Patent Document ID: 9110074
Application ID: 13102669
Patent Flag: 1

Claim One:
1. A method for identifying a subject who has a disease wherein 4E regulon activity is dysfunctional, said method comprises simultaneously determining the levels of and/or phosphorylation states of a set of target proteins or peptides in a sample obtained from the subject, said target proteins or peptides are eIF4E (NP — 001959) (NP — 001959.1), HuR (NP — 001410) (NP — 001410.2), and at least one eIF4E regulon component selected from the group consisting of: Cyclin D1(NP — 444284) (NP — 444284.1); NBS/Nibrin (NP — 002476) (NP — 002476.2); Pim-1 (NP — 002639) (NP — 002639.1); Cyclin B1 (NP — 114172) (NP — 114172.1); Cyclin A2 (NP — 001228) (NP — 001228.1); ODC (NP — 002530) (NP — 002530.1); VEGF (NP — 003367) (NP — 003367.4); Skp2 (NP — 005974, NP — 116026) (NP — 005974.2, NP — 116026.1); Cyclin E1 (P24864) (NP — 001229) (NP — 001229.1); c-myc (gi: 71774082) (NP — 002458) (NP — 002458.2); FGF2 (P09038) (NP — 002006) (NP — 001997) (NP — 002006.4) (NP — 001997.5); MMP-9 (P14780) (NP — 004985) (NP — 004985.2); mdm2 (NP — 002383) (NP — 002383.2); caspase-9 (P55211) (NP — 001220, NP — 127463) (NP — 001220.2, NP — 127463.1); bc12 (P10415) (NP — 000624, NP — 000648) (NP — 000624.2, NP — 000648.2); Bcl/xL (Q07817) (NP — 612815) (NP — 612815.1); Selenoprotein S (Q9BQE4) (NP — 060915), (NP — 982298) (NP — 060915.2), (NP — 982298.1); eIF4E-BP1 (Q13541) (NP — 004086) (NP — 004086.1); Akt1 (P31749) (NP — 001014431, NP — 005154, NP — 001014432) (NP — 001014431.1, NP — 005154.2, NP — 001014432.1); PI3K (NP — 006209, NP — 002640) (NP — 006209.2, NP — 002640.2); GSK3B (NP — 002084) (NP — 002084.2); Osteopontin (P10451) (NP — 001035149) (NP — 001035149.1) and mTOR/FRAP1 (NP — 004949) (NP — 004949.1), and at least one non-eIF4E regulon component selected from the group consisting of EGFR (P00533) (NP — 005219) (NP — 005219.2), HER2/neu (PO4626) (NP — 004439) (NP — 004439.2), ER (NP — 0001116) (NP — 000116.2) and PR (AAA60081) (AAA60081.1) in a sample, the method comprising: (a) adding at least one internal standard protein or peptide corresponding to each target protein of eIF4E, HuR, and the at least one eIF4E regulon component selected from the group consisting of Cyclin D1, NBS/Nibrin, Pim-1, Cyclin B1, Cyclin A2, ODC, VEGF, Skp2, Cyclin E1, c-myc, FGF2, MMP-9, mdm2, caspase-9, bcl2, Bcl/xL, Selenoprotein S, eIF4E-BP1, Akt1, PI3K, GSK3B, Osteopontin and mTOR/FRAP1, and the at least one non-eIF4E regulon component selected from the group consisting of EGFR, HER2/neu, ER and PR to the sample; (b) fragmenting the target proteins or peptides of eIF4E, HuR, the at least one eIF4E regulon component, and the at least one non-eIF4E component and the at least four corresponding internal standard proteins or peptides, thereby generating fragments of the eIF4E, the HuR, the at least one eIF4E regulon component, and the at least one non-eIF4E regulon component, and the at least four corresponding internal standard proteins or peptides; (c) analyzing the corresponding parent masses and determining amounts of the resultant fragments from step (b) by a mass spectrometry-based method; and (d) using the results from step (c) to determine and quantitate the levels of and/or phosphorylation states of the eIF4E, HuR, the at least one eIF4E regulon component, and the at least one non-eIF4E regulon component.