underset{j=1}{\overset{m}{\sum <br><br>}}<br><br>\text{\hspace{1em}<br><br>}<br><br>{\mathrm{\alpha <br><br>}}_j^{+}& \left(3\right)\end{array}$

(wherein i and j are subscripts of an acid dissociation constant pKa;

n is a number of pKa of a substance producing electric charges with negative values;

m is a number of pKa of a substance producing electric charges with positive values; and

pH is a pH value of an electrophoretic buffer solution to be used with the microchip electrophoresis, the capillary electrophoresis, or the capillary electrophoresis mass spectrometer).

5. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 1, wherein the migration time is a relative migration time which is obtained by normalizing the migration time of the compound measured in electrophoresis or an electrophoresis mass spectrometer with the migration time of an internal standard substance.

6. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 1, wherein the relation is learnt using a neural network of a multi-layer structure having an input layer, a hidden layer, and an output layer.

7. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 6, wherein all the descriptor values of the compound and the net charge are given to the input layer, and the relative migration time of the compound is given to the output layer.

8. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 7, wherein, when there is a big difference between the maximum and minimum of each value given to the input layer and the output layer, logarithmic normalization is performed, and, when the difference is small, linear normalization is performed.

9. The method for predicting a migration time of an ionic compound by electrophoretic measurement according to claim 6, wherein the same data are learnt by multiple neural networks, and an average value is taken as output.