Mass defect labeling for the determination of oligomer sequences

• US 20060073485A1
• Filed: 08/06/2004
• Published: 04/06/2006
• Est. Priority Date: 10/19/2000
• Status: Active Grant

• Current Assignee: Target Discovery Incorporated
• Original Assignee: Taget Discovery Incorporated
• Inventors: Schneider, Luke V., Petesch, Robert, Hall, Michael P.
• Granted Patent: US 7,316,931 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: H01J 49/0045 characterised by the fragmentation or other specific reaction
• CPC Class Codes: Y10T 436/105831 Protein or peptide standard or control [e.g., hemoglobin, etc.]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
• CPC Class Codes: Y10T 436/25125 Digestion or removing interfering materials

Abstract

Mass tagging methods are provided that lead to mass spectrometer detection sensitivities and molecular discriminations that are improved over other methods. In particular the methods are useful for discriminating tagged molecules and fragments of molecules from chemical noise in the mass spectrum. These mass tagging methods are useful for oligomer sequencing, determining the relative abundances of molecules from different samples, and identifying individual molecules or chemical processing steps in combinatorial chemical libraries. The methods provided are useful for the simultaneous analysis of multiple molecules and reaction mixtures by mass spectrometric methods.

Claims

1-50. -50. (canceled)

51. A method for identifying a labeled molecule in a mass spectrum, the method comprising the steps of:

(a) accumulating a mass spectrum of a labeled molecule using a mass spectrometer, wherein the labeled molecule is labeled with a labeling moiety, said labeling moiety comprising at least one mass defect element having an atomic number from 17 to 77;

(b) discriminating between the mass of the labeled molecule and the mass of an unlabeled molecule in said mass spectrum based on the nuclear binding energy of the labeling moiety.

52. The method of claim 51, wherein said labeling moiety comprises at least one mass defect element of atomic number 35 to 63.

53. The method of claim 52, wherein said labeling moiety comprises at least one mass defect element of atomic number 39 to 58.

54. The method of claim 52, wherein said labeling moiety comprises at least one mass defect element selected from the group consisting of bromine, iodine, europium and yttrium.

55. The method of claim 54, wherein said mass defect element is europium.

56. The method of claim 54, wherein said mass defect element is yttrium.

57. The method of claim 54, wherein said mass defect element is bromine.

58. The method of claim 54, wherein said mass defect element is iodine.

59. The method of claim 51, wherein said labeled molecule is a labeled oligomer.

60. The method of claim 59, wherein said labeled oligomer is selected from the group consisting of a labeled protein, labeled oligonucleotide, labeled oligosaccharide, labeled lipid, and labeled polymer of synthetic origin.

61. The method of claim 60, wherein said labeled polymer of synthetic origin is a member selected from the group consisting of a labeled acrylate, labeled methacrylate, labeled nylon, labeled polyester, labeled polyimide, labeled nitrile rubber, and labeled polyolefin.

62. The method of claim 59, wherein said labeled oligomer is a labeled oligonucleotide.

63. The method of claim 51, wherein several labeled molecules, each labeled with a different number of mass defect elements are mixed prior to said accumulation of the mass spectrum.

64. The method of claim 59, wherein said labeled oligomer is a labeled oligomer fragment produced using an enzymatic, chemolytic or mass spectrometric fragmentation method.

65. The method of claim 64, wherein said mass spectrometer fragmentation method is selected from the group consisting of in-source collision-induced dissociation, and collision cell collision-induced dissociation.

66. The method of claim 51, wherein several labeled molecules, each with a different number of stable isotopes, are mixed prior to said accumulation of the mass spectrum.

67. The method of claim 66, wherein the stable isotope is independently selected from the group consisting of isotopes of H, C, N, O, Cl, Br, and S.

68. The method of claim 66, wherein the stable isotope is independently selected from ⁷⁹Br and ⁸¹Br.