Reference database

• US 6,980,674 B2
• Filed: 01/04/2001
• Issued: 12/27/2005
• Est. Priority Date: 09/01/2000
• Status: Expired due to Fees

• Current Assignee: Large Scale Proteomics Corporation
• Original Assignee: Large Scale Proteomics Corporation
• Inventors: Anderson, N. Leigh, Anderson, Norman G.
• Primary Examiner(s): Mehta, Bhavesh M.
• Assistant Examiner(s): Tabatabai, Abolfazl
• Application Number:
  US09/753,678
• Publication Number:
  US 20020028005A1
• Time in Patent Office: 1,818 Days
• Field of Search: 382/128, 382/129, 382/130, 382/131, 382/132, 382/133, 424/418, 424/460, 424/477, 424/491, 435/7.1, 435/68.1, 435/6, 435/7.8, 435/23, 435/69.1, 435/69.6, 435/69.7, 435/70.1, 435/71.1, 435/152, 435/219, 435/337, 435/272, 436/15, 436/86, 204/461, 204/456, 204/466, 204/467, 204/606, 204/610, 204/612, 204/616, 204/617, 204/618, 204/626, 422/63, 422/67, 422/65, 422/68.1, 422/99, 422/100, 422/102, 930/30, 930/200, 930/210, 930/220, 930/230, 930/270, 530/352, 530/359, 530/370, 530/382
• 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: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins
• 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
• CPC Class Codes: Y10T 436/105831 Protein or peptide standard or control [e.g., hemoglobin, etc.]

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:

collecting a plurality of samples;

separating each sample into proteins and/or polypeptides to provide discrimination and resolution of the proteins and/or polypeptides using one technique selected from the following techniques;

chromatography;

immunoelectrophoresis, mass spectrometry or electrophoresis;

storing in the database data that includes at least one pattern representing the separated proteins and/or polypeptides, the data based upon a statistically significant number of samples, the data including at least one parameter of each sample;

comparing unknown data with the data stored in the database;

recording differences and similarities.

2. The method of claim 1, wherein the parameter is one selected from the group consisting of:

molecular weight and isoelectric point.

3. The method of claim 1, wherein parameter is data output from a mass spectrometry analysis.

4. The method of claim 1, wherein the samples are selected from one of the group consisting of serum, organ, tissues, cells, organelles 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 a state is classified, the state 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, further comprising the step of:

classifying a state of a sample by the steps of;

a. detecting a pattern in the sample;

b. comparing the pattern in the sample with the stored patterns in the database to identify differences and similarities; and

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

8. The method of claim 7, 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.

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