TECHNIQUES FOR HIGH THROUGHPUT TARGETED PROTEOMIC ANALYSIS AND RELATED SYSTEMS AND METHODS

• US 20190310264A1
• Filed: 06/01/2017
• Published: 10/10/2019
• Est. Priority Date: 06/03/2016
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Everley, Robert A., Erickson, Brian K., Rose, Christopher Michael, Gygi, Steven P.
• Granted Patent: US 11,085,927 B2
• Time in Patent Office: Days
• CPC Class Codes: G01N 2333/91215 with a definite EC number (2.7.1.-)
• CPC Class Codes: G01N 2458/15 Non-radioactive isotope labels, e.g. for detection by mass spectrometry
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: H01J 43/26 Box dynodes

Abstract

Described herein is a kit of materials prepared for assays that involve determining relative abundance and/or absolute abundance of various targeted peptides. The kit may comprise trigger versions of target peptides with masses offset from the respective target peptides by predetermined and known amounts. The trigger peptides may be present in amounts that may be readily detected via a mass spectrometry analysis. When mixed with samples that are analyzed, detection of the trigger peptides indicates where in the mass-spectrometer output the target peptide may be found. The kit may include a predetermined amount of synthetic versions of one or more of the target peptides. A measured relative abundance of this synthetic peptide relative to that of the target peptides yields an absolute quantitative value of the target peptide. Also disclosed is a method of preparing a plurality of samples to be submitted for mass spectrometer analysis in parallel.

Claims

1. A kit for performing an assay to determine a disease and/or condition state of an organism, the kit comprising:

a plurality of peptides proteotypic of a protein whose expression is characteristic of the disease and/or condition state, wherein the plurality of peptides are mass-tagged peptides.

2. The kit of claim 1, further comprising information identifying a first mass tag, wherein the plurality of peptides includes:

a population of a first peptide mass-tagged with the first mass tag, and

a population of a second peptide mass-tagged with the first mass tag.

3. The kit of claim 2, wherein the population of the first peptide comprises:

a first plurality of molecules of the first peptide, each molecule of the first plurality of molecules having a first mass, and

a second plurality of molecules of the first peptide, each molecule of the second plurality of molecules having a second mass, different from the first mass, and

wherein molecules of the second plurality of molecules are chemically identical to one another and to each molecule of the first plurality of molecules.

4. The kit of claim 3, further comprising:

information indicating a quantity of the first plurality of molecules of the first peptide and a quantity of the second plurality of molecules of the first peptide; and

information indicating the first mass and the second mass.

5. The kit of claim 3, further comprising:

information indicating a plurality of mass spectrometry target fragment masses.

6. The kit of claim 1, wherein the disease and/or condition state is cancer.

7. (canceled)

8. A composition of mass-tagged peptide molecules having known molecular masses for use as mass spectrometry triggers, the composition comprising:

a population of first trigger molecules, wherein each first trigger molecule of the population of first trigger molecules includes a peptide portion bonded to a tag portion, the peptide portion being a first peptide and the tag portion being a first mass tag; and

a population of second trigger molecules, wherein each second trigger molecule of the population of second trigger molecules includes a peptide portion bonded to a tag portion, the peptide portion being a second peptide, different from the first peptide, and the tag portion being the first mass tag.

9. The composition of claim 8, wherein the peptide portion of the first trigger molecules has a length of at least five amino acids and no more than fifty amino acids.

10. The composition of claim 9, wherein the peptide portion of the first trigger molecules has a length of at least ten amino acids and no more than twenty amino acids.

12. The composition of claim 8, wherein the first mass tag is a tandem mass tag.

13. A kit for performing an assay to determine a disease and/or condition state of an organism, comprising:

the composition of claim 8,

wherein the disease and/or condition state is characterized by expression of at least a first protein and a second protein,

wherein the first peptide is proteotypic of the first protein, and

wherein the second peptide is proteotypic of the second protein.

14. A kit comprising:

the composition of claim 8; and

information indicating a quantity of the first trigger molecules and a quantity of the second trigger molecules.

15. A kit comprising:

the composition of claim 8; and

information indicating a molecular mass of the first trigger molecules and a molecular mass of the second trigger molecules.

16. A kit comprising:

the composition of claim 8; and

information identifying the first mass tag.

11. (canceled)

17. A composition of mass-tagged peptide molecules having known molecular masses for use as mass spectrometry triggers, the composition comprising:

a population of trigger molecules, wherein each trigger molecule of the population of trigger molecules includes a peptide portion bonded to a tag portion, the tag portion being a first mass tag that is not isotopically substituted, wherein the peptide portion includes one or more isotopic substitutions, and wherein the trigger molecules of the population of trigger molecules are chemically identical to one another.

18. The composition of claim 17, wherein the peptide portion of the trigger molecules has a length of at least five amino acids and no more than fifty amino acids.

19. The composition of claim 18, wherein the peptide portion of the trigger molecules has a length of at least ten amino acids and no more than twenty amino acids.

21. The composition of claim 17, wherein the first mass tag is a tandem mass tag.

22. A kit comprising:

the composition of claim 17; and

information indicating a quantity of the trigger molecules.

23. A kit comprising:

the composition of claim 17; and

information indicating a molecular mass of the trigger molecules.

20. (canceled)

24-42. -42. (canceled)