Truncated HER2 SRM/MRM assay

1. A method for detecting the presence and measuring the level of full length Her2 protein and truncated Her2 protein in a human biological sample of formalin-fixed tissue, comprising detecting and quantifying the amount of a Her2 fragment peptide in a protein digest prepared from said human biological sample using mass spectrometry; and calculating the level of full length and truncated Her2 protein in said sample wherein said level is an absolute level, wherein said Her2 fragment peptide is SEQ ID NO:7.

2. The method of claim 1 , further comprising the step of fractionating said protein digest prior to detecting said Her2 fragment peptide.

3. The method of claim 2 , wherein said fractionating step is selected from the group consisting of liquid chromatography, nano-reversed phase liquid chromatography, high performance liquid chromatography, and reversed phase high performance liquid chromatography.

4. The method of claim 1 , wherein said protein digest comprises a protease digest.

5. The method of claim 4 , wherein said protein digest comprises a trypsin digest.

6. The method of claim 1 , wherein said mass spectrometry comprises tandem mass spectrometry, ion trap mass spectrometry, triple quadrupole mass spectrometry, MALDI-TOF mass spectrometry, MALDI mass spectrometry, and/or time of flight mass spectrometry.

7. The method of claim 1 , wherein the tissue is paraffin embedded tissue.

8. The method of claim 1 , wherein the tissue is obtained from a tumor.

9. The method of claim 8 , wherein the tumor is a primary tumor.

10. The method of claim 8 , wherein the tumor is a secondary tumor.

11. The method of claim 1 , wherein quantifying the amount of said Her2 fragment peptide comprises comparing the amount of said Her2 fragment peptide in a protein digest of one biological sample to the amount of the same Her2 fragment peptide in a protein digest of a different and separate biological sample.

12. The method of claim 1 , wherein quantifying the amount of said Her2 fragment peptide comprises determining the amount of said Her2 fragment peptide in a protein digest of a biological sample by comparing to a spiked internal standard peptide of known amount, wherein both the peptide in the biological sample and the internal standard peptide have the same respective amino acid sequences and wherein the internal standard peptide is an isotopically labeled peptide.

13. The method of claim 12 , wherein said isotopically labeled internal standard peptide comprises one or more heavy stable isotopes selected from 18 O, 17 O, 34 S, 15 N, 13 C, 2 H or combinations thereof.

14. The method of claim 1 , further comprising obtaining the biological sample from a subject, wherein detecting and quantifying the amount of said Her2 fragment peptide in the protein digest indicates the presence of the full-length and truncated Her2 protein and an association with cancer in the subject.

15. The method of claim 14 , further comprising correlating the amount of the full length and truncated Her2 protein to the diagnostic stage/grade/status of the cancer.

16. The method of claim 1 , further comprising selecting a treatment for the subject from whom the biological sample was obtained based on the amount of full length and truncated Her2 protein in the protein digest.

17. The method of claim 16 , further comprising administering a therapeutically effective amount of a therapeutic agent targeted specifically to the Her2 protein to said subject.

18. The method of claim 17 , wherein said therapeutic agent is selected from the group consisting of trastuzumab and lapatinib.

19. The method of claim 17 , wherein measuring the level of full-length and truncated Her2 protein is combined with detecting and quantitating other peptides from other proteins in a multiplex format so that the agent and amount of the agent used for treatment is selected based upon specific levels of truncated and full length Her2 fragment in combination with other peptides from other proteins in the biological sample.