Reference database

• US 7,133,544 B2
• Filed: 02/09/2005
• Issued: 11/07/2006
• 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): Wu, Jingge
• Assistant Examiner(s): Tabatabai, Abolfazl
• Application Number:
  US11/055,329
• Publication Number:
  US 20050170432A1
• Time in Patent Office: 636 Days
• Field of Search: 382128-134, 435/6, 435/7.1, 435/7.2, 435/7.8, 435/68.1, 435/69.1, 435/69.6, 435/69.7, 435/70.1, 435/71.1, 435/152, 435/804, 436/15, 436/85, 424/418, 424/460, 424/477, 424/491
• 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 identifying a polypeptide in a sample from a mammal of a randomly breeding population, comprising:

(a) characterizing said polypeptide by isoelectric point;

(b) characterizing said polypeptide by molecular weight; and

(c) identifying tissues of said subject where said polypeptide is found, wherein at least 5 tissues are examined, to yield distinguishing parameters of said polypeptide comprising isoelectric point, molecular weight and tissue distribution;

(d) comparing said distinguishing parameters of said polypeptide with distinguishing parameters of previously tested polypeptides of a set; and

(e) determining whether a previously tested polypeptide of said set has said distinguishing parameters of said polypeptide,

wherein said polypeptide is identified as being said previously tested polypeptide when said distinguishing parameters of said polypeptide match the parameters of said previously tested polypeptide, or adding said polypeptide and said distinguishing parameters to said set when said distinguishing parameters of said polypeptide are unique to said set.

2. The method of claim 1, wherein said set comprises identifying patterns of at least 10 proteins.

3. The method of claim 2, wherein said set comprises identifying patterns of at least 20 proteins.

4. The method of claim 3, wherein said set comprises identifying patters of at least 30 proteins.

5. The method of claim 4, wherein said set comprises identifying patterns of at 40 proteins.

6. The method of claim 5, wherein said set comprises identifying patterns of at 50 proteins.

7. The method of claim 1, further comprising characterizing said polypeptide yield one or more additional distinguishing parameters of said polypeptide.

8. The method of claim 7, wherein said additional distinguishing parameter comprises a partial primary amino acid sequence of said polypeptide, or fragment thereof.

9. The method of claim 7, wherein said additional distinguishing parameter is mass spectrometry data of said polypeptide, or fragment thereof.

10. The method of claim 9, wherein said spectrometry data is obtained by matrix-assisted laser desorption ionization (MALDI).

11. The method of claim 10, wherein said MALDI spectrometry comprises time of flight (TOF) analysis.

12. The method of claim 1, wherein at least 7 tissues are examined.

13. The method of claim 12, wherein at least 9 tissues are examined.

14. The method of claim 13, wherein at least 11 tissues are examined.

15. The method of claim 14, wherein at least 13 tissues are examined.

16. The method of claim 1, where said step (d) is conducted by a data processing means.

17. The method of claim 16, further comprising characterizing the spatial relationship of said polypeptide with one or more of said previously tested polypeptides on stained two dimensional electrophoresis gels.

18. The method of claim 1, wherein said steps (a) and (b) are obtained by two-dimensional gel electrophoresis.

19. A data processing system for determining identity of an element (N+1) to N elements of a database contained in a storage medium comprising:

(a) computer processing means for processing data;

(b) data storage means for storing data in said database contained in said storage medium; and

(c) means for processing data regarding comparing a parameter of said (N+1) element with said parameter of said N elements of said database,

wherein said element is a protein or polypeptide;

wherein step (c) is repeated at least M times, wherein each of M parameters is examined at each iteration, wherein M is 3 or more; and

wherein when said (N+1) element does not have M identical parameters of one of said N elements, said data storage means (b) adds data of said (N+1) element and of said M parameters thereof to said database to produce a new database comprising (N+1) elements.

20. The system of claim 19, wherein said element is a protein or polypeptide.

21. The system of claim 20, wherein said two of said three parameters are molecular weight and isoelectric point.

22. The system of claim 20, wherein one of said three elements is a mass spectrometry analysis of said element.