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First Claim
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1. A method for creating a peptide and/or protein database comprising the steps of:
- 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 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;
analyzing the two 2-D separation of peptides and/or proteins of the first and second sources to determine peptide and/or protein spots common to both tissues;
confirming commonality of at least a portion of the peptide and/or protein spots common in both the two 2-D separation of peptides and/or proteins;
recording in a peptide and/or protein database all peptide and/or protein spots common to both tissues as being the same in response to positive confirmation of the portion of the spots common to both 2-D separation of peptides and/or proteins;
analyzing peptide and/or protein spots not common to both 2-D separations; and
recording in the peptide and/or protein database results of said analyzing the peptide and/or protein spots not common to both 2-D separations.
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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.
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Citations
70 Claims
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1. A method for creating a peptide and/or protein database comprising the steps of:
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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 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;
analyzing the two 2-D separation of peptides and/or proteins of the first and second sources to determine peptide and/or protein spots common to both tissues;
confirming commonality of at least a portion of the peptide and/or protein spots common in both the two 2-D separation of peptides and/or proteins;
recording in a peptide and/or protein database all peptide and/or protein spots common to both tissues as being the same in response to positive confirmation of the portion of the spots common to both 2-D separation of peptides and/or proteins;
analyzing peptide and/or protein spots not common to both 2-D separations; and
recording in the peptide and/or protein database results of said analyzing the peptide and/or protein spots not common to both 2-D separations. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method for identifying a polypeptide in a sample from a mammal of a randomly breeding population, comprising:
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(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. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29)
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30. An ordered set of elements comprising at least N elements, wherein each of said N elements is a polypeptide or a protein, wherein presence or absence of each of said N elements is determined in at least 5 tissues from a single subject;
- each of said elements is analyzed by mass spectrometry and N is at least 10.
- View Dependent Claims (31, 32, 33, 34, 35, 36, 37, 38, 39)
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40. A machine readable storage medium comprising digitized data of an ordered array of N elements, wherein said N elements are proteins;
- and wherein said digitized data comprises expression of each of said N elements in at least 5 tissues of a single subject and a mass spectrometry scan of each of said elements; and
N is at least 10. - View Dependent Claims (41, 42, 43, 44, 45, 46, 47)
- and wherein said digitized data comprises expression of each of said N elements in at least 5 tissues of a single subject and a mass spectrometry scan of each of said elements; and
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48. A data processing system for determining identity of an element (N+1) to N elements of a database contained in a storage medium comprising:
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(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. - View Dependent Claims (49, 50, 51)
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52. A method for determining whether a protein spot on a first two dimensional gel (2DG) is the same or different from a spot on a second 2DG, when protein containing samples for said first and second gel are from different sources, comprising;
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establishing location of at least 10 landmark spots on each of said first 2DG and said second 2DG, obtaining an image of said first 2DG and said second 2DG, aligning said landmark image positions so that said landmark image positions of said second 2DG are in register with corresponding landmark image positions of said first 2DG; and
identifying a provisional identical spot image on said second 2DG that about aligns with said image of said protein spot on said first 2DG;
wherein said protein of said provisional identical spot image on said second 2DC is identified as the same protein of said protein spot of said first 2DG. - View Dependent Claims (53, 54, 55, 56, 57)
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58. Hierarchical dissection or separation method comprising the steps of:
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acquiring whole tissue samples from a statistically significant number of identified individuals;
analyzing the whole tissues by high resolution two-dimensional electrophoresis,;
acquiring images of the resulting gels;
processing said images by superimposing landmarks of said images, wherein same images are manipulated so that all landmarks are in register;
comparing the superimposed patterns to detect differences and similarities; and
recording said differences and similarities in a database. - View Dependent Claims (59, 60, 61, 62)
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63. A method of detecting proteins that have correlated expression, comprising:
comparing images of two-dimensional gels of a tissue sample from genetically similar or genetically identical individuals to detect two or more proteins with coordinated expression. - View Dependent Claims (64, 65)
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66. A method of removing proteins from a tissue sample prior to a method for separating the remaining proteins in said sample comprising;
- exposing said tissue sample to a solid matrix comprising a plurality of antibodies, wherein each of said antibodies specifically binds to a tissue protein, wherein said antibodies bind to at least five tissue proteins;
removing said tissue sample from said solid matrix; and
separating said remaining tissue proteins. - View Dependent Claims (67, 68, 69, 70)
- exposing said tissue sample to a solid matrix comprising a plurality of antibodies, wherein each of said antibodies specifically binds to a tissue protein, wherein said antibodies bind to at least five tissue proteins;
Specification