Reference database

• US 6,539,102 B1
• Filed: 09/01/2000
• Issued: 03/25/2003
• Est. Priority Date: 09/01/2000
• Status: Expired due to Fees

• Current Assignee: Large Scale Proteomics Corporation
• Original Assignee: Large Scale Proteomics, Inc.
• Inventors: Anderson, N. Leigh, Anderson, Norman G.
• Primary Examiner(s): Chang, Jon
• Assistant Examiner(s): MILLER, MARTIN E
• Application Number:
  US09/654,133
• Time in Patent Office: 935 Days
• Field of Search: 382/128, 382/129, 382/133, 435/6, 204/452, 204/461, 702/19-23
• 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 creating a peptide and/or protein database comprising the steps of:

providing a first source of peptides and/or proteins and providing a second source of peptides and/or proteins wherein the first source and the second source are from different tissues, cells, organelles or fractions of each;

generating a 2-D separation of peptides and/or proteins of a first source;

generating a 2-D separation of peptides and/or proteins of a second source;

generating an electronic image of the 2-D separation of peptides and/or proteins of the first source;

generating an electronic image of the 2-D separation of peptides and/or proteins of the second source;

warping one of the electronic images of the 2-D separation of peptides and/or proteins to the other image;

determining peptides and/or proteins common to both the sources after said warping one of the electronic images by analyzing the two 2-D separations of peptides and/or proteins of the first and second sources;

characterizing a physical, chemical or biological property of the peptides and/or proteins previously determined to be common by a technique other than by the 2-D separation of peptides and/or proteins to establish protein identity, thereby confirming commonality of at least a portion of the peptides and/or proteins common to both of the 2-D separations of peptides and/or proteins;

after said confirming, recording in a peptide and/or protein database all peptides and/or said proteins common to both sources as being the same in response to positive confirmation of the portion of the peptides and/or proteins common to both 2-D separations of peptides and/or proteins, thereby generating a database or part of a database of peptides and/or proteins common to both sources;

analyzing peptides and/or proteins not common to both 2-D separations; and

recording in the peptides and/or proteins database results of said analyzing the peptides and/or proteins not common to both 2-D separations, thereby generating a database or part of a database of peptides and/or proteins in one source and not in another source or in a significantly different amount in another source, wherein said proteins and/or peptides not common to both 2-D separations or in a significantly different amount in another source distinguishes one source from another source.

2. The method for creating a peptide and/or protein database as set forth in claim 1, wherein said steps of generating the electronic images of the 2-D separation of peptides and/or proteins of the first and second sources comprises scanning 2-D electrophoresis gels.

3. The method for creating a peptide and/or protein database as set forth in claim 2, wherein said step of warping one of the electronic images of the 2-D separation of peptides and/or proteins to the other comprises electronically stretching, rotating and/or shrinking portions of the one of the electronic images so that at least a portion of spots on the 2-D electrophoresis gels are brought into alignment with one another.

4. The method for creating a peptide and/or protein database as set forth in claim 3, wherein said step of analyzing the two 2-D separations of peptides and/or proteins of the first and second sources to determine peptide and/or protein spots common to both tissues comprises the step of determining which peptide and/or protein spots in the two gel images are aligned with one another.

5. The method for creating a peptide and/or protein database as set forth in claim 4, wherein said step of confirming commonality between at least a portion of the peptide and/or protein spots common in both the two 2-D separations of peptides and/or proteins comprises the steps of:

excising several of the aligned spots common to both 2-D electrophoresis gels from the gels; and

subjecting the excised spots to mass spectrometry analysis.

6. The method for creating a peptide and/or protein database as set forth in claim 4, wherein said step of analyzing peptide and/or protein spots not common to both 2-D separations comprises the steps of:

excising plural spots not common to both 2-D electrophoresis gels from the gels; and

subjecting the excised spots to mass spectrometry analysis.

7. The method of claim 1, wherein said first source and said second source are two different tissues.

8. The method of claim 1, wherein said first source and said second source are samples obtained from two individuals of a population.

9. The method of claim 7, wherein said tissues are from one individual or from genetically identical individuals.

10. The method of claim 1, wherein said first source and said second source are two different cell types.

11. The method of claim 1, wherein said first source and said second source are two different organelles.

12. A method for creating a peptide and/or protein database comprising the steps of:

providing a first source of peptides and/or proteins and providing a second source of peptides and/or proteins wherein the second source is the same as the first source except wherein said second source comprises exposure of tissues, cells, organelles or fractions of each to varying conditions selected from the group consisting of environmental, chemical, disease and aging;

generating a 2-D separation of peptides and/or proteins of a first source;

generating a 2-D separation of peptides and/or proteins of a second source;

generating an electronic image of the 2-D separation of peptides and/or proteins of the first source;

generating an electronic image of the 2-D separation of peptides and/or proteins of the second source;

warping one of the electronic images of the 2-D separation of peptides and/or proteins to the other image;

determining peptides and/or proteins common to both the sources after said warping one of the electronic images by analyzing the two 2-D separations of peptides and/or proteins of the first and second sources;

characterizing a physical, chemical or biological property of the peptides and/or proteins previously determined to be common by a technique other than by the 2-D separation of peptides and/or proteins to establish protein identity, thereby confirming commonality of at least a portion of the peptides and/or proteins common to both of the 2-D separations of peptides and/or proteins;

after said confirming, recording in a peptide and/or protein database all peptides and/or said proteins common to both sources as being the same in response to positive confirmation of the portion of the peptides and/or proteins common to both 2-D separations of peptides and/or proteins, thereby generating a database or part of a database of peptides and/or proteins common to both sources;

analyzing peptides and/or proteins not common to both 2-D separations; and

recording in the peptides and/or proteins database results of said analyzing the peptides and/or proteins not common to both 2-D separations, thereby generating a database or part of a database of peptides and/or proteins in one source and not in another source or in a significantly different amount in another source, wherein said proteins and/or peptides not common to both 2-D separations or in a significantly different amount in another source distinguishes one source from another source.

13. The method for creating a peptide and/or protein database as set forth in claim 12, wherein said steps of generating the electronic images of the 2-D separation of peptides and/or proteins of the first and second sources comprises scanning 2-D electrophoresis gels.

14. The method for creating a peptide and/or protein database as set forth in claim 13, wherein said step of warping one of the electronic images of the 2-D separation of peptides and/or proteins to the other comprises electronically stretching, rotating and/or shrinking portions of the one of the electronic images so that at least a portion of spots on the 2-D electrophoresis gels are brought into alignment with one another.

15. The method for creating a peptide and/or protein database as set forth in claim 14, wherein said step of analyzing the two 2-D separations of peptides and/or proteins of the first and second sources to determine peptide and/or protein spots common to both tissues comprises the step of determining which peptide and/or protein spots in the two gel images are aligned with one another.

16. The method for creating a peptide and/or protein database as set forth in claim 15, wherein said step of confirming commonality between at least a portion of the peptide and/or protein spots common in both the two 2-D separations of peptides and/or proteins comprises the steps of:

excising several of the aligned spots common to both 2-D electrophoresis gels from the gels; and

subjecting the excised spots to mass spectrometry analysis.

17. The method for creating a peptide and/or protein database as set forth in claim 15, wherein said step of analyzing peptide and/or protein spots not common to both 2-D separations comprises the steps of:

excising plural spots not common to both 2-D electrophoresis gels from the gels; and

subjecting the excised spots to mass spectrometry analysis.

18. The method of claim 12, wherein said first source and said second source are samples obtained from two individuals of a population.

19. The method of claim 12, wherein said tissues are from one individual or from genetically identical individuals.