SRM/MRM assay for the receptor tyrosine-protein kinase erbB-4 protein (HER4)
Specific peptides, and derived ionization characteristics of the peptides, from the Receptor Tyrosine-Protein Kinase erbB-4 Protein (HER4) protein are provided that are particularly advantageous for quantifying the HER4 protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample using the Liquid Tissue™ reagents and protocol and the HER4 protein is quantitated in the Liquid Tissue™ sample by SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of an HER4 peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
1. A method for measuring the level of the human Receptor Tyrosine-Protein Kinase erbB-4 Protein (HER4) protein in a human biological sample of formalin-fixed tissue, comprising detecting and quantifying the amount of an HER4 fragment peptide in a protein digest prepared from said biological sample using mass spectrometry; and calculating the level of HER4 protein in said sample; wherein the HER4 fragment peptide consists of the peptide of SEQ ID NO: 4, and
wherein said amount is a relative amount or an absolute amount.
2. The method of claim 1 , further comprising the step of fractionating said protein digest prior to detecting and quantifying the amount of said HER4 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 reverse 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 the tissue is paraffin embedded tissue.
7. The method of claim 1 , wherein the tissue is obtained from a tumor.
8. The method of claim 1 wherein quantifying said HER4 fragment peptide comprises comparing an amount of said HER4 fragment peptide in one biological sample to the amount of the same HER4 fragment peptide in a different and separate biological sample.
9. The method of claim 1 , wherein quantifying said HER4 fragment peptide comprises determining the amount of said HER4 fragment peptide in a biological sample by comparison to an added internal standard peptide of known amount having the same amino acid sequence.
10. The method of claim 9 , wherein the internal standard peptide is an isotopically labeled peptide.
11. The method of claim 10 , wherein the 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.
12. The method of claim 1 , wherein detecting and quantifying the amount of said HER4 fragment peptide in the protein digest indicates the presence of HER4 protein and an association with cancer in the subject.
13. The method of claim 12 , further comprising correlating the results of said detecting and quantifying the amount of said HER4 fragment peptide, or the amount of said HER4 protein to the diagnostic stage/grade/status of the cancer.
14. The method of claim 13 , wherein correlating the results of said detecting and quantifying the amount of said HER4 fragment peptide, or the amount of said HER4 protein to the diagnostic stage/grade/status of the cancer is combined with detecting and/or quantifying the amount of other proteins or peptides from other proteins in a multiplex format to provide additional information about the diagnostic stage/grade/status of the cancer.
15. The method of claim 1 , further comprising selecting for the subject from which said biological sample was obtained a treatment based on the presence, absence, or amount of said HER4 fragment peptide or the amount of HER4 protein.
16. The method of claim 1 , further comprising administering to the patient from which said biological sample was obtained a therapeutically effective amount of a therapeutic agent, wherein the therapeutic agent and/or amount of the therapeutic agent administered is based upon the amount of said HER4 fragment peptide or the amount of HER4 protein.
17. The method of claim 15 , wherein the treatment or the therapeutic agent is directed to cancer cells expressing the HER4 protein.