Reference database

• US 7,130,459 B2
• Filed: 11/18/2002
• Issued: 10/31/2006
• Est. Priority Date: 09/01/2000
• Status: Expired due to Fees

• Current Assignee: Large Scale Biology Corporation
• Original Assignee: Large Scale Biology Corporation
• Inventors: Anderson, N. Leigh, Anderson, Norman G.
• Primary Examiner(s): Bali, Vikkram
• Application Number:
  US10/295,840
• Publication Number:
  US 20030059095A1
• Time in Patent Office: 1,443 Days
• Field of Search: 382/128, 382/129, 382/133, 435/6, 204/459, 204/461, 702/19, 702/20, 702/21, 702/22, 702/23, 707/104.1, 436/86, 436/89
• US Class Current: 382/128
• CPC Class Codes: G01N 2800/52 Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G06V 20/69 Microscopic objects, e.g. biological cells or cellular parts
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

Data acquisition and cataloging are used to classify polypeptides into a reference index or database. The database can be used to identify previously unidentified samples. New polypeptides are characterized and added to the database.

Claims

1. A method for processing data in a database contained in a storage medium, comprising the steps of:

(a) storing in the database, data that includes at least one pattern of a plurality of molecules found in a sample containing a plurality of molecules, the data based upon a statistically significant number of different samples, the data including at least one parameter, which is data output from a mass spectrometry analysis, for each of the molecules found in each sample;

(b) comparing unknown data that comprises at least one parameter, which is data output from a mass spectrometry analysis, for each molecule found in a test sample with the data stored in the database;

(c) recording differences and similarities between the unknown data and data stored in the database;

(d) classifying a state of a sample by the steps of;

1) detecting a test pattern in the unknown data;

2) comparing the test pattern in the unknown data with the stored patterns in the database to identify differences and similarities; and

3) using the identified differences and similarities to confirm the state thereof.

2. The method of claim 1, wherein the at least one pattern represents multiple proteins or polypeptides found in a single sample.

3. The method of claim 1, wherein the parameter is molecular weight.

4. The method of claim 1, wherein the samples are selected from the group consisting of serum, organ, tissues, cells, organdies and fractions.

5. The method of claim 1, wherein the differences and similarities in the database indicate one of the following states:

aging, disease, presence of a toxin and presence of a pathogen.

6. The method of claim 1, wherein the state is selected from the group consisting of:

a disease state, the presence of a toxin, the presence of a pathogen and aging.

7. The method of claim 1, wherein the pattern is a discriminatory pattern.

8. A computer program embedded on a computer readable medium storing a program for performing the steps comprising:

(a) storing in the database, data that includes at least one pattern of a plurality of molecules found in a sample containing a plurality of molecules, the data based upon a statistically significant number of different samples, the data including at least one parameter, which is data output from a mass spectrometry analysis, for each of the molecules found in each sample;

(b) comparing unknown data that comprises at least one parameter, which is data output from a mass spectrometry analysis, for each molecule found in a test sample with the data stored in the database;

(c) recording differences and similarities between the unknown data and data stored in the database;

(d) classifying a state of a sample by the steps of;

1) detecting a test pattern in the unknown data;

2) comparing the test pattern in the unknown data with the stored patterns in the database to identify differences and similarities; and

using the identified differences and similarities to confirm the state thereof.

9. The computer program of claim 8, wherein the data includes or indicates the molecular weights of the proteins or polypeptides in the patterns.

10. The computer program of claim 8, wherein the sample is selected from the group consisting of blood, urine, feces, saliva, sputum, tears, sweat, cerebral spinal fluid, pleural fluid, serums organ, tissue, cell, organelle and fractions thereof.

11. The computer program of claim 8, wherein the state is selected from the group consisting of:

a disease state, the presence of a toxin, the presence of a pathogen and aging.

12. The computer program of claim 8, wherein the pattern is a discriminatory pattern.

13. A method for processing data in a database contained in a storage medium, comprising the steps of:

i) storing a pattern in the database, based on data, which is output from mass spectrometry analysis, that includes at least one pattern, a) said pattern being the presence of and abundance of a plurality of molecules and at least one parameter for each of said plurality of molecule, b) said pattern being found in a sample that contains the plurality of molecules, c) the data being based upon a statistically significant number of different samples previously analyzed wherein each different sample corresponds to a particular reference state, and d) the data including at least one parameter for each of the molecules found in each sample;

ii) comparing unknown data from an output from mass spectrometry analysis that comprises the presence and abundance and at least one parameter for each of a plurality of molecules found in a test sample, with the data stored in the database by determining a test pattern in the unknown data that corresponds to plural molecules in a test sample;

iii) classifying a state of a test sample by the steps of;

detecting a test pattern in the unknown data;

comparing the test pattern in the unknown data with the stored patterns in the database to identify differences and similarities; and

using the identified differences and similarities to confinn the state of the test sample, and;

iv) reporting the state of the test sample.

14. The method of claim 13, wherein the parameter is molecular weight.

15. The method of claim 13, wherein the samples are selected from the group consisting of serum, organ, tissues, cells, organelles and fractions.

16. The method of claim 13, wherein the differences and similarities in the database indicate one of the following states:

aging, disease, presence of a toxin and presence of a pathogen.

17. The method of claim 13, wherein the state is selected from the group consisting of:

a disease state, the presence of a toxin, the presence of a pathogen and aging.

18. The method of claim 13, wherein the pattern is a discriminatory pattern.