Fourier transform mass spectrometry of complex biological samples

• US 6,680,203 B2
• Filed: 12/12/2000
• Issued: 01/20/2004
• Est. Priority Date: 07/10/2000
• Status: Expired due to Fees

• Current Assignee: Esperion Therapeutics, Inc.
• Original Assignee: Esperion Therapeutics, Inc.
• Inventors: Dasseux, Jean-Louis H., Rea, Thomas J., Bisgaier, Charles L., Newton, Roger S., Pape, Michael E.
• Primary Examiner(s): Warden, Jill
• Assistant Examiner(s): GAKH, YELENA G
• Application Number:
  US09/735,707
• Publication Number:
  US 20020019023A1
• Time in Patent Office: 1,134 Days
• Field of Search: 436/86, 436/173
• US Class Current: 436/86
• CPC Class Codes: G01N 33/5008 for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
• CPC Class Codes: G01N 33/5011 for testing antineoplastic activity
• CPC Class Codes: G01N 33/502 for testing non-proliferative effects
• CPC Class Codes: G01N 33/5038 involving detection of metabolites per se
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

The present invention relates to methods for high information content (HIC) analysis or screening of complex biological systems using Fourier transform mass spectrometry (FTMS). The present methods are useful for analyzing complex biological mixtures containing both high molecular weight molecules (e.g., polynucleotides, proteins, polysaccharides) and low molecular weight molecules (e.g., oligonucleotides, peptides, lipids, oligosaccharides, steroid hormones, catabolic and metabolic intermediates) permit the elucidation of molecular differences between complex biological samples, and permit the identification of biologically active molecules (e.g. therapeutically active drugs, etc.).

Claims

1. A method for identifying one or more endogenous molecules that differ in abundance between a first cell population and a second cell population, comprising:

(a) comparing a first Fourier Transform Mass Spectrometry (FTMS) peak profile obtained from the first cell population with a second FTMS peak profile obtained from the second cell population;

(b) identifying one or more peaks that differ in intensity in the first FTMS peak profile relative to the second FTMS peak profile, which one or more peaks correspond to one or more molecules that differ in abundance between a first cell population and a second cell population; and

(c) identifying said one or more said endogenals molecules that differ in abundance between a first cell population and a second cell population either directly from mass-to-charge (m/z) ratio or through additional fragmentation of said one or more molecules.

2. The method of claim 1, wherein the first and second cell populations do not contain a label.

3. The method of claim 1, further comprising:

(c) prior to step (a), obtaining the first FTMS peak profile from the first cell population by subjecting said first cell population to FTMS.

4. The method of claim 1, further comprising:

(c) prior to step (a), obtaining the second FTMS peak profile from the second cell population by subjecting said second cell population to FTMS.

5. The method of claim 3, further comprising:

(d) prior to step (a), obtaining the second FTMS peak profile from the second cell population by subjecting said second cell population to FTMS.

6. The method of any one of claims 1-5, wherein the first cell population is a reference cell population and the second cell population is a test cell population.

7. The method of claim 6, wherein the first and second cell population are of different cell types.

8. The method of claim 7, wherein the first and second cell populations are of different tissue types from the same organism.

9. The method of claim 7, wherein the first and second cell populations are of the same tissue type from different organisms.

10. The method of claim 6, wherein the first and second cell populations are of the same cell type.

11. The method of claim 10, wherein the first cell population is a normal cell population, the second cell population is a diseased cell population and the one or more molecules are markers for the disease.

12. The method of claim 11, wherein the diseased cell population is a cancerous cell population and said markers are the markers for cancer.

13. The method of claim 12, wherein the cancerous cell population is a population of melanoma, myeloid leukemia, or carcinoma cells.

14. The method of claim 13, wherein the carcinoma is lung, breast, ovarian, colon, kidney, prostate, pancreatic, stomach, brain, lymphatic system, thymic, thyroid, adrenal or testicular carcinoma.

15. The method of claim 11, wherein the diseased cell population is from an individual with cardiovascular disease and said markers are the markers for cardiovascular disease.

16. The method of claim 15, wherein the diseased cell population is a population of cardiomyocytes, endothelial cells, macrophages, hepatocytes, adipocytes, smooth muscle cells or intestinal cells.

17. The method of claim 11, wherein the diseased cell population is from an individual with diabetes and said markers are the markers for diabetes.

18. The method of claim 17, wherein the diseased cell population is a population of cardiomyocytes, endothelial cells, macrophages, pancreatic cells, hepatocytes, adipocytes, smooth muscle cells or intestinal cells.

19. The method of claim 11, wherein the diseased cell population is from an obese individual.

20. The method of claim 19, wherein the diseased cell population is a population of cardiomyocytes, endothelial cells, macrophages, hepatocytes, adipocytes, smooth muscle cells or intestinal cells.

21. The method of claim 10, wherein the first cell population has not been subjected to a test agent and the second cell population has been subjected to the test agent.

22. The method of claim 21, wherein the test agent is a known drug.

23. The method of claim 21, wherein the test agent is a drug candidate.

24. The method of claim 21, wherein the test agent is a small molecule.

25. The method of claim 21, wherein the test agent is a protein.

26. The method of claim 25, wherein the protein is a hormone, a growth factor, a cytokine, a ligand, or an antibody.

27. The method of claim 21, wherein the test agent is a nucleic acid.

28. The method of claim 27, wherein the nucleic acid is a DNA, an RNA, or a DNA-RNA hybrid.

29. The method of claim 6, wherein the first FTMS peak profile is a historical control.

30. The method of claim 6, wherein the first FTMS peak profile is a concurrent control.

31. The method of any one of claims 1-5, wherein the first and second cell populations are populations of primary cells from a tissue or organ.

32. The method of claim 31, wherein in the primary cells are primary brain, skin, lung, endothelial, epithelial, adipose, muscle, bone, stomach, colon, spleen, pancreas, kidney, bladder, heart, lymphatic system, blood, or liver cells.