Imaging mass spectrometer with mass tags

1. A method of analyzing biological material for cancer prognosis or drug effectiveness determinations, wherein said biological material has at least one region of interest area, comprising the steps of:

exposing the biological material to a recognition element,

exposing the biological material to a mass tag element,

exposing said recognition element, said mass tag element, and the biological material to a cleavable linker resulting in said recognition element and said mass tag element, being connected by said cleavable linker,

cleaving said cleavable linker,

using a time-of-flight secondary ion mass spectrometer and directing an ion beam of said time-of-flight secondary ion mass spectrometer to the biological material producing secondary ions,

interrogating the at least one region of interest area from the biological material by accelerating said secondary ions into said time-of-flight mass spectrometer where they are analyzed for mass by measuring the time-of-flight of said secondary ions from the biological material to the detector,

producing data, and

analyzing said data for cancer prognosis or drug effectiveness determinations.

2. The method of analyzing biological material of claim 1 wherein said step of cleaving said cleavable linker comprises using ultraviolet light to cleave said cleavable linker.

3. The method of analyzing biological material of claim 1 wherein said step of directing an ion beam to the biological material comprises directing an ion beam of a finely focused energetic primary-ion beam of a time- of-flight secondary ion mass spectrometer to the biological material.

4. The method of analyzing biological material of claim 1 wherein said step of directing an ion beam to the biological material comprises directing an ion beam of a matrix-assisted laser desorption/ionization mass spectrometer.

5. The method of analyzing biological material of claim 1 wherein said step of analyzing said data for cancer prognosis or drug effectiveness determinations includes distributing said data in plots indicating measures of similarity.

6. The method of analyzing biological material of claim 1 wherein said step of analyzing said data for cancer prognosis or drug effectiveness determinations includes producing a chemical map of the biological material.

7. The method of analyzing biological material of claim 1 wherein said step of analyzing said data for cancer prognosis or drug effectiveness determinations includes obtaining known data and comparing said data with said known data.

8. The method of analyzing biological material of claim 1 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to a chemical recognition element.

9. The method of analyzing biological material of claim 1 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to a protein recognition element.

10. The method of analyzing biological material of claim 1 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to an antibody recognition element.

11. The method of analyzing biological material of claim 1 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to an oligo recognition element.

12. The method of analyzing biological material of claim 1 wherein said step of exposing the biological material to a mass tag element comprises exposing the biological material to a multiplexed mass tag element.

13. The method of analyzing biological material of claim 1 wherein said step of exposing said recognition element, said mass tag element, and the biological material to a cleavable linker comprises exposing said recognition element, said mass tag element, and the biological material to an ultraviolet light cleavable linker.

14. The method of analyzing biological material of claim 1 wherein said step of exposing said recognition element, said mass tag element, and the biological material to a cleavable linker comprises exposing said recognition element, said mass tag element, and the biological material to an ultraviolet light cleavable linker and including the step of cleaving said ultraviolet light cleavable linker.

15. The method of analyzing biological material of claim 1 wherein said step of exposing said recognition element, said mass tag element, and the biological material to a cleavable linker comprises exposing said recognition element, said mass tag element, and the biological material to an ultraviolet light cleavable linker and including the step of cleaving said cleavable linker by exposing said ultraviolet light cleavable linker to ultraviolet light and cleaving said ultraviolet light cleavable linker that connect said recognition element, said mass tag element, and the biological material.

16. A method of analyzing biological material for cancer prognosis or drug effectiveness determinations, wherein said biological material has at least one region of interest area, comprising the steps of:

exposing the biological material to a recognition element,

exposing the biological material to a mass tag element,

connecting said recognition element and said mass tag element with a cleavable linker,

using a time-of-flight secondary ion mass spectrometer and directing an ion beam of said time-of-flight secondary ion mass spectrometer to the biological material producing secondary ions,

cleaving said cleavable linker,

interrogating at least one region of interest area from the biological material by accelerating said secondary ions into said time-of-flight mass spectrometer where they are analyzed for mass by measuring the time-of-flight of said secondary ions from the biological material to the detector and producing data, and

analyzing said data to provide information about the biological material for cancer prognosis or drug effectiveness determinations.

17. The method of analyzing biological material of claim 16 wherein said step of directing an ion beam to the biological material comprises directing an ion beam of a finely focused energetic primary-ion beam of a time-of-flight secondary ion mass spectrometer to the biological material.

18. The method of analyzing biological material of claim 16 including obtaining known data and comparing said data with said known data.

19. The method of analyzing biological material of claim 16 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to a chemical recognition element.

20. The method of analyzing biological material of claim 16 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to a protein recognition element.

21. The method of analyzing biological material of claim 16 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to an antibody recognition element.

22. The method of analyzing biological material of claim 16 wherein said step of exposing the biological material to a recognition element comprises exposing the biological material to an oligo recognition element.

23. The method of analyzing biological material of claim 16 wherein said step of exposing the biological material to a mass tag element comprises exposing the biological material to a multiplexed mass tag element.