METHOD FOR DETERMINING THE QUALITY OF A BIOLOGICAL SAMPLE

• US 20090137063A1
• Filed: 11/28/2006
• Published: 05/28/2009
• Est. Priority Date: 11/29/2005
• Status: Abandoned Application

• Current Assignee: Denator Aktiebolag
• Original Assignee: Denator Aktiebolag
• Inventors: Svenningsson, Per, Svensson, Marcus, Skold, Karl, Andren, Per
• Application Number:
  US12/091,344
• Publication Number:
  US 20090137063A1
• Time in Patent Office: Days
• US Class Current: 436/501
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6842 Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G01N 33/6851 Methods of protein analysis involving laser desorption ionisation mass spectrometry
• CPC Class Codes: G01N 33/96 involving blood or serum control standard

Abstract

The present invention relates to a method of determining the quality of a biological sample. A method according to the invention may be used to determine if a biological sample is suitable to use in a further biological assay demanding samples of good quality to render an accurate result. The method comprises detecting the presence of protein fragments in the biological sample by using appropriate means. The invention also relates to a kit for determining the quality of a biological sample.

Claims

1. A method for identifying a biological marker for the quality of a biological sample comprising the steps;

a) detecting the presence and amount of degradation products of proteins and peptides in a test sample at one or more time points within 10 minutes post sampling, and

b) identifying a degradation product which is formed in a time dependent manner within 10 minutes post sampling as a biological marker for the quality of a biological sample.

2. A method according to claim 1, wherein said detection is performed by a method selected from, mass spectrometry, gel electrophoresis alone or in combination with mass spectrometry, two-dimensional difference gel electrophoresis (2D DIGE) alone or in combination with matrix-assisted laser desorption ionization mass spectrometry, liquid chromatography alone or in combination with mass spectrometry, capillary nanoscale liquid chromatography alone or in combination with electrospray ionization (quadrupole) time-of-flight (nanoLC/ESI Q-TOF) MS, surface plasmone resonance (SPR), quartz crystal microbalance-dissipation (QCM-D), and other immunological assays using antibodies directed to one or more of said protein, peptide and/or degradation product.

3. A method according to any of claims 1 to 2, wherein said sample originates from a tissue or a bodily fluid.

4. A method for determining the quality of a biological sample, wherein said quality is determined by detecting the presence and/or amount of a degradation product of a protein or a peptide, wherein said degradation product has been identified to be formed in a time dependent manner within 10 minutes post sampling in a comparable test sample.

5. A method according to claim 4, wherein said protein or peptide has a distinctive temporal degradation profile.

6. A method according to any of claims 4 to 5, wherein said peptide is a neuropeptide.

7. A method according to any of claims 4 to 5, wherein said protein is an acetylated protein.

8. A method according to any of claims 4 to 7 wherein said degradation product is peptide fragment.

9. A method according to claim 8 wherein said peptide fragment is a fragment of the protein stathmin.

10. A method according to claim 9 wherein said peptide fragment is an N-terminal fragment of the protein stathmin.

11. A method according to claim 10 wherein said peptide fragment is the peptide SEQ ID NO:

2.

12. A method according to any of claims 9 to 11, wherein the amount of a fragment of stathmin is compared with the amount of intact stathmin in said sample.

13. A method according to claim 12, wherein the fragments of stathmin in the biological sample are separated from intact stathmin in said sample before detection by means of size exclusion chromatography or ultrafiltration

14. A method according to any of claims 4 to 13, wherein said sample is taken from plasma, serum, urine, cerebrospinal fluid and/or a tissue biopsy

15. A method according to any of claims 4 to 14, wherein said biological sample is of mammalian origin.

16. A method according to claim 15, wherein said sample is of human origin.

17. A method according to any of claims 4 to 16, wherein said detection is preceded by an inactivation of said sample.

18. A method according to any of claims 4 to 17, wherein said detection is performed by a method selected from mass spectrometry, gel electrophoresis alone or in combination with mass spectrometry, two-dimensional difference gel electrophoresis (2D DIGE) alone or in combination with matrix-assisted laser desorption ionization mass spectrometry, liquid chromatography alone or in combination with mass spectrometry, capillary nanoscale liquid chromatography alone or in combination with electrospray ionization (quadrupole) time-of-flight (nanoLC/ESI Q-TOF) MS, surface plasmone resonance (SPR), quartz crystal microbalance-dissipation (QCM-D), and other immunological methods using antibodies directed to one or more of said protein, peptide and/or degradation product.

19. The peptide SEQ ID NO:

2.

20. An antibody directed to the peptide SEQ ID NO:

2.

21. Use of an antibody according to claim 20, for determining the quality of a biological sample.

23. A kit according to claim 22, comprising the antibody according to claim 20.

22. A kit for determining the quality of a biological sample, comprising an antibody to stathmin, optionally in combination with suitable reagents, for detecting the presence of stathmin and/or a fragment of stathmin in said sample.

24. A biological marker for determining the quality of a biological sample, characterized by:

a) being formed post sampling as a degradation product of a protein or a peptide present in said biological sample, and

b) being formed in a time dependent manner within 10 minutes post sampling in a comparable untreated test sample at 25°

C.

25. A biological marker according to claim 24, wherein said protein or peptide has a distinctive temporal degradation profile.

26. A biological marker according to any of claims 24 to 25, wherein said peptide is a neuropeptide.

27. A biological marker according to any of claims 24 to 25, wherein said protein is an acetylated protein.

28. A biological marker according to any of claims 24 to 27 which is a peptide fragment.

29. A biological marker according to claim 28 which is a fragment of the protein stathmin.

30. A biological marker according to claim 29 which is an N-terminal fragment of the protein stathmin.

31. A biological marker according to claim 30 which is the peptide SEQ ID NO:

2.

32. A method for determining the quality of a biological sample, wherein said quality is determined by detecting the total amount of degradation products of proteins and peptides in said sample, wherein

a) said degradation products are peptide fragments with a molecular weight less than 10 kDa, and

b) the quality of said biological sample is determined by comparing the total amount of peptide fragments present in the biological sample with the standard amount of peptide fragments and endogenous peptides present in comparable biological samples of high quality.

33. A method according to claim 32, wherein the ratio between the amount of peptides fragments and the amount of proteins and peptides is calculated, and wherein said ratio is compared to standard ratios for comparable biological samples of high quality.

34. A method according to any of claims 32 to 33, wherein said degradation products are peptide fragments with a molecular weight less than 5 kDa, preferably less than 3 kDa.

35. A method according to any of claims 32 to 34, wherein said detection is performed using a specific N-terminal or specific C-terminal reagent.

36. A method according to any of claims 32 to 35, wherein the peptide fragments in the biological sample are separated from the proteins and peptides of said sample before detection by means of size exclusion chromatography or ultrafiltration.