Methods and systems for analyzing complex biological systems

• US 20040018500A1
• Filed: 11/20/2002
• Published: 01/29/2004
• Est. Priority Date: 11/21/2001
• Status: Abandoned Application

• Current Assignee: Icoria, Inc. (Abbvie Incorporated)
• Original Assignee: Icoria, Inc. (Abbvie Incorporated)
• Inventors: Winfield, Stephanie, Beecher, Christopher, Glassbrook, Norman, Nye, Gordon James, Ranasinghe, Yasmin, Broadwell, David, Popa-Burke, Ioana
• Application Number:
  US10/300,543
• Publication Number:
  US 20040018500A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 30/72 Mass spectrometers mass spectrometers per se H01J49/00
• CPC Class Codes: G01N 30/8655 Details of data formats
• CPC Class Codes: G01N 30/8658 Optimising operation parameters
• CPC Class Codes: G01N 30/8662 Expert systems; optimising a large number of parameters
• CPC Class Codes: G01N 30/8679 Target compound analysis, i.e. whereby a limited number of peaks is analysed
• CPC Class Codes: G01N 30/8693 Models, e.g. prediction of retention times, method development and validation
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface

Abstract

The present invention provides methods and systems for organizing complex and disparate data. More specifically, the present invention provides methods and systems for organizing complex and disparate data into coherent data sets. Coherent data sets resulting from the methods and systems of the present invention serve as models for biological systems. Methods and systems for integrating data and creating coherent data sets are useful for numerous biological applications, such as, for example, determining gene function, identifying and validating drug and pesticide targets, identifying and validating drug and pesticide candidate compounds, profiling drug and pesticide compounds, producing a compilation of health or wellness profiles, determining compound site(s) of action, identifying unknown samples, and numerous other applications in the agricultural, pharmaceutical, forensic, and biotechnology industries.

Claims

1. A method for examining chemical components in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least two processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier; and

d) characterizing and/or identifying said chemical components.

4. The method according to claim 1, wherein said plurality of peaks comprises at least 100 peaks.

5. The method according to claim 1, wherein said plurality of peaks comprises at least 500 peaks.

6. The method according to claim 1, wherein said plurality of peaks comprises at least 1000 peaks.

7. The method according to claim 1, wherein said characterized and/or identified chemical component is linked to a metabolite in a biochemical pathway.

8. The method according to claim 7, wherein said linkage with a biochemical pathway enables disease diagnosis or prognosis.

9. The method according to claim 1, wherein said characterized and/or identified chemical component is correlated with a phenotype.

10. The method according to claim 1, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

11. The method according to claim 1, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

12. The method according to claim 11, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

13. The method according to claim 12, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

14. The method according to claim 13, wherein the biological sample is the human HepG2 cell line.

15. The method according to claim 11, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

16. The method according to claim 11, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

17. The method according to claim 11, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

18. The method according to claim 11, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

111. The method according to claim 110, wherein the biological sample is the human HepG2 cell line.

118. The method according to claim 117, wherein two of said three processes are LC-MS and GC-MS.

19. A method for examining chemical components in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least three processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier; and

d) characterizing and/or identifying said chemical components.

2. The method according to claim 34, wherein said two processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

3. The method according to claim 2, wherein said two processes are LC-MS and GC-MS.

20. The method according to claim 19, wherein said three processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

21. The method according to claim 20, wherein two of said three processes are LC-MS and GC-MS.

22. The method according to claim 20, wherein said three processes are LC-MS, GC-MS, and FT-MS.

23. The method according to claim 20, wherein said three processes are LC-MS, GC-MS, and NMR.

24. The method according to claim 20, wherein said three processes are LC-MS, GC-MS, and ICP-MS.

25. The method according to claim 19, wherein said plurality of peaks comprises at least 100 peaks.

26. The method according to claim 19, wherein said plurality of peaks comprises at least 500 peaks.

27. The method according to claim 19, wherein said plurality of peaks comprises at least 1000 peaks.

28. The method according to claim 19, wherein said characterized and/or identified chemical component is linked to a metabolite in a biochemical pathway.

29. The method according to claim 28, wherein said linkage with a biochemical pathway enables disease diagnosis or prognosis.

30. The method according to claim 19, wherein said characterized and/or identified chemical component is correlated with a phenotype.

31. The method according to claim 19, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

32. The method according to claim 19, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

33. The method according to claim 32, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

34. The method according to claim 33, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

35. The method according to claim 34, wherein the biological sample is the human HepG2 cell line.

36. The method according to claim 32, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

37. The method according to claim 32, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

38. The method according to claim 19, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

39. The method according to claim 19, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

40. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component;

c) storing in said computer tracking system said chemical component data, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways.

41. The method according to claim 40, wherein said data are selected from the group consisting of liquid chromatography (LC) data, high-pressure liquid chromatography (HPLC) data, mass spectroscopy (MS) data, gas chromatography (GC) data, liquid chromatography/mass spectroscopy (LC-MS) data, gas chromatography/mass spectroscopy (GC-MS) data, Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS) data, nuclear magnetic resonance (NMR) data, magnetic resonance imaging (MRI) data, Fourier Transform InfraRed (FT-IR) data, and inductively coupled plasma mass spectrometry (ICP-MS) data.

42. The method according to claim 40, wherein said plurality of peaks comprises at least 100 peaks.

43. The method according to claim 40, wherein said plurality of peaks comprises at least 500 peaks.

44. The method according to claim 40, wherein said plurality of peaks comprises at least 1000 peaks.

45. The method according to claim 40, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

46. The method according to claim 40, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

47. The method according to claim 46, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

48. The method according to claim 47, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

49. The method according to claim 48, wherein the biological sample is the human HepG2 cell line.

50. The method according to claim 46, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

51. The method according to claim 46, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

52. The method according to claim 40, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

53. The method according to claim 40, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

54. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least two processes;

c) storing in said computer tracking system said chemical component data, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways.

55. The method according to claim 54, wherein said two processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

56. The method according to claim 55, wherein said two processes are LC-MS and GC-MS.

57. The method according to claim 54, wherein said plurality of peaks comprises at least 100 peaks.

58. The method according to claim 54, wherein said plurality of peaks comprises at least 500 peaks.

59. The method according to claim 54, wherein said plurality of peaks comprises at least 1000 peaks.

60. The method according to claim 54, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

61. The method according to claim 54, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

62. The method according to claim 61, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

63. The method according to claim 62, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

64. The method according to claim 63, wherein the biological sample is the human HepG2 cell line.

65. The method according to claim 61, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

66. The method according to claim 61, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

67. The method according to claim 54, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

68. The method according to claim 54, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

69. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least three processes;

c) storing in said computer tracking system said chemical component data, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways.

70. The method according to claim 69, wherein said three processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

71. The method according to claim 70, wherein two of said three processes are LC-MS and GC-MS.

72. The method according to claim 70, wherein said three processes are LC-MS, GC-MS, and FT-MS.

73. The method according to claim 70, wherein said three processes are LC-MS, GC-MS, and NMR.

74. The method according to claim 70, wherein said three processes are LC-MS, GC-MS, and ICP-MS.

75. The method according to claim 69, wherein said plurality of peaks comprises at least 100 peaks.

76. The method according to claim 69, wherein said plurality of peaks comprises at least 500 peaks.

77. The method according to claim 69, wherein said plurality of peaks comprises at least 1000 peaks.

78. The method according to claim 69, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

79. The method according to claim 69, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

80. The method according to claim 79, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

81. The method according to claim 80, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

82. The method according to claim 81, wherein the biological sample is the human HepG2 cell line.

83. The method according to claim 79, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

84. The method according to claim 79, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

85. The method according to claim 69, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

86. The method according to claim 69, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

87. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways or to phenotypes.

88. The method according to claim 87, wherein said data are selected from the group consisting of liquid chromatography (LC) data, high-pressure liquid chromatography (HPLC) data, mass spectroscopy (MS) data, gas chromatography (GC) data, liquid chromatography/mass spectroscopy (LC-MS) data, gas chromatography/mass spectroscopy (GC-MS) data, Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS) data, nuclear magnetic resonance (NMR) data, magnetic resonance imaging (MRI) data, Fourier Transform InfraRed (FT-IR) data, and inductively coupled plasma mass spectrometry (ICP-MS) data.

89. The method according to claim 87, wherein said plurality of peaks comprises at least 100 peaks.

90. The method according to claim 87, wherein said plurality of peaks comprises at least 500 peaks.

91. The method according to claim 87, wherein said plurality of peaks comprises at least 1000 peaks.

92. The method according to claim 87, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

93. The method according to claim 87, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

94. The method according to claim 93, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

95. The method according to claim 94, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

96. The method according to claim 95, wherein the biological sample is the human HepG2 cell line.

97. The method according to claim 93, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

98. The method according to claim 93, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

99. The method according to claim 87, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

100. The method according to claim 87, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

101. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least two processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways or to phenotypes.

102. The method according to claim 101, wherein said two processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

103. The method according to claim 102, wherein said two processes are LC-MS and GC-MS.

104. The method according to claim 101, wherein said plurality of peaks comprises at least 100 peaks.

105. The method according to claim 101, wherein said plurality of peaks comprises at least 500 peaks.

106. The method according to claim 101, wherein said plurality of peaks comprises at least 1000 peaks.

107. The method according to claim 101, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

108. The method according to claim 101, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

109. The method according to claim 108, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

110. The method according to claim 109, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

112. The method according to claim 108, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

113. The method according to claim 108, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

114. The method according to claim 101, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

115. The method according to claim 101, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

116. A method for examining metabolites in a biological sample, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least three processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) characterizing and/or identifying said chemical components; and

e) linking said characterized and/or identified chemical components to metabolites in biochemical pathways or to phenotypes.

117. The method according to claim 116, wherein said three processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

119. The method according to claim 117, wherein said three processes are LC-MS, GC-MS, and FT-MS.

120. The method according to claim 117, wherein said three processes are LC-MS, GC-MS, and NMR.

121. The method according to claim 117, wherein said three processes are LC-MS, GC-MS, and ICP-MS.

122. The method according to claim 116, wherein said plurality of peaks comprises at least 100 peaks.

123. The method according to claim 116, wherein said plurality of peaks comprises at least 500 peaks.

124. The method according to claim 116, wherein said plurality of peaks comprises at least 1000 peaks.

125. The method according to claim 116, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

126. The method according to claim 116, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

127. The method according to claim 126, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, and rodent.

128. The method according to claim 127, wherein the biological sample is selected from the group consisting of liver tissue, liver spheroids, or liver cells.

129. The method according to claim 128, wherein the biological sample is the human HepG2 cell line.

130. The method according to claim 126, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

131. The method according to claim 126, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

132. The method according to claim 116, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

133. The method according to claim 116, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

134. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) storing in said computer tracking system data from said sample, wherein said data are linked to said unique identifier;

c) comparing said linked data to a reference; and

d) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

135. The method according to claim 134, wherein said data are selected from the group consisting of RNA data, DNA data, protein data, metabolite data, and phenotypic data.

136. The method according to claim 134, wherein said data consist of two types of data.

137. The method according to claim 134, wherein said data consist of three types of data.

138. The method according to claim 134, wherein said data consist of four types of data.

139. The method according to claim 134, wherein said data consist of five types of data.

140. The method according to claim 134, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

141. The method according to claim 134, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

142. The method according to claim 141, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

143. The method according to claim 141, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

144. The method according to claim 141, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

145. The method according to claim 134, wherein said signature profile is indicative of a particular disease or disease stage.

146. The method according to claim 134, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

147. The method according to claim 134, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

148. The method according to claim 134, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

149. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) storing in said computer tracking system metabolite data from said sample, wherein said data are linked to said unique identifier;

c) comparing said linked data to a reference; and

d) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

150. The method according to claim 149, wherein said data are selected from the group consisting of liquid chromatography (LC) data, high-pressure liquid chromatography (HPLC) data, mass spectroscopy (MS) data, gas chromatography (GC) data, liquid chromatography/mass spectroscopy (LC-MS) data, gas chromatography/mass spectroscopy (GC-MS) data, Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS) data, nuclear magnetic resonance (NMR) data, magnetic resonance imaging (MRI) data, Fourier Transform InfraRed (FT-IR) data, and inductively coupled plasma mass spectrometry (ICP-MS) data.

151. The method according to claim 149, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

152. The method according to claim 149, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

153. The method according to claim 152, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

154. The method according to claim 152, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

155. The method according to claim 152, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

156. The method according to claim 149, wherein said signature profile is indicative of a particular disease or disease stage.

157. The method according to claim 149, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

158. The method according to claim 149, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

159. The method according to claim 149, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

160. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) storing in said computer tracking system metabolite data from said sample, wherein said data are from at least two different processes and are linked to said unique identifier;

c) comparing said linked data to a reference; and

d) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

161. The method according to claim 160, wherein said two processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

162. The method according to claim 161, wherein said two processes are LC-MS and GC-MS.

163. The method according to claim 160, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

164. The method according to claim 160, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

165. The method according to claim 164,. wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

166. The method according to claim 164, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

167. The method according to claim 164, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

168. The method according to claim 160, wherein said signature profile is indicative of a particular disease or disease stage.

169. The method according to claim 160, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

170. The method according to claim 160, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

171. The method according to claim 160, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

172. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) storing in said computer tracking system metabolite data from said sample, wherein said data are from at least three different processes and are linked to said unique identifier;

c) comparing said linked data to a reference; and

d) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

173. The method according to claim 172, wherein said three processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

174. The method according to claim 173, wherein two of said three processes are LC-MS and GC-MS.

175. The method according to claim 173, wherein said three processes are LC-MS, GC-MS, and FT-MS.

176. The method according to claim 173, wherein said three processes are LC-MS, GC-MS, and NMR.

177. The method according to claim 173, wherein said three processes are LC-MS, GC-MS, and ICP-MS.

178. The method according to claim 172, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

179. The method according to claim 172, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

180. The method according to claim 179, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

181. The method according to claim 179, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

182. The method according to claim 179, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

183. The method according to claim 172, wherein said signature profile is indicative of a particular disease or disease stage.

184. The method according to claim 172, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

185. The method according to claim 172, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

186. The method according to claim 172, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

187. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) comparing said linked data to a reference; and

e) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

188. The method according to claim 187, wherein said data are selected from the group consisting of liquid chromatography (LC) data, high-pressure liquid chromatography (HPLC) data, mass spectroscopy (MS) data, gas chromatography (GC) data, liquid chromatography/mass spectroscopy (LC-MS) data, gas chromatography/mass spectroscopy (GC-MS) data, Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS) data, nuclear magnetic resonance (NMR) data, magnetic resonance imaging (MRI) data, Fourier Transform InfraRed (FT-IR) data, and inductively coupled plasma mass spectrometry (ICP-MS) data.

189. The method according to claim 187, wherein said plurality of peaks comprises at least 100 peaks.

190. The method according to claim 187, wherein said plurality of peaks comprises at least 500 peaks.

191. The method according to claim 187, wherein said plurality of peaks comprises at least 1000 peaks.

192. The method according to claim 187, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

193. The method according to claim 187, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

194. The method according to claim 193, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

195. The method according to claim 193, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

196. The method according to claim 193, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

197. The method according to claim 193, wherein said signature profile is indicative of a particular disease or disease stage.

198. The method according to claim 193, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

199. The method according to claim 193, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

200. The method according to claim 193, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

201. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least two processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) comparing said linked data to a reference; and

e) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

202. The method according to claim 201, wherein said two processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

203. The method according to claim 202, wherein said two processes are LC-MS and GC-MS.

204. The method according to claim 201, wherein said plurality of peaks comprises at least 100 peaks.

205. The method according to claim 201, wherein said plurality of peaks comprises at least 500 peaks.

206. The method according to claim 201, wherein said plurality of peaks comprises at least 1000 peaks.

207. The method according to claim 201, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

208. The method according to claim 201, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

209. The method according to claim 208, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

210. The method according to claim 208, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

211. The method according to claim 208, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

212. The method according to claim 201, wherein said signature profile is indicative of a particular disease or disease stage.

213. The method according to claim 201, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

214. The method according to claim 201, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

215. The method according to claim 201, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.

216. A method for establishing a signature profile indicative of the physiological status of an individual, comprising:

a) entering a unique identifier of at least one biological sample into a computer tracking system;

b) simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least three processes;

c) storing said data in said computer tracking system, wherein said data are linked to said unique identifier;

d) comparing said linked data to a reference; and

e) determining the most informative of said compared data;

wherein said most informative data are a signature profile indicative of physiological status.

217. The method according to claim 216, wherein said three processes are selected from the group consisting of liquid chromatography (LC), high-pressure liquid chromatography (HPLC), mass spectroscopy (MS), hyphenated mass spectroscopy (MS-MS), gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

218. The method according to claim 217, wherein two of said three processes are LC-MS and GC-MS.

219. The method according to claim 217, wherein said three processes are LC-MS, GC-MS, and FT-MS.

220. The method according to claim 217, wherein said three processes are LC-MS, GC-MS, and NMR.

221. The method according to claim 217, wherein said three processes are LC-MS, GC-MS, and ICP-MS.

222. The method according to claim 216, wherein said plurality of peaks comprises at least 100 peaks.

223. The method according to claim 216, wherein said plurality of peaks comprises at least 500 peaks.

224. The method according to claim 216, wherein said plurality of peaks comprises at least 1000 peaks.

225. The method according to claim 216, wherein the computer tracking system is a Laboratory Information Management System (LIMS).

226. The method according to claim 216, wherein the biological sample is selected from the group consisting of animalia, plantae, protista, monera, and fungi.

227. The method according to claim 226, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.

228. The method according to claim 226, wherein the biological sample is selected from the group consisting of Arabidopsis, corn, wheat, barley, rye, legumes, mint, tobacco, tomatoes, rice, spinach, and peas.

229. The method according to claim 226, wherein the biological sample is selected from the group consisting of Magnaporthe, Candida, Mycosphaerella, Botrytis, Saccharomyces, Aspergillus, Puccinia, Erysiphe, Ustilago, Fursarium, Phytophthora and Penicillium.

230. The method according to claim 216, wherein said signature profile is indicative of a particular disease or disease stage.

231. The method according to claim 216, wherein said signature profile is indicative of the efficacy of a therapeutic program or exposure to a particular chemical.

232. The method according to claim 216, wherein the biological sample is selected from the group consisting of a healthy organism, a diseased organism, a drug-treated organism, and a genetically altered organism.

233. The method according to claim 216, wherein the biological sample is an organism having received an environmental insult or an organism having received a chemical insult.