Patent Publication Number: US-2022211828-A1

Title: Target peptides for ovarian cancer therapy and diagnostics

Description:
CROSS-REFERENCE TO RELATED APPLICATION 
     This application is a continuation of U.S. patent application Ser. No. 14/651,932, filed Jun. 12, 2015 (now pending), which itself claims the benefit of U.S. Provisional Patent Application Ser. No. 61/736,815, filed Dec. 13, 2012 (expired), the disclosure of each of which is incorporated herein by reference in its entirety. 
    
    
     GRANT STATEMENT 
     This invention was made with government support under Grant No. AI 033993 awarded by National Institutes of Health. The Government has certain rights in the invention. 
    
    
     REFERENCE TO SEQUENCE LISTING 
     The Sequence Listing associated with the instant disclosure has been electronically submitted to the United States Patent and Trademark Office as International Receiving Office as a 64 kilobyte ASCII text file created on Feb. 22, 2021 and entitled “3062_11_2_PCT_US_CON_ST25.txt”. The Sequence Listing submitted via EFS-Web is hereby incorporated by reference in its entirety. 
     TECHNICAL FIELD 
     The presently disclosed subject matter relates to diagnostics and therapeutics. In particular, it relates to immunotherapies and diagnostics in the context of proliferative diseases such as cancer. 
     BACKGROUND 
     The mammalian immune system has evolved a variety of mechanisms to protect the host from cancerous cells. An important component of this response is mediated by cells referred to as T cells. Cytotoxic T lymphocytes (CTL) are specialized T cells that primarily function by recognizing and killing cancerous cells or infected cells, but they can also function by secreting soluble molecules referred to as cytokines that can mediate a variety of effects on the immune system. T helper cells primarily function by recognizing antigen on specialized antigen presenting cells, and in turn secreting cytokines that activate B cells, T cells, and macrophages. A variety of evidence suggests that immunotherapy designed to stimulate a tumor-specific CTL response would be effective in controlling cancer. For example, it has been shown that human CTL recognize sarcomas (Slovin et al. (1986)  J Jmmunol  137:3042-3048), renal cell carcinomas (Schendel et al. (1993)  J Immunol  151:4209-4220), colorectal carcinomas (Jacob et al. (199.7)  Int J Cancer  71:325-332), ovarian carcinomas (Peoples et al. (1993)  Surgery  114:227-234), pancreatic carcinomas (Peiper el al. (1997)  Eur J Immunol  27:1115-1123), squamous tumors of the head and neck (Yasumura et al. (1993)  Cancer Res  53:1461-1468), and squamous carcinomas of the lung (Slingluff et al. (1994)  Cancer Res  54:2731-2737; Yoshino et al. (1994)  Cancer Res  54:3387-3390). The largest number of reports of human tumor-reactive CTLs, however, has concerned melanomas (Boon et al (1994)  Annu Rev Immunol  12:337-365). The ability of tumor-specific CTL, to mediate tumor regression, in both human (Parmiani et al. (2002).  J Natl Cancer Inst  94:805-818; Weber (2002)  Cancer Invest  20:208-221) and animal models, suggests that methods directed at increasing CTL activity would likely have a beneficial effect with respect to tumor treatment. 
     Ovarian cancer is a cancer that starts in the ovaries, the female reproductive organ that produces eggs. It is the ninth most common cancer among women and causes more deaths than any other type of female reproductive cancer. Ovarian cancer accounts for 3% of all cancers in women. While the cause of ovarian cancer is unknown, several factors appear to affect a woman&#39;s risk for developing ovarian cancer. Age, obesity, estrogen therapy, family histories of ovarian, breast or colorectal cancer, among other factors have been found to increase a woman&#39;s chance for ovarian cancer. Also, some gene defects, such as BRCA1 and BRCA2, appear to be responsible for a small number of ovarian cancer cases. On the other hand, some factors appear to decrease the risk including, taking birth control pills and having children. Symptoms of ovarian cancer are usually vague, but can include tiredness, back pain, upset stomach, menstrual changes, pelvic discomfort or pain, and constipation. Screening can include pelvic examinations, imaging including CT scans, MRI, or ultrasound of the pelvis, blood tests including CA125 blood test, and pelvic laparoscopy or exploratory laparotoiny. Surgery is used to treat all stages of ovarian cancer. Additionally, chemotherapy has also been used to treat any remaining disease after surgery or if the cancer comes back. 
     According to the American Cancer Society, only about 20% of ovarian cancers are found at an early stage. Among those women, about 9 out of 10 women treated for early ovarian cancer will longer than 5 years after the cancer is found. The survival rates differ among different types of ovarian cancer. For example, for invasive epithelial ovarian cancer, the American Cancer Society reports the following 5 year survival rates: Stage I: 89%; IA, 94%; Stage IB: 91%; IC: 80%; Stage II: 66%; JIB: 67-/%; IIC: 57%; III: 34%; IIA: 45%; IIIB: 39%; IIIC: 35%; IV: 18%. For ovarian tumors of low malignant potential, the 5 year survival rates are reported to be as follows: Stage I 99%; II: 98%; III: 96%; and IV: 77%. Nevertheless, additional therapeutics which are safer and more effective than current therapies are in high demand. 
     In order for CTL to kill or secrete cytokines in response to a cancer cell, the CTL must first recognize the cancer cell (Townsend &amp; Bodmer (1989)  Ann Rev Immunol  7:601-624). This process involves the interaction of the T cell receptor, located on the surface of the CTL, with what is generically referred to as an MHC-peptide complex which is located on the surface of the cancerous cell. MHC (major histocompatibility-complex)-encoded molecules have been subdivided into two types, and are referred to as class I and class II MHC-encoded molecules. In the human immune system, MHC molecules are referred to as human leukocyte antigens (HLA). Within the MHC complex, located on chromosome six, are three different loci that encode for class I MHC molecules. MHC molecules encoded at these loci are referred to as HLA-A, HLA-B, and HLA-C. The genes that can be encoded at each of these loci are extremely polymorphic, and thus, different individuals within the population express different class I MHC molecules on the surface of their cells. HLA-A1, HLA-A2, HLA-A3, HLA-B7, HLA-B14, HLA-B27, and HLA-B44 are examples of different class I MHC molecules that can be expressed from these loci. 
     The peptides which associate with the MHC molecules can either be derived from proteins made within the cell, in which case they typically associate with class I MHC molecules (Rock &amp; Goldberg (1999)  Annu Rev Immunol  17:739-779); or they can be derived from proteins which are acquired from outside of the cell, in which case they typically associate with class II MHC molecules (Watts (1997)  Annu Rev Immunol  15:821-850). The peptides that evoke a cancer-specific CTL response most typically associate with class I MHC molecules. The peptides themselves are typically nine amino acids in length, but can vary from a minimum length of eight amino acids to a maximum of fourteen amino acids in length. Tumor antigens can also bind to class II MIC molecules on antigen presenting cells and provoke a T helper cell response. The peptides that bind to class II MHC molecules are generally twelve to nineteen amino acids in length, but can be as short as ten amino acids and as long as thirty amino acids. 
     The process by which intact proteins are degraded into peptides is referred to as antigen processing. Two major pathways of antigen processing occur within cells (Rock &amp; Goldberg (1999)  Annu Rev Immunol  17:739-779). One pathway, which is largely restricted to professional antigen presenting cells such as dendritic cells, macrophages, and B cells, degrades proteins that are typically phagocytosed or endocytosed into the cell. Peptides derived from this pathway can be presented on either class I or to class II MHC molecules. A second pathway of antigen processing is present in essentially all cells of the body. This second pathway primarily degrades proteins that are made within the cells, and the peptides derived from this pathway primarily bind to class I MHC molecules. Antigen processing by this latter pathway involves polypeptide synthesis and proteolysis in the cytoplasm, followed by transport of peptides to the plasma membrane for presentation. These peptides, initially being transported into the endoplasmic reticulum of the cell, become associated with newly synthesized class I MHC molecules and the resulting complexes are then transported to the cell surface. Peptides derived from membrane and secreted proteins have also been identified. In some cases these peptides correspond to the signal sequence of the proteins which is cleaved from the protein by the signal peptidase. In other cases, it is thought that some fraction of the membrane and secreted proteins are transported from the endoplasmic reticulum into the cytoplasm where processing subsequently occurs. Once bound to the class I MHC molecule, the peptides are recognized by antigen-specific receptors on CTL. Several methods have been developed to identify the peptides recognized by CTL, each method of which relies on the ability of a CTL to recognize and kill only those cells expressing the appropriate class I MHC molecule with the peptide bound to it. Mere expression of the class I MHC molecule is insufficient to trigger the CTL to kill the target cell if the antigenic peptide is not bound to the class I MHC molecule. Such peptides can be derived from a non-self source, such as a pathogen (for example, following the infection of a cell by a bacterium or a virus) or from a self-derived protein within a cell, such as a cancerous cell. The tumor antigens from which the peptides are derived can broadly be categorized as differentiation antigens, cancer/testis antigens, mutated gene products, widely expressed proteins, viral antigens and most recently, phosphopeptides derived from dysregulated signal transduction pathways. (Zarling et al. (2006)  Proc Natl Acad Sci USA  103:12889-14894). 
     Immunization with melanoma-derived, class I or class II MHC-encoded molecule associated peptides, or with a precursor polypeptide or protein that contains the peptide, or with a gene that encodes a polypeptide or protein containing the peptide, are forms of immunotherapy that can be employed in the treatment of ovarian cancer. Identification of the immunogens is a necessary first step in the formulation of the appropriate immunotherapeutic agent or agents. Although a large number of tumor-associated peptide antigens recognized by tumor reactive CTL, have been identified, there are few examples of antigens that are derived from proteins that are selectively expressed on a broad array of tumors, as well as associated with cellular proliferation and/or transformation. 
     Attractive candidates for this type of antigen are peptides derived from proteins that are differentially phosphorylated on serine (Ser), threonine (Thr), and tyrosine (Tyr; Zarling et al. (2000)  J Exp Med  192:1755-1762). Due to the increased and dysregulated phosphorylation of cellular proteins in transformed cells as compared to normal cells, tumors are likely to present a unique subset of phosphorylated peptides on the cell surface that are available for recognition by cytotoxic T-lymphocytes (CTL). Presently, there is no way to predict which protein phosphorylation sites in a cell will be unique to tumors, survive the antigen processing pathway, and be presented to the immune system in the context of 8-14 residue phosphopeptides bound to class I MHC molecules. 
     Thirty-six phosphopeptides were disclosed as presented in association with HLA A*0201 on cancer cells. Sec Table 1 of Zarling et al. (2006)  Proc Natl Acad Sci USA  103:14889-14894. Parent proteins for four of these peptides (beta-catenin, insulin receptor substrate-2 (IRS-2), tensin-3 and Jun-C/D) are associated with cytoplasmic signaling pathways and cellular transformation. 
     Until the present disclosure, no studies have examined MHC class-I-bound phosphopeptide displayed on primary human tumor samples and there is only limited evidence of a human immune response against class-I restricted phosphopeptides. 
     There is a need in the art for class I therapeutic peptide antigen based immunotherapies in general and for ovarian cancer in particular. 
     SUMMARY 
     This Summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features. 
     In some embodiments, the presently disclosed subject matter relates to compositions comprising at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more synthetic target peptides each of which are about or at least 8, 9, 10, 11, 12, 13, 14 or 15 amino acids long wherein the target peptides comprise for example, amino acid sequences as set forth in any of SEQ ID NOs.: 1-193; and wherein the composition has the ability to stimulate a T cell mediated immune response to at least one of the target synthetic peptides. 
     In some embodiments, at least one serine residue in any of the peptides is replaced with a homo-serine. In some embodiments, the composition comprises a non-hydrolyzable phosphate. In some embodiments, the composition is immunologically suitable for at least 60 to 88% of ovarian cancer patients. In some embodiments, the composition comprises at least 5 different target peptides. In some embodiments, the composition comprises at least 10 different target peptides. In some embodiments, the composition comprises at least 15 different target peptides. In some embodiments, the composition comprises a peptide capable of binding to an MHC class I molecule of the HLA-A*0201 allele. 
     In some embodiments, the composition is capable of increasing the 5-year survival rate of ovarian cancer patients treated with the composition by at least 20 percent relative to average 5-year survival rates that could have been expected without treatment with the composition. In some embodiments, the composition is capable of increasing the survival rate of ovarian cancer patients treated with the composition by at least 20 percent relative to a survival rate that could have been expected without treatment with the composition. In some embodiments, the composition is capable of increasing the treatment response rate of ovarian cancer patients treated with the composition by at least 20 percent relative to a treatment rate that could have been expected without treatment with the composition. In some embodiments, the composition is capable of increasing the overall median survival of patients of ovarian cancer patients treated with the composition by at least two months relative to an overall median survival that could have been expected without treatment with the composition. 
     In some embodiments, the composition comprises at least one peptide derived from MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, p15(58), CEA, RAGE, NY-ESO (LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HFPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, p16, TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4, 791Tgp72, alpha-fetoprotein, ρ-HCG, BCA225, BTAA, CA 125, CA 15-3 (CA 27.29\BCAA), CA 195, CA 242, CA-50, CAM43, CD68\KP1, CO-029, FGF-5, G250, Ga733 (EpCAM), HTgp-175, M344, MA-50 MG7-Ag, MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding protein\cyclophilin C-associated protein), TAAL6, TAG72, TLP and TPS. 
     In some embodiments, the composition comprises an adjuvant selected from the group consisting of montanide ISA-51 (Seppic Inc., Fairfield, N.J., United States of America), QS-21 (Aquila Biophannaceuticals, Inc., Frarmingham, Nassachusetts, United States of America), tetanus helper peptides (such as but not limited to QYIKANSKFIGITEL (SEQ ID NO: 242) and/or AQYIKANSKFIGITEL (SEQ ID NO: 234), GM-CSF, cyclophosamide,  bacillus  Calmette-Guerin (BCG),  Corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrchlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, diphtheria toxin (DT). 
     In some embodiments, the presently disclosed subject matter relates to an in vitro population of dendritic cells comprising the aforementioned compositions or a composition comprising at least one target peptide. 
     In some embodiments, the presently disclosed subject matter relates to an in vitro population of CD8′T cells capable of being activated upon being brought into contact with a population of dendritic cells, wherein the dendritic cells comprise the aforementioned compositions. 
     In some embodiments, the presently disclosed subject matter relates to an antibody or antibody-like molecule that specifically binds to both a first complex of MHC class I molecule and a target peptide. In some embodiments, the antibody or antibody-like molecule is a member of the immunoglobulin superfamily. In some embodiments, the antibody or antibody-like molecule comprises a binding member selected from the group consisting an Fab, Fab′, F(ab′), Fv, and a single-chain antibody. 
     In some embodiments, the antibody or antibody-like molecule comprises a therapeutic agent selected from the group consisting of an alkylating agent, an antimetabolite, a mitotic inhibitor, a taxoid, a vinca alkaloid and an antibiotic. In some embodiments, the antibody or antibody-like molecule is a T cell receptor, optionally linked to a CD3 agonist. 
     In some embodiments, the presently disclosed subject matter relates to an in vitro population of T cells transfected with mRNA encoding the aforementioned target peptide-specific T cell receptors. 
     In some embodiments, the presently disclosed subject matter relates to methods of treating or preventing cancer comprising administering to a patient in need thereof a dose of the aforementioned compositions. 
     In some embodiments, the presently disclosed subject matter relates to methods of treating or preventing ovarian cancer comprising administering to a patient in need thereof a dose of the aforementioned compositions with a pharmaceutically acceptable carrier. 
     In some embodiments, the presently disclosed subject matter relates to methods of treating or preventing cancer comprising administering to a patient in need thereof a dose of the aforementioned CD8 +  T in combination with a pharmaceutically acceptable carrier. 
     In some embodiments, the presently disclosed subject matter relates to methods of treating or preventing cancer comprising administering to a patient in need thereof the population of the aforementioned dendritic cells in combination with a pharmaceutically acceptable carrier. 
     In some embodiments, the presently disclosed subject matter relates to methods of treating or preventing cancer comprising administering to a patient in need thereof the aforementioned population T cells in combination with a pharmaceutically acceptable carrier. 
     In some embodiments, the presently disclosed subject matter relates to methods of making a cancer vaccine comprising combining the aforementioned compositions with the aforementioned adjuvant and a pharmaceutically acceptable carrier; and placing the composition, adjuvant and pharmaceutical carrier into a syringe. 
     In some embodiments, the presently disclosed subject matter relates to methods of methods of screening target peptides for inclusion in an immunotherapy composition comprising administering the target peptide to a human; determining whether the target peptide is capable of inducing a target peptide-specific memory T cell response in the human; selecting the target peptide for inclusion in an immunotherapy composition if the target peptide elicits a memory T cell response in the human. 
     In some embodiments, the presently disclosed subject matter relates to a method of determining the prognosis of a cancer patient comprising: administering a target peptide associated with the patient&#39;s cancer to the patient; determining whether the target peptide is capable of inducing a target peptide-specific memory T cell response in the patient; determining that the patient has a better prognosis if the patient mounts a memory T cell response to the target peptide than if the patient did not mount a memory T cell response to the target peptide. 
     In some embodiments, the presently disclosed subject matter relates to a kit comprising at least one target peptide composition comprising at least one target peptide and a cytokine and/or an adjuvant. In some embodiments, the kit comprises at least 2, 3, 4 or 5 or more compositions. 
     In some embodiments, the cytokine is selected from the group consisting of transforming growth factors (TGFs) such as TGF-alpha and TGF-beta; insulin-like growth factor-I and -II; erythropoietin (EPO); osteoinductive factors; interferons such as interferon-alpha -beta, and -gamma; colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF). 
     In some embodiments, the adjuvant selected from the group consisting of montanide ISA-51 (Seppic, Inc.), QS-21 (Aquila Pharmaceuticals, Inc.), tetanus helper peptides, GM-CSF, cyclophosamide,  bacillus  Calmette-Guerin (BCG), corynbacterium  parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, diphtheria toxin (DT). 
     In some embodiments, the cytokine is selected from the group consisting of nerve growth factors such as NGF-beta; platelet-growth factor; transforming growth factors (TGFs) such as TGF-alpha and TGF-beta; insulin-like growth factor-I and -II; erythropoietin (EPO); osteoinductive factors; interferons such as interferon-alpha -beta, and -gamma; colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1, IL-1 alpha, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, LIF, G-CSF, GM-CSF, M-CSF, EPO, kit-ligand, or FLT-3, angiostatin, thrombospondin, endostatin, tumor necrosis factor, and LT. 
     In some embodiments, the kit comprises at least one additional peptide derived from MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, CAGE-2, p15(58), CEA, RAGE, NY-ESO (LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, p16, TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4, 791Tgp72, alpha-fetoprotein, β-HCG, BCA225, BTAA, CA 125, CA 15-3 (CA 27.29\BCAA), CA 195, CA 242, CA-50, CAM43, CD68\KP1, CO-029, FGF-5, G250, Ga733 (EpCAM), HTgp-175, M344, MA-50, MG7-Ag. MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding protein\cyclophilin C-associated protein), TAAL6, TAG72, TLP, and TPS. 
     In some embodiments, the kit comprises at least one target peptide that comprises an amino acid as set forth in any of SEQ ID NOs: 1-193. 
     These and other aspects and embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with immunological tools and agents useful for diagnosing, prognosing, monitoring, and/or treating human cancers. 
     BRIEF DESCRIPTION OF THE SEQUENCE LISTING 
     A more complete understanding of the presently disclosed subject matter can be obtained by reference to the accompanying Sequence Listing, when considered in conjunction with the subsequent Detailed Description. The embodiments presented in the Sequence Listing are intended to be exemplary only and should not be construed as limiting the presently disclosed subject matter to the listed embodiments, in which SEQ ID NOs: 1-193 provide a listing of exemplary MHC class I target peptides associated with ovarian cancer. Additional details with respect to SEQ ID NOs: 1-193 are provided in Table 3 herein below. 
    
    
     DETAILED DESCRIPTION 
     While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. 
     All technical and scientific terms used herein, unless otherwise defined below, are intended to have the same meaning as commonly understood by one of ordinary skill in the art. Mention of techniques employed herein are intended to refer to the techniques as commonly understood in the art, including variations on those techniques or substitutions of equivalent techniques that would be apparent to one of skill in the art. While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. Thus, unless defined otherwise, all technical and scientific terms and any acronyms used herein have the same meanings as commonly understood by one of ordinary skill in the art in the field of the presently disclosed subject matter. Although any compositions, methods, kits, and means for communicating information similar or equivalent to those described herein can be used to practice the presently disclosed subject matter, particular compositions, methods, kits, and means for communicating information are described herein. It is understood that the particular compositions, methods, kits, and means for communicating information described herein are exemplary only and the presently disclosed subject matter is not intended to be limited to just those embodiments. 
     Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, in some embodiments the phrase “a peptide” refers to one or more peptides. 
     The term “about”, as used herein to refer to a measurable value such as an amount of weight, time, dose (e.g., therapeutic dose), etc., is meant to encompass in some embodiments variations of 20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.1%, in some embodiments ±0.5%, and in some embodiments ±0.01% from the specified amount, as such variations are appropriate to perform the disclosed methods. 
     As used herein, the term “and/or” when used in the context of a list of entities, refers to the entities being present singly or in any and every possible combination and subcombination. Thus, for example, the phrase “A, B, C, and/or D” includes A, B, C, and D individually, but also includes any and all combinations and subcombinations of A, B, C, and D. It is further understood that for each instance wherein multiple possible options are listed for a given element (i.e., for all “Markush Groups” and similar listings of optional components for any element), in some embodiments the optional components can be present singly or in any combination or subcombination of the optional components. It is implicit in these forms of lists that each and every combination and subcombination is envisioned and that each such combination or subcombination has not been listed simply merely for convenience. Additionally, it is further understood that all recitations of “or” are to be interpreted as “and/or” unless the context clearly requires that listed components be considered only in the alternative (e.g., if the components would be mutually exclusive in a given context and/or could not be employed in combination with each other). 
     As used herein, the phrase “amino acid sequence as set forth in any of SEQ ID NOs: [A]-[B]” refers to any amino acid sequence that is disclosed in any one or more of SEQ ID NOs: A-B. In some embodiments, the amino acid sequence is any amino acid sequence that is disclosed in any of the SEQ ID NOs. that are present in the Sequence Listing. In some embodiments, the phrase refers to the full length sequence of any amino acid sequence that is disclosed in any of the SEQ ID NOs. that are present in the Sequence Listing, such that an “amino acid sequence as set forth in any of SEQ ID NOs: [A]-[B]” refers to the full length sequence of any of the sequences disclosed in the Sequence Listing. By way of example and not limitation, in some embodiments an “amino acid sequence as set forth in any of SEQ ID NOs: 1-193” refers to the full length amino acid sequence disclosed in any of SEQ ID NOs: 1-193 and not to a subsequence of any of SEQ ID NOs: 1-193. 
     The presently disclosed subject matter relates in some embodiments to post-translationally-modified immunogenic therapeutic target peptides, e.g., phosphopeptides and/or O-GlcNAc peptides, for use in immunotherapy and diagnostic methods of using the target peptides, as well as methods of selecting the same to make compositions for immunotherapy, e.g., in vaccines and/or in compositions useful in adaptive cell transfer. 
     I. Target Peptides 
     In some embodiments, the target peptides of the presently disclosed subject matter are post-translationally-modified by being provided with a phosphate group (referred to herein as “phosphopeptides”) and/or an O-linked beta-N-acetylglucosamine (“O-GlcNAc”) moiety (referred to herein as “O-GlcNAc peptides”). 
     The target peptides of the presently disclosed subject matter are in some embodiments not the entire proteins from which they are derived. They are in some embodiments from 8 to 50 contiguous amino acid residues of the native human protein. They can in some embodiments contain exactly, about, or at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids. The peptides of the presently disclosed subject matter can also in some embodiments have a length that falls in the ranges of 8-10, 9-12, 10-13, 11-14, 12-15, 15-20, 20-25, 25-30, 30-35, 35-40, and 45-50 amino acids. Exactly, about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or more of the amino acid residues within the recited sequence of a target peptide can phosphorylated and/or contain an O-GlcNAc moiety. 
     Target peptides can be modified and analogs (using for example, beta-amino acids, L-amino acids, N-methylated amino acids, amidated amino acids, non-natural amino acids, retro inverse peptides, peptoids, PNA, halogenated amino acids) can be synthesized that retain their ability to stimulate a particular immune response, but which also gain one or more beneficial features, such as those described below. Thus, particular target peptides can, for example, have use for treating and vaccinating against multiple cancer types. 
     In some embodiments, substitutions can be made in the target peptides at residues known to interact with the MHC molecule. Such substitutions can in some embodiments have the effect of increasing the binding affinity of the target peptides for the MHC molecule and can also increase the half-life of the target peptide-T/MHC complex, the consequence of which is that the analog is in some embodiments a more potent stimulator of an immune response than is the original peptide. 
     Additionally, the substitutions can in some embodiments have no effect on the immunogenicity of the target peptide per se, but rather can prolong its biological half-life or prevent it from undergoing spontaneous alterations which might otherwise negatively impact on the immunogenicity of the peptide. 
     The target peptides disclosed herein can in some embodiments have differing levels of immunogenicity, MHC binding and ability to elicit CTL responses against cells displaying a native target peptide, e.g., on the surface of a tumor cell. 
     The amino acid sequences of the target peptides can in some embodiments be modified such that immunogenicity and/or binding is enhanced. In some embodiments, the modified target peptide binds an MHC class I molecule about or at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, 110%, 125%, 150%, 175%, 200%, 225%, 250%, 275%, 300%, 350%, 375%, 400%, 450%, 500%, 600%, 700%, 800%, 1000%, or more tightly than its native (unmodified) counterpart. 
     However, given the exquisite sensitivity of the T-cell receptor, it cannot be foreseen whether such enhanced binding and/or immunogenicity will render a modified target peptide still capable of inducing an activated CTL that will cross react with the native target peptide being displayed on the surface of a tumor. Indeed, it is disclosed herein that the binding affinity of a target peptide does not predict its functional ability to elicit a T cell response. 
     Target peptides of the presently disclosed subject matter can in some embodiments be mixed together to form a cocktail. The target peptides can in some embodiments be in an admixture, or they can in some embodiments be linked together in a concatamer as a single molecule. Linkers between individual target peptides can in some embodiments be used; these can, for example, in some embodiments be formed by any 10 to 20 amino acid residues. The linkers can in some embodiments be random sequences, or they can in some embodiments be optimized for degradation by dendritic cells. 
     In certain specified positions, a native amino acid residue in a native human protein can in some embodiments be altered to enhance the binding to the MHC class I molecule. These can occur in “anchor” positions of the target peptides, often in positions 1, 2, 3, 9, or 10. Valine, alanine, lysine, leucine tyrosine, arginine, phenylalanine, proline, glutamic acid, threonine, serine, aspartic acid, tryptophan, and methionine can also be used in some embodiments as improved anchoring residues. Anchor residues for different HLA molecules are listed below. Anchor residues for HLA molecules are listed in Table 1. 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 Anchor Residues for Different HLA Molecules 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 HLA A*0201 
                 Residue 2 = L, M 
               
               
                   
                   
                 Residue 9 or last residue = V 
               
               
                   
                 HLA A*0301 
                 Residue 2 = L, M 
               
               
                   
                   
                 Residue 9 or last residue = K 
               
               
                   
                 HLA A*0101 
                 Residue 2 = T, S 
               
               
                   
                   
                 Residue 3 = D, E 
               
               
                   
                   
                 Residue 9 or last residue = Y 
               
               
                   
                 HLA B*2705 
                 Residue 1 = R 
               
               
                   
                   
                 Residue 2 = R 
               
               
                   
                   
                 Residue 9 or last residue L, F, K, R, M 
               
               
                   
                 HLA B*0702 
                 Residue 2 = P 
               
               
                   
                   
                 Residue 9 or last residue = L, M, V, F 
               
               
                   
                 HLA B*4402 
                 Residue 2 = E 
               
               
                   
                   
                 Residue 9 or last residue = F, Y, W 
               
               
                   
                   
               
            
           
         
       
     
     In some embodiments, the immunogenicity of a target peptide is measured using transgenic mice expressing human MHC class I genes. For example, “ADD Tg mice” express an interspecies hybrid class I MHC gene, AAD, which contains the alpha-1 and alpha-2 domains of the human HLA-A2.1 gene and the alpha-3 transmembrane and cytoplasmic domains of the mouse H-2Dd gene, under the direction of the human HLA-A2.1 promoter. Immunodetection of the HLA-A2.1 recombinant transgene established that expression was at equivalent levels to endogenous mouse class I molecules. The mouse alpha-3 domain expression enhances the immune response in this system. Compared to unmodified HLA-A2.1, the chimeric HLA-A2.1/H2-Dd MHC Class I molecule mediates efficient positive selection of mouse T cells to provide a more complete T cell repertoire capable of recognizing peptides presented by HLA-A2.1 Class I molecules. The peptide epitopes presented and recognized by mouse T cells in the context of the HLA-A2.1/H2-Dd class I molecule are the same as those presented in HLA-A2.1 +  humans. This transgenic strain facilitates the modeling of human T cell immune responses to HLA-A2 presented antigens, and identification of those antigens. This transgenic strain is a preclinical model for design and testing of vaccines for infectious diseases or cancer therapy involving optimal stimulation of CD8 +  cytolytic T cells. 
     In some embodiments, the immunogenicity of a modified target peptide is determined by the degree of Interferon gamma and/or TNF-alpha production of T-cells from ADD Tg mice immunized with the target peptide, e.g., by immunization with target peptide pulsed bone marrow derived dendritic cells. 
     In some embodiments, the modified target peptides are about or at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, 110%, 125%, 150%, 175%, 200%, 225%, 250%, 275%, 300%, 350%, 375%, 400%, 450%, 500%, 600%, 700%, 800%, 1000%, 1500%, 2000%, 2500%, 3000%, 4000%, 5000%, or more immunogenic, e.g., in terms of numbers of Interferon gamma and/or TNF-alpha positive (i.e., “activated”) T-cells relative to numbers elicited by native target peptides in ADD Tg mice immunized with target peptides pulsed bone marrow derived dendritic cells. In some embodiments, the modified target peptides are able to elicit CD8 +  T cells which are cross-reactive with the modified and the native target peptide in general and when such modified and native target peptides are complexed with MHC class I molecules in particular. In some embodiments, the CD8 +  T cells which are cross-reactive with the modified and the native target peptides are able to reduce tumor size by about or at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 99% in a NOD/SCID/IL-2Rγc −/−  knock out mouse (which has been provided transgenic T cells specific form an immune competent donor) relative to IL-2 treatment without such cross-reactive CD8 +  T cells. 
     The term “capable of inducing a target peptide-specific memory T cell response in a patient” as used herein relates to eliciting a response from memory T cells (also referred to as “antigen-experienced T cell”) which are a subset of infection- and cancer-fighting T cells that have previously encountered and responded to their cognate antigen. Such T cells can recognize foreign invaders, such as bacteria or viruses, as well as cancer cells. Memory T cells have become “experienced” by having encountered antigen during a prior infection, encounter with cancer, or previous vaccination. At a second encounter with the cognate antigen, e.g., by way of an initial inoculation with a target peptide of the invention, memory T cells can reproduce to mount a faster and stronger immune response than the first time the immune system responded to the invader (e.g., through the body&#39;s own consciously unperceived recognition of a target peptide being associated with diseased tissue). This behavior can be assayed in T lymphocyte proliferation assays, which can reveal exposure to specific antigens. Memory T cells comprise two subtypes: central memory T cells (T CM  cells) and effector memory T cells (T EM  cells). Memory cells can be either CD4 +  or CD8 + . Memory T cells typically express the cell surface protein CD45RO. Central memory T CM  cells generally express L-selectin and CCR7, they secrete IL-2, but not IFNγ or IL-4. Effector memory T EM  cells, however, generally do not express L-selectin or CCR7 but produce effector cytokines like IFNγ and IL-4. 
     A memory T cell response generally results in the proliferation of memory T cell and/or the upregulation or increased secretion of the factors such as CD45RO, L-selectin, CCR7, IL-2, IFNγ, CD45RA, CD27 and/or IL-4. In some embodiments, the target peptides of the presently disclosed subject matter are capable of inducing a T CM  cell response associated with L-selectin, CCR7, IL-2 (but not IFNγ or IL-4) expression and/secretion. See e.g., Hamann et al. (1997)  J Exp Med  186:1407-1418. In some embodiments, a T CM  cell response is associated with an at least or about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, 99%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000%, 1500%, 2000%, or more increase in T cell CD45RO/RA, L-selectin, CCR7, or IL-2 expression and/secretio. 
     In some embodiments, the target peptides of the presently disclosed subject matter are capable of inducing a CD8 +  T CM  cell response in a patient the first time that patient is provided the composition including the selected target peptides. As such, the target peptides of the presently disclosed subject matter can in some embodiments be referred to as “neo-antigens”. Although target peptides might be considered “self” for being derived from self-tissue, they generally are only found on the surface of cells with a dysregulated metabolism, e.g., aberrant phosphorylation, they are likely never presented to immature T cells in the thymus. As such, these “self” antigens act are neo-antigens because they are nevertheless capable of eliciting an immune response. 
     In some embodiments, about or at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, or 99% of T cells activated by particular target peptide in a particular patient sample are T CM  cells. In some embodiments, a patient sample is taken exactly, about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more days after an initial exposure to a particular target peptide and then assayed for target peptide specific activated T cells and the proportion of T CM  cells thereof. In some embodiments, the compositions of the presently disclosed subject matter are able to elicit a CD8 +  T CM  cell response in at least or about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, 99%, or 100% of patients and/or healthy volunteers. In some embodiments, the compositions of the presently disclosed subject matter are able to elicit a CD8 +  T CM  cell response in a patient about or at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, 99%, or 100% of patients and/or healthy volunteers specific to all or at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 target peptides in the composition. In some embodiments, the aforementioned T cell activation tests are done by ELISpot assay. 
     II. O-GlcNAc Peptides 
     The term “O-GlcNAc peptides” includes MHC class I and MHC class II specific O-GlcNAc peptides. 
     Modification of proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) was previously technically difficult to detect. However, it rivals phosphorylation in both abundance and distribution of the protein targets for this modification. Like phosphorylation, O-GlcNAcylation is a reversible modification of nuclear and cytoplasmic proteins and consists of the attachment of a single β-N-acetyl-glucosamine moiety to hydroxyl groups of serine or threonine residues. Modification by O-GlcNAcylation is often competitive with phosphorylation at the same sites or at proximal sites on proteins. Furthermore, crosstalk between O-GlcNAcylation and phosphorylation affects the posttranslational state of hundreds of proteins in response to nutrients and stress and plays an important role in chronic diseases of metabolism, such as diabetes and neurodegeneration. 
     O-GlcNAc transferase (OGT) catalyzes the addition of the sugar moiety from the donor substrate uridine 5′-diphosphate (UDP)-GlcNAc to proteins. During M phase, OGT localizes to discrete structures, such as centrosomes (metaphase) and the spindle (anaphase), and then moves to the midbody during cytokinesis. OGT, along with O-GlcNAcase (OGA), the enzyme that removes the sugar, dynamically interacts with AURKB and PP1 at the midbody. Together, these proteins form a complex regulating M-phase O-GlcNAcylation, which in turn influences the phosphorylation state, of vimentin. However, the identity of other OGT mitotic substrates is currently not known. 
     Peptides modified with O-GlcNAc can be difficult to detect by standard mass spectrometric methods. The modification is usually present at sub-stoichiometric amounts, modified and unmodified peptides co-elute during high-performance liquid chromatography (HPLC), and ionization of the modified peptide is suppressed in the presence of unmodified peptides. Consequently, sample enrichment is often required to successfully detect and characterize O-GlcNAcylated peptides. Enrichment can be achieved through chemoenzymatic approaches that biotinylate O-GlcNAc peptides and capture them by avidin chromatography. Alternatively, a chemoenzymatic approach using a photocleavable biotin-alkyne reagent (PCbiotin-alkyne) tag can be used (see FIG. S1A of Wang et al. (2010)  Sci Signal  3(104):ra2 (hereinafter “Wang”, incorporated herein by reference). Photocleavage not only allows efficient and quantitative recovery from the affinity column, but also tags the peptide with a charged moiety that facilitates O-GlcNAc site mapping by electron-transfer dissociation (ETD) mass spectrometry. This tagging approach also makes it possible to use conventional collision-activated dissociation mass spectrometry (CAD MS) to screen samples for the presence of O-GlcNAc-modified peptides by monitoring for two-signature fragment ions characteristic of the tag (see FIG. S1B of Wang). 
     O-GlcNAcylation rivals phosphorylation in both abundance and distribution of the modified proteins and alterations in O-GlcNAcylation disrupt both the chromosomal passenger complex, containing AURKB, INCENP, PP1, Borealin, and Surviven, and the circuits regulating CDK1 activity. 
     O-GlcNAc is nearly as abundant as phosphate on proteins associated with the spindle and midbody. Many of the O-GlcNAcylation sites identified are identical or proximal to known phosphorylation sites. O-GlcNAcylation and phosphorylation work together to control complicated mitotic processes, such as spindle formation. For example, OGT overexpression altered the abundance of transcripts and proteins encoded by several mitotic genes, changed the localization of NuMA1, and disrupted the chromosomal passenger complex and the CDK1 activation circuit. 
     An interplay exists between O-GlcNAcylation and phosphorylation for several protein classes, most noticeably transcriptional regulators and cytoskeletal proteins. Many of the O-GlcNAcylation and phosphorylation sites are located in the regulatory head domains of intermediate filament proteins. Phosphorylation of these sites causes filament disassociation during M phase. For example, vimentin is phosphorylated at multiple sites during M phase and there is an O-GlcNAcylation site that is also a mitotic phosphorylation site (Ser55; Slawson et al. (2005)  J Biol Chem  280:32944-32956; Slawson et al. (2008)  Mol Biol Cell  19:4130-4140; Wang et al. (2007)  Mol Cell Proteomics  6:1365-1379; Molina et al. (2007)  Proc Natl Acad Sci USA  104:2199-2204). There are three additional O-GlcNAcylation sites on vimentin at Ser7, Thr33, and Ser34 (see Tables S5 and S6 of Wan), all of which are in the regulatory head domain of the protein. Two of these, Ser7 and Ser34, are also phosphorylation sites (Dephoure et al. (2008)  Proc Natl Acad Sci USA  105:10762-10767; Molina et al (2007)  Proc Natl Acad Sci USA  104:2199-2204). Signaling pathways involving cytoskeletal proteins are regulated by reciprocal occupancy on specific sites by phosphate and O-GlcNAc. In these classes of molecules, areas of multiple phosphorylation are also likely to be targeted for OGlcNAcylation. 
     OGT overexpression profoundly affects multiple mitotic signaling circuits. Although overexpression of OGT does not interfere with the formation of the midbody complex or localization of AURKB, AURKB activity is altered toward the cytoskeletal protein, vimentin. The reduction in the abundance of AURKB or INCENP dampens kinase activity to a point that retards mitotic progression especially during anaphase and telephase. Furthermore, OGT overexpression reduced phosphorylation of INCENP and borealin, but to what extent this alters the function of the midbody complex is unclear. 
     Multiple components of the cyclin B-CDK1 activation circuit were disrupted by the overexpression of OGT. The loss of PLK1 inhibitory phosphorylation on MYT1 and the increase in the abundance of MYT1 are likely contributors to the loss in cyclin B-CDK1 activity observed in OGT-overexpressing cells (see FIG. 7 of Wang). However, the reduction in cyclin B-CDK1 activity is likely only partially due to the increase in MYT1 activity, because the mRNA for CDCl25C, the key CDK1 dual-specific phosphatase, is substantially reduced. The “on” switch for CDK1 activation, the reduction of MYT1 and the increase in CDCl25C activity, is pushed toward “off” by OCT overexpression. Both MYT1 and CDCl25C are substrates for PLK1. The protein and transcript abundance of PLK1 is substantially reduced in response to OGT overexpression, but there is little change in the extent of activating phosphorylation of PLK1. 
     Because O-GlcNAcylation is directly coupled to nutrient uptake and metabolism, the sugar residue is an ideal metabolic sensor for regulating mitotic progression. Whereas, phosphorylation might act as a master switch initiating the mitotic process, O-GlcNAcylation might act as an adjuster of signals to make these processes more responsive to environmental cues. How O-GlcNAcylation exerts control on specific mitotic proteins and how OGlcNAcylation will integrate into well-known signaling pathways represent another layer of cellular regulation. 
     III. Phosphopeptides 
     The term “phosphopeptides” includes MHC class I and MHC class II specific phosphopeptides. Exemplary MHC class I phosphopeptides of the presently disclosed subject matter are set forth in SEQ ID NOs: 1-193, for example. 
     In some embodiments, the phosphopeptides of the presently disclosed subject matter comprise the sequences of at least one of the MHC class I binding peptides listed in SEQ ID NOs: 1-193. Moreover, in some embodiments about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more of the serine, homo-serine, threonine, or tyrosine residues within the recited sequence is phosphorylated. The phosphorylation can in some embodiments be with a natural phosphorylation (—CH—O—PO 3 H) or with an enzyme non-degradable, modified phosphorylation, such as (—CH 2 —CF 2 —PO 3 H or —CH 2 —CH 2 —PO 3 H). Some phosphopeptides can contain more than one of the peptides listed in SEQ ID NOs: 1-193, for example, if they are overlapping, adjacent, or nearby within the native protein from which they are derived. 
     The chemical structure of a phosphopeptide mimetic appropriate for use in the presently disclosed subject matter can in some embodiments closely approximate the natural phosphorylated residue which is mimicked, and also can in some embodiments be chemically stable (e.g., resistant to dephosphorylation by phosphatase enzymes). This can be achieved with a synthetic molecule in which the phosphorous atom is linked to the amino acid residue, not through oxygen, but through carbon. In some embodiments, a CF 2  group links the amino acid to the phosphorous atom. Mimetics of several amino acids which are phosphorylated in nature can be generated by this approach. Mimetics of phosphoserine, phosphothreonine, and phosphotyrosine can be generated by placing a CF 2  linkage from the appropriate carbon to the phosphate moiety. The mimetic molecule L-2-amino-4 (diethylphosphono)-4,4-difluorobutanoic acid (F2Pab) can in some embodiments substitute for phosphoserine (Otaka et al., Tetrahedron Letters 36: 927-930 (1995)). L-2-amino-4-phosphono-4,4difloro-3-methylbutanoic acid (F2Pmb) can in some embodiments substitute for phosphothreonine. L-2-amino-4-phosphono (difluoromethyl) phenylalanine (F2Pmp) can in some embodiments substitute for phosphotyrosine (Akamatsu et al. (1997)  Bioorg Med Chem  5:157-163; Smyth et al. (1992)  Tetrahedron Lett  33:4137-4140). Alternatively, the oxygen bridge of the natural amino acid can in some embodiments be replaced with a methylene group. In some embodiments, serine and threonine residues are substituted with homo-serine and homo-threonine residues, respectively. A phosphomimetic can in some embodiments also include vanadate, pyrophosphate or fluorophosphates. 
     IV. Immunosuitablity 
     In some embodiments, the target peptides of the presently disclosed subject matter are combined into compositions which can be used in vaccine compositions for eliciting anti-tumor immune responses or in adoptive T-cell therapy of ovarian cancer patients. Table 3 provides target peptides presented on the surface of cancer cells. 
     Although individuals in the human population display hundreds of different HLA alleles, some are more prevalent than others. For example, 88% of melanoma patients carry at least one of the six HLA alleles: HLA-A*0201 (51%), HLA-A*0101(29%), HLA-A*0301 (21%), HLA-A*4402 (27%), HLA-A*0702 (30%′), and HLA-A*2705 (7%). 
     The presently disclosed subject matter provides in some embodiments target peptides which are immunologically suitable for each of the foregoing HLA alleles and, in particular, HLA-A*0201. “Immunologically suitable” means that a target peptide will bind at least one allele of an MIC class I molecule in a given patient. Compositions of the presently disclosed subject matter are in some embodiments immunologically suitable for a patient when at least one target peptide of the composition will bind at least one allele of an MHC class I molecule in a given patient. Compositions of multiple target peptides presented by each of the most prevalent alleles used in a cocktail, ensures coverage of the human population and to minimize the possibility that the tumor will be able to escape immune surveillance by down-regulating expression of any one class I target peptide. 
     The compositions of the presently disclosed subject matter can in some embodiments have at least one target peptide specific for HLA-A*0201. The compositions can in some embodiments have at least one phosphopeptide specific from at least the HLA-A*0201 allele. In some embodiments, the compositions can further comprise additional phosphopeptides from other MHC class I alleles. 
     As such, the compositions of the presently disclosed subject matter containing various combinations of target peptides will in some embodiments be immunologically suitable for between or about 3-88%, 80-89%, 70-79%, 60-69%, 57-59%, 55-57%, 53-55% or 51-53% or 5-90%, 10-80%, 15-75%, 20-70%, 25-65%, 30-60%, 35-55%, or 40-50% of the population of a particular cancer, e.g., ovarian cancer. In some embodiments, the compositions of the presently disclosed subject matter are able to act as vaccine compositions for eliciting anti-tumor immune responses or in adoptive T-cell therapy of ovarian cancer patients, wherein the compositions are immunologically suitable for about or at least 88, 87, 86, 85, 84, 83, 82, 81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67, 66, 65, 64, 63, 62, 61, 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4 or 3 percent of cancer, e.g., ovarian cancer, patients. 
     V. Compositions 
     “Target peptide compositions” as used herein refers to at least one target peptide formulated for example, as a vaccine; or as a preparation for pulsing cells in a manner such that the pulsed cells, e.g., dendritic cells, will display the at least one target peptide in the composition on their surface, e.g., to T-cells in the context of adoptive T-cell therapy. 
     The compositions of the presently disclosed subject matter can include in some embodiments about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50-55, 55-65, 65-80, 80-120, 90-150, 100-175, or 175-250 different target peptides. 
     The compositions of the presently disclosed subject matter generally include MHC class I specific target peptide(s) but in some embodiments can also include one or more target peptides specific for MHC class II or other peptides associated with tumors, e.g., tumor-associated antigen (“TAA”). 
     Compositions comprising the presently disclosed target peptide are typically substantially free of other human proteins or peptides. They can be made synthetically or by purification from a biological source. They can be made recombinantly. In some embodiments, they are at least 90%, 92%, 93%, 94%, at least 95%, or at least 99% pure. For administration to a human body, in some embodiments they do not contain other components that might be harmful to a human recipient. The compositions are typically devoid of cells, both human and recombinant producing cells. However, as noted below, in some cases, it can be desirable to load dendritic cells with a target peptide and use those loaded dendritic cells as either an immunotherapy agent themselves, or as a reagent to stimulate a patient&#39;s T cells cx vivo. The stimulated T cells can be used as an immunotherapy agent. In some embodiments, it can be desirable to form a complex between a target peptide and an HLA molecule of the appropriate type. Such complexes can in some embodiments be formed in vitro or in vivo. Such complexes are typically tetrameric with respect to an HLA-target peptide complex. Under certain circumstances it can be desirable to add additional proteins or peptides, for example, to make a cocktail having the ability to stimulate an immune response in a number of different HLA type hosts. Alternatively, additional proteins or peptide can provide an interacting function within a single host, such as an adjuvant function or a stabilizing function. As a non-limiting example, other tumor antigens can be used in admixture with the target peptides, such that multiple different immune responses are induced in a single patient. 
     Administration of target peptides to a mammalian recipient can in some embodiments be accomplished using long target peptides, e.g., longer than 15 residues, or using target peptide loaded dendritic cells. See Melief (2009)  J Med Sci  2:43-45. The immediate goal is to induce activation of CD8 +  T cells. Additional components which can be administered to the same patient, either at the same time or close in time (e.g. within 21 days of each other) include TLR-ligand oligonucleotide CpG and related target peptides that have overlapping sequences of at least 6 amino acid residues. To ensure efficacy, mammalian recipients should express the appropriate human HLA molecules to bind to the target peptides. Transgenic mammals can be used as recipients, for example, if they express appropriate human HLA molecules. If a mammal&#39;s own immune system recognizes a similar target peptide then it can be used as model system directly, without introducing a transgene. Useful models and recipients can in some embodiments be at increased risk of developing metastatic cancer, such as metastatic ovarian cancer. Other useful models and recipients can be predisposed, e.g., genetically or environmentally, to develop ovarian cancer or other cancer. 
     V.A. Selection of Target Peptides 
     Disclosed herein is the finding that immune responses can be generated against phosphorylated peptides tested in healthy and diseased individuals. The T-cells associated with these immune responses, when expanded in vitro, are able to recognize and kill malignant tissue (both established cells lines and primary tumor samples). Cold-target inhibition studies reveal that these target peptide-specific T-cell lines kill primary tumor tissue in a target peptide-specific manner. 
     When selecting target peptides of the presently disclosed subject matter for inclusion in immunotherapy, e.g., in adaptive cell therapy or in the context of a vaccine, one can preferably pick target peptides that in some embodiments: 1) are associated with a particular cancer/tumor cell type; 2) are associated with a gene/protein involved in cell proliferation; 3) are specific for an HLA allele carried the group of patients to be treated; and/or 4) are capable of inducing a target peptide-specific memory T cell response in the patients to be treated upon a first exposure to a composition including the selected target peptides. 
     V.B. Target Peptide Vaccines 
     The antigen target peptides can also in some embodiments be used to vaccinate an individual. The antigen target peptides can be injected alone or in some embodiments can be administered in combination with an adjuvant and a pharmaceutically acceptable carrier. Vaccines are envisioned to prevent or treat certain diseases in general and cancers in particular. 
     The target peptides compositions of the presently disclosed subject matter can in some embodiments be used as a vaccine for cancer, and more specifically for melanoma, leukemia, ovarian, breast, colorectal, or lung squamous cancer, sarcoma, renal cell carcinoma, pancreatic carcinomas, squamous tumors of the head and neck, brain cancer, liver cancer, prostate cancer, and cervical cancer. The compositions can in some embodiments include target peptides. The vaccine compositions can in some embodiments include only the target peptides, or peptides disclosed herein, or they can include other cancer antigens that have been identified. 
     The vaccine compositions can in some embodiments be used prophylactically for the purposes of preventing, reducing the risk of, and/or delaying initiation of a cancer in an individual that does not currently have cancer. Alternatively, they can be used to treat an individual that already has cancer, so that recurrence or metastasis is delayed and/or prevented. Prevention relates to a process of prophylaxis in which the individual is immunized prior to the induction or onset of cancer. For example, individuals with a history of poor life style choices and at risk for developing ovarian cancer can in some embodiments be immunized prior to the onset of the disease. 
     Alternatively or in addition, individuals that already have cancer can be immunized with the antigens of the presently disclosed subject matter so as to stimulate an immune response that would be reactive against the cancer. A clinically relevant immune response would be one in which the cancer partially or completely regresses and/or is eliminated from the patient, and it would also include those responses in which the progression of the cancer is blocked without being eliminated. Similarly, prevention need not be total, but can in some embodiments result in a reduced risk, delayed onset, and/or delayed progression or metastasis. 
     The target peptide vaccines of the presently disclosed subject matter can in some embodiments be given to patients before, after, or during any of the aforementioned stages of ovarian cancer. In some embodiments, they are given to patients with stage malignant ovarian cancer. 
     In some embodiments, the 5-year survival rate of patients treated with the vaccines of the presently disclosed subject matter is increased by a statistically significant amount, e.g., by about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more percent, relative to the average 5-year survival rates described above. 
     In some embodiments, the target peptide vaccine composition of the presently disclosed subject matter will increase survival rates in patients with metastatic ovarian cancer by a statistically significant amount of time, e.g., by about or at least, 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.5, 4.0, 4.25, 4.5, 4.75, 5.0, 5.25, 5.5, 5.75, 6.0, 6.25, 6.5, 6.75, 7.0, 7.25, 7.5, 7.75, 8.0, 8.25, 8.5, 8.75, 9.0, 9.25, 9.50, 9.75, 10.0, 10.25, 10.5, 10.75, 11.0, 11.25, 11.5, 11.75, or 12 months or more compared to what could have been expected without vaccine treatment at the time of filing of this disclosure. 
     In some embodiments, the survival rate, e.g., the 1, 2, 3, 4, or 5-year survival rate, of patients treated with the vaccines of the presently disclosed subject matter is increased by a statistically significant amount, e.g., by about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 percent, relative to the average 5-year survival rates described above. 
     The target peptide vaccines of the presently disclosed subject matter are in some embodiments envisioned to illicit a T cell associated immune response, e.g., generating activated CD8 m  T cells specific for native target peptide/MHC class 1 expressing cells, specific for at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the target peptides in the vaccine in a patient for about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 07, 98, 99, or 100 days after providing the vaccine to the patient. 
     In some embodiments, the treatment response rates of patients treated with the target peptide vaccines of the presently disclosed subject matter are increased by a statistically significant amount, e.g., by about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 07, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, or more percent, relative to treatment without the vaccine. 
     In some embodiments, overall median survival of patients treated with the target peptide vaccines of the presently disclosed subject matter is increased by a statistically significant amount, e.g., by about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, or more percent, relative to treatment without the vaccine. In some embodiments, the overall median survival of ovarian cancer patients treated the target peptide vaccines is envisioned to be about or at least 10.0, 10.25, 10.5, 10.75, 11.0, 11.25, 11.5, 11.75, 12, 12.25, 12.5, 12.75, 13, 13.25, 135, 13.75, 14, 14.25, 145, 14.75, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, or more months. 
     In some embodiments, tumor size of patients treated with the target peptide vaccines of the presently disclosed subject matter is decreased by a statistically significant amount, e.g. by about, or by at least, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, or more percent, relative to treatment without the vaccine. 
     In some embodiments, the compositions of the presently disclosed subject matter provide an clinical tumor regression by a statistically significant amount, e.g., in about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 percent of patients treated with a composition of the presently disclosed subject matter. 
     In some embodiments, the compositions of the presently disclosed subject matter provide a CTL response specific for the cancer being treated (such as but not limited to ovarian cancer) by a statistically significant amount, e.g., in about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 percent of patients treated with a composition of the presently disclosed subject matter. 
     In some embodiments, the compositions of the presently disclosed subject matter provide an increase in progression free survival in the cancer being treated, e.g., ovarian cancer, of about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, or more percent compared to the progression free survival or patients not treated with the composition. 
     In some embodiments, progression free survival, CTL response rates, clinical tumor regression rates, tumor size, survival rates (including but not limited to overall survival rates), and/or response rates are determined, assessed, calculated, and/or estimated weekly, monthly, bi-monthly, quarterly, semi-annually, annually, and/or bi-annually over a period of about or at least 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15 or more years or about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 3, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, or more weeks. 
     V.C. Compositions for Priming T Cells 
     Adoptive cell transfer is the passive transfer of cells, in some embodiments immune-derived cells, into a recipient host with the goal of transferring the immunologic functionality and characteristics into the host. Clinically, this approach has been exploited to transfer either immune-promoting or tolergenic cells (often lymphocytes) to patients to enhance immunity against cancer. The adoptive transfer of autologous tumor infiltrating lymphocytes (TIL) or genetically re-directed peripheral blood mononuclear cells has been used to successfully treat patients with advanced solid tumors, including melanoma and ovarian carcinoma, as well as patients with CD19-expressing hematologic malignancies. In some embodiments, adoptive cell transfer (ACT) therapies achieve T-cell stimulation ex vivo by activating and expanding autologous tumor-reactive T-cell populations to large numbers of cells that are then transferred back to the patient. See e.g., Gattinoni et al (2006)  Nature Rev Immunol  6:383-393. 
     The target peptides of the presently disclosed subject matter can in some embodiments take the form of antigen peptides formulated in a composition added to autologous dendritic cells and used to stimulate a T helper cell or CTL response in vitro. The in vitro generated T helper cells or CTL can then be infused into a patient with cancer (Yee et al. (2002)  Proc Natl Acad Sci USA  99:16168-16173), and specifically a patient with a form of cancer that expresses one or more of antigen target peptides. 
     Alternatively or in addition, the target peptides of the presently disclosed subject matter can be added to dendritic cells in vitro, with the loaded dendritic cells being subsequently transferred into an individual with cancer in order to stimulate an immune response. Alternatively or in addition, the loaded dendritic cells can be used to stimulate CD8 +  T cells ex vivo with subsequent reintroduction of the stimulated T cells to the patient. Although a particular target peptide can be identified on a particular cancer cell type, it can be found on other cancer cell types. 
     The presently disclosed subject matter envisions treating cancer by providing a patient with cells pulsed with a composition of target peptides. The use of dendritic cells (“DCs”) pulsed with target peptide antigens allows for manipulation of the immunogen in two ways: varying the number of cells injected and varying the density of antigen presented on each cell. Exemplary methods for DC-based based treatments can be found for example in Mackensen et cal. (2000)  Int J Cancer  86:385-392. 
     V.D. Additional Peptides Present in Target Peptide Compositions 
     The target peptide compositions (or target peptide composition kits) of the presently disclosed subject matter can in some embodiments also include at least one additional peptide derived from tumor-associated antigens. Examples of tumor-associated antigens include MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, p15(58), CEA, RAGE, NY-ESO (LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H14-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, p16, TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4, 791Tgp72, alpha-fetoprotein, β-HCG, BCA225, BTAA, CA 125, CA 15-3 (CA 27.29\BCAA), CA 195, CA 242, CA-50, CAM43, CD68\KP1, CO-029, FGF-5, G250, Ga733 (EpCAM), HTgp-175, M344, MA-50, MG7-Ag, MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding protein/cyclophilin C-associated protein), TAAL6, TAG72, TLP, TPS, prostatic acid phosphatase, and the like. Particular examples of additional peptides derived from tumor-associated antigens that can be employed alone or in combination with the compositions of the presently disclosed subject matter those set forth in Table 2 below. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Exemplary Peptides Derived from Tumor-associated Antigens 
               
            
           
           
               
               
               
            
               
                   
                   
                 Exemplary GENBANK ® 
               
               
                 Polypeptide Name a   
                 Amino Acid Sequence b   
                 Acc. No(s). c   
               
               
                   
               
               
                 CEA 61-69   
                 HLFGYSWYK (SEQ ID NO: 194) 
                 NP_001264092.1 
               
               
                   
                   
                 XP_005278431.1 
               
               
                   
               
               
                 CEA 604-612   
                 YLSGADLNL (SEQ ID NO: 195) 
                 XP_005278431.1 
               
               
                   
               
               
                 FBP/FOLR1 191-199   
                 EIWTHSYKV (SEQ ID NO: 196) 
                 NP_000793.1 
               
               
                   
               
               
                 gp100 17-25   
                 ALLAVGATK (SEQ ID NO: 197) 
                 NP_001186982.1 
               
               
                   
               
               
                 gp100 44-59   
                 WNRQLYPEWTEAQRLD 
                 NP_008859.1 
               
               
                   
                 (SEQ ID NO: 198) 
                   
               
               
                   
               
               
                 gp100 87-95   
                 ALNFPGSQK (SEQ ID NO: 199) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 89-95   
                 SQNFPGSQK (SEQ ID NO: 200) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 154-162   
                 KTWGQYWQV (SEQ ID NO: 201) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 209-217   
                 ITDQVPFSV (SEQ ID NO: 202) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 209-217   
                 IMDQVPFSV (SEQ ID NO: 203) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 280-288   
                 YLEPGPVTA (SEQ ID NO: 204) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 476-485   
                 VLYRYGSFSV (SEQ ID NO: 205) 
                 NP_008859.1 
               
               
                   
               
               
                 gp100 614-622   
                 LIYRRRLMK (SEQ ID NO: 206) 
                 NP_008859.1 
               
               
                   
               
               
                 Her2/neu 369-377   
                 KIFGSLAFL (SEQ ID NO: 207) 
                 NP_004439.2 
               
               
                   
               
               
                 Her2/neu 754-762   
                 VLRENTSPK (SEQ ID NO: 208) 
                 NP_004439.2 
               
               
                   
               
               
                 MAGE-A1 114-127   
                 LLKYRAREPVTKAE 
                 NP_004979.3 
               
               
                 MAGE-A2,3,6 121-134   
                 (SEQ ID NO: 209) 
                 NP_005352.1 
               
               
                   
                   
                 NP_005353.1 
               
               
                   
                   
                 NP_005354.1 
               
               
                   
               
               
                 MAGE-A1 96-104   
                 SLFRAVITK (SEQ ID NO: 210) 
                 NP_004979.3 
               
               
                   
               
               
                 MAGE-A1 161-169   
                 EADPTGHSY (SEQ ID NO: 211) 
                 NP_004979.3 
               
               
                   
               
               
                 MAGE-A3 168-176   
                 EVDPIGHLY (SEQ ID NO: 212) 
                 NP_005353.1 
               
               
                   
               
               
                 MAGE-A3 281-295   
                 TSYVKVLHHMVKISG 
                 NP_005353.1 
               
               
                   
                 (SEQ ID NO: 213) 
                   
               
               
                   
               
               
                 MAGE-A10 254-262   
                 GLYDGMEHL (SEQ ID NO: 214) 
                 NP_001011543.2 
               
               
                   
               
               
                 MART-1/MelanA 27-35   
                 AAGIGILTV (SEQ ID NO: 215) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 51-73   
                 RNGYRALMDKSLHVGTQCALTRR 
                 NP_005502.1 
               
               
                   
                 (SEQ ID NO: 216) 
                   
               
               
                   
               
               
                 MART-1/MelanA 97-116   
                 VPNAPPAYEKLsAEQSPPPY 
                 NP_005502.1 
               
               
                   
                 (SEQ ID NO: 217) 
                   
               
               
                   
               
               
                 MART-1/MelanA 98-109   
                 PNAPPAYEKLsA (SEQ ID NO: 218) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 99-110   
                 PNAPPAYEKLsA (SEQ ID NO: 219) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 100-108   
                 APPAYEKLs (SEQ ID NO: 220) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 100-111   
                 APPAYEKLsAEQ (SEQ ID NO: 221) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 100-114   
                 APPAYEKLsAEQSPP 
                 NP_005502.1 
               
               
                   
                 (SEQ ID NO: 222) 
                   
               
               
                   
               
               
                 MART-1/MelanA 100-115   
                 APPAYEKLsAEQSPPP 
                 NP_005502.1 
               
               
                   
                 (SEQ ID NO: 223) 
                   
               
               
                   
               
               
                 MART-1/MelanA 100-116   
                 APPAYEKLsAEQSPPPY 
                 NP_005502.1 
               
               
                   
                 (SEQ ID NO: 224) 
                   
               
               
                   
               
               
                 MART-1/MelanA 101-109   
                 PPAYEKLsA (SEQ ID NO: 225) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 101-112   
                 PPAYEKLsAEQS (SEQ ID NO: 226) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 102-110   
                 PAYEKLsAE (SEQ ID NO: 227) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 102-113   
                 PAYEKLsAEQSP (SEQ ID NO: 228) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 103-114   
                 AYEKLsAEQSPP (SEQ ID NO: 229) 
                 NP_005502.1 
               
               
                   
               
               
                 MART-1/MelanA 104-115   
                 YEKLsAEQSPPP (SEQ ID NO: 230) 
                 NP_005502.1 
               
               
                   
               
               
                 NY-ESO-1 
                 AAQERRVPR (SEQ ID NO: 231) 
                 AAD05203.1 
               
               
                   
                   
                 CAA10193.1 
               
               
                   
               
               
                 NY-ESO-1 
                 LLGPGRPYR (SEQ ID NO: 232) 
                 NP_001913.2 
               
               
                   
               
               
                 NY-ESO-1 53-62   
                 ASGPGGGAPR (SEQ ID NO: 233) 
                 NP_001318.1 
               
               
                   
               
               
                 p2 830-844   
                 AQYIKANSKFIGITEL 
                 NP_783831.1 
               
               
                   
                 (SEQ ID NO: 234) 
                   
               
               
                   
               
               
                 TAG-1,2 
                 RLSNRLLLR (SEQ ID NO: 235) 
                   
               
               
                   
               
               
                 Tyr 56-70   
                 AQNILLSNAPLGPQFP 
                 NP_000363.1 
               
               
                   
                 (SEQ ID NO: 236) 
                   
               
               
                   
               
               
                 Tyr 146-156   
                 SSDYVIPIGTY (SEQ ID NO: 237) 
                 NP_000363.1 
               
               
                   
               
               
                 Tyr 240-251   
                 SDAEKSDICTDEY (SEQ ID NO: 238) 
                 NP_000363.1 
               
               
                   
               
               
                 Tyr 243-251   
                 KCDICTDEY (SEQ ID NO: 239) 
                 NP_000363.1 
               
               
                   
               
               
                 Tyr 369-377   
                 YMDGTMSQV (SEQ ID NO: 240) 
                 NP_000363.1 
               
               
                   
               
               
                 Tyr 388-406   
                 FLLHHAFVDSIFEQWLQRHRP 
                 NP_000363.1 
               
               
                   
                 (SEQ ID NO: 241) 
               
               
                   
               
               
                   a Numbers listed in subscript are the amino acids positions of the listed peptide sequence in the corresponding polypeptide including, but not limited to the amino acid sequences provided in the GENBANK ® biosequence database. 
               
               
                   b lower case amino acids in this column are optionally phosphorylated. 
               
               
                   c GENBANK ® biosequence database Accession Numbers listed here are intended to be exemplary only and should not be interpreted to limit the disclosed peptide sequences to only these polypeptides. 
               
            
           
         
       
     
     Such tumor specific peptides (including the MHC class I phosphopeptides disclosed in SEQ D NOs: 1-193 and in Table 3 can be added to the target peptide compositions in a manner, number, and/or in an amount as if they were an additional target peptide added to the target peptide compositions as described herein. 
     V.E. Combination Therapies 
     In some embodiments, the target peptide compositions (or target peptide composition kits) of the presently disclosed subject matter are administered as a vaccine or in the form of pulsed cells as first, second, third, or fourth line treatment for the cancer. In some embodiments, the compositions of the presently disclosed subject matter are administered to a patient in combination with one or more therapeutic agents, e.g., anti-CA 125 (or oregovomab Mab B43.13), anti-idiotype Ab (ACA-125), anti-HER-2 (trastuzumab, pertuzumab), anti-MUC-1 idiotypic Ab (HMFG1), HER-2/neu peptide, NY-ESO-1, anti-Programed Death-1 (“PD1”) (or PD1-antagonists such as BMS-936558), anti-CTLA-4 (or CTLA-4 antagonists), vermurafenib, ipilimumab, dacarbazine, IL-2, IFN-α, IFN-γ, temozolomide, receptor tyrosine kinase inhibitors (e.g., imatinib, gefitinib, erlotinib, sunitinib, tyrphostins, telatinib), sipileucel-T, tumor cells transfected with GM-CSF, a platinum-based agent, a taxane, an alkylating agent, an antimetabolite and/or a vinca alkaloid or combinations thereof. In an embodiment, the cancer is sensitive to or refractory, relapsed or resistant to one or more chemotherapeutic agents, e.g., a platinum-based agent, a taxane, an alkylating agent, an anthracycline (e.g., doxorubicin (e.g., liposomal doxorubicin)), an antimetabolite and/or a  vinca  alkaloid. In some embodiments, the cancer is, e.g., ovarian cancer, and the ovarian cancer is refractory, relapsed or resistant to a platinum-based agent (e.g., carboplatin, cisplatin, oxaliplatin), a taxane (e.g., paclitaxel, docetaxel, larotaxel, cabazitaxel) and/or an anthracycline (e.g., doxorubicin (e.g., liposomal doxorubicin)). In some embodiments, the cancer is, e.g., ovarian cancer, and the cancer is refractory, relapsed or resistant to an antimetabolite (e.g., an antifolate (e.g., pemetrexed, floxuridine, raltitrexed) and a pyrimidine analogue (e.g., capecitabine, cytrarabine, gemcitabine, 5FU)) and/or a platinum-based agent (e.g., carboplatin, cisplatin, oxaliplatin). In some embodiments, the cancer is, e.g., lung cancer, and the cancer is refractory, relapsed or resistant to a taxane (e.g., paclitaxel, docetaxel, larotaxel, cabazitaxel), a platinum-based agent (e.g. carboplatin, cisplatin, oxaliplatin), a  vinca  alkaloid (e.g., vinblastine, vincristine, vindesine, vinorelbine), a vascular endothelial growth factor (VEGF) pathway inhibitor, an epidermal growth factor (EGF) pathway inhibitor) and/or an antimetabolite (e.g., an antifolate (e.g., pemetrexed, floxuridine, raltitrexed) and a pyrimidine analogue (e.g., capecitabine, cytrarabine, gemcitabine, 5FU. In some embodiments, the cancer is, e.g. breast cancer, and the cancer is refractory, relapsed or resistant to a taxane (e.g., paclitaxel, docetaxel, larotaxel, cabazitaxel), a vascular endothelial growth factor (VEGF) pathway inhibitor, an anthracycline (e.g., daunorubicin, doxorubicin (e.g., liposomal doxorubicin), epirubicin, valrubicin, idarubicin), a platinum-based agent (e.g., carboplatin, cisplatin, oxaliplatin), and/or an antimetabolite (e.g., an antifolate (e.g. pemetrexed, floxuridine, raltitrexed) and a pyrimidine analogue (e.g., capecitabine, cytrarabine, gemcitabine, 5FU)). In some embodiments, the cancer is, e.g., gastric cancer, and the cancer is refractory, relapsed or resistant to an antiretabolite (e.g., an antifolate (e.g., pemetrexed, floxuridine, raltitrexed) and a pyrimidine analogue (e.g. capecitabine, cytrarabine, gemcitabine, 5FU)) and/or a platinum-based agent (e.g., carboplatin, cisplatin, oxaliplatin). 
     In some embodiments, the target peptide compositions (or target peptide composition kits) of the presently disclosed subject matter are associated with agents that inhibit T cell apoptosis or anergy thus potentiating a T cell response (“T cell potentiator”). Such agents include B7RP1 agonists, B7-H3 antagonists, B7-H4 antagonists, HVEM antagonists, HVEM antagonists, GAL9 antagonists or alternatively CD27 agonists, OX40 agonists, CD137 agonists, BTLA agonists, ICOS agonists CD28 agonists, or soluble versions of PDL1, PDL2, CD80, CD96, B7RP1, CD137L, OX40 or CD70. See Pardoll, National Reviews of Cancer, Focus on Tumour Immunology &amp; Immunotherapy, 254, April 2012, Volume 12. 
     In some embodiments, the T cell potentiator is a PD1 antagonist. Programmed death 1 (PD-1) is a key immune checkpoint receptor expressed by activated T cells, and it mediates immunosuppression. PD-1 functions primarily in peripheral tissues, where T cells can encounter the immunosuppressive PD-1 ligands PD-L1 (B7-H1) and PD-L2 (B7-DC), which are expressed by tumor cells, stromal cells, or both. In some embodiments, the anti-PD-1 monoclonal antibody BMS-936558 (also known as MDX-1106 and ONO-4538) is used. In some embodiments, the T cell potentiator, e.g., PD1 antagonist, is administered as an intravenous infusion at least or about every 1, 1.5, 2, 2.5, 3, 3.5, or 4 weeks of each 4, 5, 6, 7, 8, 9, or 10-week treatment cycle of about for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more cycles. Exemplary, non-limiting doses of the PD1 antagonists are envisioned to be exactly, about, or at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mg/kg. See Brahmer el al., N Engl J Med 2012; 366:2455-65. 
     The exemplary therapeutic agents disclosed herein above are envisioned to be administered at a concentration of, e.g., about 1 to 100 mg/m 2 , about 10 to 80 mg/m 2 , about 40 to 60 mg/m 2 , e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more mg/mm 2 . Alternatively, the exemplary therapeutic agents disclosed herein above are envisioned to be administered at a concentration of, e.g., about or at least 0.001 to 100 mg/kg or 0.1 to 1 mg/kg. In some embodiments, the exemplary therapeutic agents disclosed herein above are envisioned to be administered at a concentration of, e.g., about or at least from 0.01 to 10 mg/kg. 
     The target peptide compositions (or target peptide composition kits) of the presently disclosed subject matter can in some embodiments also be provided with administration of cytokines such as lymphokines, monokines, growth factors and traditional polypeptide hormones. Included among the cytokines are growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); hepatic growth factor; prostaglandin, fibroblast growth factor; prolactin; placental lactogen, OB protein; tumor necrosis factor-alpha and -beta; mullerian-inhibiting substance; mouse gonadotropin-associated peptide; inhibin; activin; vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF-beta; platelet-growth factor; transforming growth factors (TGFs) such as TGF-alpha and TGF-beta; insulin-like growth factor-I and -II; erythropoietin (EPO); osteoinductive factors; interferons such as interferon-alpha -beta, and -gamma; colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1, IL-1alpha, IL-2, IL-3, L-4, LL-5, IL-6, IL-7, IL-8, II-9, IL-10, IL-11, IL-12; IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, LIF, G-CSF, GM-CSF, M-CSF, EPO, kit-ligand or FLT-3, angiostatin, thrombospondin, endostatin, tumor necrosis factor and LT. As used herein, the term cytokine includes proteins from natural sources or from recombinant cell culture and biologically active equivalents of the native sequence cytokines. 
     The target peptide compositions of the presently disclosed subject matter can in some embodiments be provided with administration of cytokines around the time, (e.g., about or at least 1, 2, 3, or 4 weeks or days before or after) of the initial dose of a target peptide composition. 
     Exemplary, non-limiting doses of a cytokine would be about or at least 1-100, 10-80, 20-70, 30-60, 40-50, or 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 Mu/in/day over about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 days. The cytokine can in some embodiments be delivered at least or about once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 hours. Cytokine treatment can in some embodiments be provided in at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 cycles of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, wherein each cycle has at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 cytokine doses. Cytokine treatment can be on the same schedule as administration of the target peptide compositions or on a different (but in some embodiments overlapping) schedule. 
     In some embodiments, the cytokine is IL-2 and is dosed in an amount of about or at least 100,000 to 1,000,000; 200,000-900,000; 300,000-800,000; 450,000-750,000; 600,000-800,000; or 700,000-800,000; or 720,000 units (IU)/kg administered, e.g., as a bolus, every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 hours for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days, in a cycle, for example. 
     VI Types of Proliferative Disease 
     The compositions of the presently disclosed subject matter are envisioned to useful in the treatment of benign and malignant proliferative diseases. Excessive proliferation of cells and turnover of cellular matrix can contribute significantly to the pathogenesis of several diseases, including but not, limited to cancer, atherosclerosis, rheumatoid arthritis, psoriasis, idiopathic pulmonary fibrosis, scleroderma and cirrhosis of the liver, ductal hyperplasia, lobular hyperplasia, papillomas, and others. 
     In some embodiments, the proliferative disease is cancer, which in some embodiments is selected from the group consisting of breast cancer, colorectal cancer, squamous carcinoma of the lung, sarcoma, renal cell carcinoma, pancreatic carcinomas, squamous tumors of the head and neck, leukemia, brain cancer, liver cancer, prostate cancer, ovarian cancer, and cervical cancer. In some embodiments, the compositions of the presently disclosed subject matter are used to treat colorectal cancer, acute myelogenous leukemia (AML), acute lymphocytic leukemia (ALL), chronic lymphocytic lymphoma (CLL), chronic myelogenous leukemia (CML), breast cancer, renal cancer, pancreatic cancer, and/or ovarian cancer. 
     The target peptide compositions of the presently disclosed subject matter are in some embodiments used to treat ovarian cancer. When metastatic, the ovarian cancer is in the lung, bone, liver, and/or brain. 
     In some embodiments, the cancer is a cancer of the bladder (including accelerated and metastatic bladder cancer), breast (e.g., estrogen receptor positive breast cancer, estrogen receptor negative breast cancer, HER-2 positive breast cancer, HER-2 negative breast cancer, triple negative breast cancer, inflammatory breast cancer), colon (including colorectal cancer), kidney (e.g., renal cell carcinoma), liver, lung (including small cell lung cancer and non-small cell lung cancer (including adenocarcinoma, squamous cell carcinoma, bronchoalveolar carcinoma and large cell carcinoma)), genitourinary tract, e.g., ovary (including fallopian, endometrial and peritoneal cancers), cervix, prostate and testes, lymphatic system, rectum, larynx, pancreas (including exocrine pancreatic carcinoma), stomach (e.g., gastroesophageal, upper gastric or lower gastric cancer), gastrointestinal cancer (e.g., anal cancer), gall bladder, thyroid, lymphoma (e.g., Burkitt&#39;s, Hodgkin&#39;s, or non-Hodgkin&#39;s lymphoma), leukemia (e.g., acute myeloid leukemia), Ewing&#39;s sarcoma, nasoesophageal cancer, nasopharyngeal cancer, neural and glial cell cancers (e.g., glioblastoma multiforme), and head and neck. Exemplary cancers include but are not limited to melanoma, breast cancer (e.g., metastatic or locally advanced breast cancer), prostate cancer (e.g., hormone refractory prostate cancer), renal cell carcinoma, lung cancer (e.g., small cell lung cancer and non-small cell lung cancer (including adenocarcinoma, squamous cell carcinoma, bronchoalveolar carcinoma and large cell carcinoma)), pancreatic cancer, gastric cancer (e.g., gastroesophageal, upper gastric or lower gastric cancer), colorectal cancer, squamous cell cancer of the head and neck, ovarian cancer (e.g., advanced ovarian cancer, platinum-based agent resistant or relapsed ovarian cancer), lymphoma (e.g., Burkitt&#39;s, Hodgkin&#39;s, or non-Hodgkin&#39;s lymphoma), leukemia (e.g., acute myeloid leukemia) and gastrointestinal cancer. 
     VII. Administration of Vaccine Compositions 
     VII.A. Routes of Administration 
     The target peptide compositions of the presently disclosed subject matter can in some embodiments be administered parenterally, systemically, and/or topically. By way of example and not limitation, composition injection can be performed by intravenous (i.v). injection, sub-cutaneous (s.c). injection, intradermal (i.d). injection, intraperitoneal (i.p). injection, and/or intramuscular (i.m). injection. One or more such routes can be employed. Parenteral administration can be, for example, by bolus injection or by gradual perfusion over time. Alternatively or concurrently, administration can be by the oral route. 
     In some embodiments, intradermal (i.d). injection is employed. The target peptide compositions of the presently disclosed subject matter are suitable for administration of the peptides by any acceptable route such as oral (enteral), nasal, ophthal, or transdermal. In some embodiments, the administration is subcutaneous and can be administered by an infusion pump. 
     VII.B. Formulation 
     Pharmaceutical carriers, diluents, and excipients are generally added to the target peptide compositions or (target peptide compositions kits) that are compatible with the active ingredients and acceptable for pharmaceutical use. Examples of such carriers include, but are not limited to, water, saline solutions, dextrose, and/or glycerol. 
     Combinations of carriers can also be used. The vaccine compositions can further incorporate additional substances to stabilize pH and/or to function as adjuvants, wetting agents, and/or emulsifying agents, which can serve to improve the effectiveness of the vaccine. 
     The target peptide compositions can include one or more adjuvants such but not limited to montanide ISA-51 (Seppic, Inc.); QS-21 (Aquila Pharmaceuticals, Inc.); Arlacel A; oeleic acid; tetanus helper peptides (e.g., QYIKANSKFIGITEL (SEQ ID NO: 242) or AQYIKANSKFIGITEL (SEQ ID NO: 234); GM-CSF; cyclophosamide;  bacillus  Calmette-Guerin (BCG); corynbacterium  parvum ; levamisole, azimezone; isoprinisone; dinitrochlorobenezene (DNCB); keyhole limpet hemocyanins (KLH) including Freunds adjuvant (complete and incomplete); mineral gels; aluminum hydroxide (Alum); lysolecithin; pluronic polyols; polyanions; peptides; oil emulsions; nucleic acids (e.g., dsRNA) dinitrophenol; diphtheria toxin (DT); toll-like receptor (TLR, e.g., TLR3, TLR4, TLR7, TLR8 or TLR9) agonists (e.g., endotoxins such as lipopolysaccharide (LPS); monophosphoryl lipid A (MPL); polyinosinic-polycytidylic acid (poly-ICLC/HILTONOL®; Oncovir, Inc., Washington, D.C., United States of America); IMO-2055, glucopyranosyl lipid A (GLA), QS-21—a saponin extracted from the bark of the Quillaja  saponaria  tree, also known as the soap bark tree or Soapbark; resiquimod (TLR7/8 agonist), CDX-1401—a fusion protein consisting of a fully human monoclonal antibody with specificity for the dendritic cell receptor DEC-205 linked to the NY-ESO-1 tumor antigen; Juvaris&#39; Cationic Lipid-DNA Complex; Vaxfectin; and combinations thereof. 
     Polyinosinic-Polycytidylic acid (Poly IC) is a double-stranded RNA (dsRNA) that acts as a TLR3 agonist. To increase half-life, it has been stabilized with polylysine and carboxymethylcellulose as poly-ICLC. It has been used to induce interferon in cancer patients, with intravenous doses up to 300 μg/kg. Like poly-IC, poly-ICLC is a TLR3 agonist. TLR3 is expressed in the early endosome of myeloid DC; thus poly ICLC preferentially activates myeloid dendritic cells, thus favoring a Th1 cytotoxic T-cell response. Poly ICLC activates natural killer (NC) cells, induces cytolytic potential, and induces IFN-gamma from myeloid DC. 
     In some embodiments, the adjuvant is provided at about or at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 micrograms per dose or per kg in each dose. In some embodiments, the adjuvant is provided at least or about 0.1, 0.2, 0.3, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 0.100, 1.10, 1.20, 1.30, 1.40, 1.50, 1.60, 1.70, 1.80, 1.90, 2.00, 2.10, 2.20, 2.30, 2.40, 2.50, 2.60, 2.70, 2.80, 2.90, 3.00, 3.10, 3.20, 3.30, 3.40, 3.50, 3.60, 3.70, 3.80, 3.90, 4.00, 4.10, 4.20, 4.30, 4.40, 4.50, 4.60, 4.70, 4.80, 4.90, 5.00, 5.10, 5.20, 5.30, 5.40, 5.50, 5.60, 5.70, 5.80, 5.90, 6.00, 6.10, 6.20, 6.30, 6.40, 6.50, 6.60, 6.70, 6.80, 6.90, 7.00, 7.10, 7.20, 7.30, 7.40, 7.50, 7.60, 7.70, 7.80, 7.90, 8.00, 8.10, 8.20, 8.30, 8.40, 8.50, 8.60, 8.70, 8.80, 8.90, 9.00, 9.10, 9.20, 9.30, 9.40, 9.50, 9.60, 9.70, 9.80, or 9.90 grains per dose or per kg in each dose. In some embodiments, the adjuvant is given at about or at least 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 500, 525, 550, 575, 600, 625, 675, 700, 725, 750, 775, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, or 2000 endotoxin units (“EU”) per dose. 
     The target peptide compositions of the presently disclosed subject matter can in some embodiments be provided with an administration of cyclophosamide around the time, (e.g., about or at least 1, 2, 3, or 4 weeks or days before or after) the initial dose of a target peptide composition. An exemplary dose of cyclophosamide would in some embodiments be about or at least 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 mg/m 2 /day over about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. 
     The compositions of the presently disclosed subject matter can in some embodiments comprise the presently disclosed target peptides in the free form and/or in the form of a pharmaceutically acceptable salt. 
     As used herein, “a pharmaceutically acceptable salt” refers to a derivative of the disclosed target peptides wherein the target peptide is modified by making acid or base salts of the target peptide. For example, acid salts are prepared from the free base (typically wherein the neutral form of the drug has a neutral —NH 2  group) involving reaction with a suitable acid. Suitable acids for preparing acid salts include both organic acids such as but not limited to acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like, as well as inorganic acids such as but not limited to hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Conversely, basic salts of acid moieties which can be present on a target peptide are prepared using a pharmaceutically acceptable base such as sodium hydroxide, potassium hydroxide, ammonium hydroxide, calcium hydroxide, trimmethylamine or the like. By way of example and not limitation, the compositions can in some embodiments comprise the target peptides as salts of acetic acid (acetates), ammonium, or hydrochloric acid (chlorides). 
     In some embodiments, a composition can include one or more sugars, sugar alcohols, amino acids such a glycine, arginine, glutaminic acid, and others as framework former. The sugars can be mono-, di- or trisaccharide. These sugars can be used alone, as well as in combination with sugar alcohols. Examples of sugars include glucose, mannose, galactose, fructose or sorbose as monosaccharides, sucrose, lactose, maltose or trehalose as disaccharides and raffinose as a trisaccharide. A sugar alcohol can be, for example, mannitose. In some embodiments, the composition comprises sucrose, lactose, maltose, trehalose, mannit and/or sorbit. In some embodiments, the composition comprises mannitol. 
     Furthermore, in some embodiments the presently disclosed compositions can include physiological well-tolerated excipients (see e.g., the  Handbook of Pharmaceutical Excipients,  5 th  ed. (2006) Rowe et al. (eds)., Pharmaceutical Press, London, United Kingdom), such as antioxidants like ascorbic acid or glutathione, preserving agents such as phenol, m-cresole, methyl- or propylparabene, chlorobutanol, thiomersal or benzalkoniumchloride, stabilizer, framework former such as sucrose, lactose, maltose, trehalose, mannitose, mannitol and/or sorbitol, mannitol and/or lactose and solubilizer such as polyethyleneglycols (PEG), i.e. PEG 3000, 3350, 4000, or 6000, or cyclodextrines, i.e. hydroxypropyle-β-cyclodextrine, sulfobutylethyl-β-cyclodextrine or γ-cyclodextrine, or dextranes or poloxaomers, i.e. poloxaomer 407, poloxamer 188, or TWEEn™20, TWEEN™ 80. In some embodiments, one or more Well tolerated excipients can be included, selected from the group consisting of antioxidants, framework formers, and stabilizers. 
     In some embodiments, the pH for intravenous and intramuscular administration is selected from pH 2 to pH 12, while the pH for subcutaneous administration is selected from pH 2.7 to pH 9.0 as the rate of in vivo dilution is reduced resulting in more potential for irradiation at the injection site. (Strickley (2004)  Pharm Res  21:201-230). 
     VII.C. Dosage 
     It is understood that a suitable dosage of a target peptide composition vaccine immunogen will depend upon the age, sex, health, and weight of the recipient, the kind of concurrent treatment, if any, the frequency of treatment, and the nature of the effect desired. However, a desired dosage can be tailored to the individual subject, as determined by the researcher or clinician. The total dose employed for any given treatment can typically be determined with respect to a standard reference dose based on the experience of the researcher or clinician, such dose being administered either in a single treatment or in a series of doses, the success of which can depend on the production of a desired immunological result (i.e., successful production of a T helper cell and/or CTL-mediated response to the target peptide immunogen composition, which response gives rise to the prevention and/or treatment desired). Thus, in some embodiments the overall administration schedule can be considered in determining the success of a course of treatment and not whether a single dose, given in isolation, would or would not produce the desired immunologically therapeutic result or effect. As such, a therapeutically effective amount (i.e., that producing the desired T helper cell and/or CTL-mediated response) can in some embodiments depend on the antigenic composition of the vaccine used, the nature of the disease condition, the severity of the disease condition, the extent of any need to prevent such a condition where it has not already been detected, the manner of administration dictated by the situation requiring such administration, the weight and state of health of the individual receiving such administration, and/or the sound judgment of the clinician or researcher. Needless to say, the efficacy of administering additional doses and of increasing or decreasing the interval can be re-evaluated on a continuing basis, in view of the recipient&#39;s immunocompetence (for example, the level of T helper cell and/or CTL activity with respect to tumor-associated or tumor-specific antigens). 
     The concentration of the T helper or CTL stimulatory target peptides of the invention in pharmaceutical formulations are subject to wide variation, including anywhere from less than 0.01% by weight to as much as 50% or more. Factors such as volume and viscosity of the resulting composition can also be considered. The solvents, or diluents, used for such compositions can include one or more of water, phosphate buffered saline (PBS), saline itself, and/or other possible carriers and/or excipients. The immunogens of the presently disclosed subject matter can in some embodiments also be contained in artificially created structures such as liposomes, which structures can in some embodiments contain additional molecules, such as proteins or polysaccharides, inserted in the outer membranes of the structures and having the effect of targeting the liposomes to particular areas of the body, or to particular cells within a given organ or tissue. Such targeting molecules can in some embodiments be some type of immunoglobulin. Antibodies can work particularly well for targeting the liposomes to tumor cells. 
     Single i.d., i.m., s.c., i.p., and i.v. doses of e.g., about 1 to 50 μg, 1 to 100 μg, 1 to 500 μg, 1 to 1000 μg, or about 1 to 50 mg, 1 to 100 mug, 1 to 500 mg, or 1 to 1000 mg of a target peptide composition of the presently disclosed subject matter can in some embodiments be given and in some embodiments can depend from the respective compositions of target peptides with respect to total amount for all target peptides in the composition or alternatively for each individual target peptide in the composition. A single dose of a target peptide vaccine composition of the presently disclosed subject matter can in some embodiments have a target peptide amount (e.g., total amount for all target peptides in the composition or alternatively for each individual target peptide in the composition) of about or at least 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, or 950 μg. Alternatively, a single dose of a target peptide composition of the presently disclosed subject matter can in some embodiments have a total target peptide amount (e.g., total amount for all target peptides in the composition or alternatively for each individual target peptide in the composition) of about or at least 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, or 950 mg. In some embodiments, the target peptides of a composition of the presently disclosed subject matter are present in equal amounts of about 100 micrograms per dose in combination with an adjuvant peptide present in an amount of about 200 micrograms per dose. 
     In a single dose of the target peptide composition of the presently disclosed subject matter, the amount of each target peptide in the composition is in some embodiments equal or is in some embodiments substantially equal. Alternatively, the ratio of the target peptides present in the least amount relative to the target peptide present in the greatest amount is in some embodiments about or at least 1:1.25, 1:1.5, 1:1.75, 1:2.0, 1:2.25, 1:2.5, 1:2.75, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:20, 1:30; 1:40, 1:50, 1:100, 1:200, 1:500, 1:1000, 1:5000; 1:10,000; or 1:100,000. Alternatively, the ratio of the target peptides present in the least amount relative to the target peptide present in the greatest amount is in some embodiments about or at least 1 or 2 to 25; 1 or 2 to 20; 1 or 2 to 15; 1 or 2 to 10; 1 to 3; 1 to 4; 1 to; 1 to 6; 1 to; 1 to 10; 2 to 3; 2 to 4; 2 to 5; 2 to 6; 2 to 7; 2 to 10; 3 to 4; 3 to 5; 3 to 6; 3 to 7; 3 to 10; 5 to 10; 10 to 15; 15 to 20; 20 to 25; 1 to 40; 1 to 30; 1 to 20; 1 to 15; 10 to 40; 10 to 30; 10 to 20; 10 to 15; 20 to 40; 20 to 30; or 20 to 25; 1 to 100; 25 to 100; 50 to 100; 75 to 100; 25 to 75, 25 to 50, or 50 to 75; 25 to 40; 25 to 50; 30 to 50; 30 to 40; or 30 to 75. 
     Single dosages can in some embodiments be given to a patient about or at least 1, 2, 3, 4, or 5 times per day. Single dosages can in some embodiments be given to a patient about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 36, 48, 60, or 72 hours subsequent to a previous dose. 
     Single dosages can in some embodiments be given to a patient about or at least 1, 2, 3, 4, 5, 6, or 7 times per week or every other, third, fourth, or fifth day. Single doses can in some embodiments also be given every week, every other week, or only during 1, 2, or 3 weeks per month. A course of treatment can in some embodiments last about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. 
     In some embodiments, single dosages of the compositions of the presently disclosed subject matter are provided to a patient in at least two phases, e.g., during an initial phase and then a subsequent phase. An initial phase can in some embodiments be about or at least 1, 2, 3, 4, 5, or 6 weeks in length. The subsequent phase can in some embodiments last at least or about 1, 2, 3, 4, 5, 6, 7, or 8 times as long as the initial phase. The initial phase can in some embodiments be separated from the subsequent phase by about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks or months. 
     The target peptide composition dosage during the subsequent phase can in some embodiments be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 times greater than during the initial phase. The target peptide composition dosage during the subsequent phase can in some embodiments be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 times lower than during the initial phase. 
     In some embodiments, the initial phase is about three weeks and the second phase is about 9 weeks. In some embodiments, the target peptide compositions would be administered to the patient on or about days 1, 8, 15, 36, 57, and 78. 
     VII.D. Kits and Storage 
     In some embodiments, the presently disclosed subject matter provides a kit. In some embodiments the kit comprises (a) a container that contains at least one target peptide composition as described above in solution or in lyophilized form-; (b) optionally, a second container containing a diluent or reconstituting solution for the lyophilized formulation; and (c) also optionally, instructions for (i) use of the solution; and/or (ii) reconstitution and/or use of the lyophilized formulation. The kit can in some embodiments further comprise one or more of (iii) a buffer, (iv) a diluent, (v) a filter, (vi) a needle, and/or (v) a syringe. In some embodiments, the container is selected from the group consisting of a bottle, a vial, a syringe, a test tube, and a multi-use container. In some embodiments, the target peptide composition is lyophilized. 
     The kits can in some embodiments contain exactly, about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, or more target peptide-containing compositions. Each composition in the kit can in some embodiments be administered at the same time or at different times to a subject. 
     In some embodiments, the kits can comprise a lyophilized formulation of the presently disclosed compositions and/or vaccines in a suitable container and instructions for its reconstitution and/or use. Suitable containers include, for example, bottles, vials (e.g. dual chamber vials), syringes (such as dual chamber syringes), and test tubes. The container can in some embodiments be formed from a variety of materials such as glass or plastic. In some embodiments, the kit and/or container include instructions on or associated with the container that indicate directions for reconstitution and/or use. For example, the label can in some embodiments indicate that the lyophilized formulation is to be reconstituted to target peptide concentrations as described above. The label can in some embodiments further indicate that the formulation is useful or intended for subcutaneous administration. Lyophilized and liquid formulations are in some embodiments stored at −20° C. to −80° C. 
     The container holding the target peptide composition(s) can in some embodiments be a multi-use vial, which allows for repeat administrations (e.g., from 2-6 administrations) of the reconstituted formulation. The kit can in some embodiments further comprise a second container comprising a suitable diluent such as, but not limited to a sodium bicarbonate solution. 
     In some embodiments, upon mixing of the diluent and the lyophilized formulation, the final peptide concentration in the reconstituted formulation is at least or about 0.15, 0.20, 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.50, 3.75, 4.0, 4.25, 4.5, 4.75, 5.0, 6.0, 7.0, 8.0, 9.0, or 10 mg/mL/target peptide. In some embodiments, upon mixing of the diluent and the lyophilized formulation, the final peptide concentration in the reconstituted formulation is at least or about 0.15, 0.20, 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.50, 3.75, 4.0, 4.25, 4.5, 4.75, 5.0, 6.0, 7.0, 8.0, 9.0 or 10 μg/mL/target peptide. 
     The kit can in some embodiments further comprise other materials desirable from a commercial and user standpoint, including but not limited to other buffers, diluents, filters, needles, syringes, and/or package inserts with instructions for use. 
     The kits can in some embodiments have a single container that comprises the formulation of the target peptide compositions with or without other components (e.g. other compounds or compositions of these other compounds) or can in some embodiments have a distinct container for each component. 
     Additionally, the kits can in some embodiments comprise a formulation of the presently disclosed target peptide compositions and/or vaccines packaged for use in combination with the co-administration of a second compound such as but not limited to adjuvants (e.g. imiquimod), a chemotherapeutic agent, a natural product, a hormone or antagonist, an anti-angiogenesis agent or inhibitor, an apoptosis-inducing agent, or a chelator or a composition thereof. The components of the kit can in some embodiments be pre-complexed or each component can in some embodiments be in a separate distinct container prior to administration to a patient. The components of the kit can in some embodiments be provided in one or more liquid solutions. In some embodiments, the liquid solution is an aqueous solution. In some embodiments, the liquid solution is a sterile aqueous solution. The components of the kit can in some embodiments also be provided as solids, which in some embodiments are converted into liquids by addition of suitable solvents, which can in some embodiments be provided in another distinct container. 
     The container of a therapeutic kit can in some embodiments be a vial, a test tube, a flask, a bottle, a syringe, or any other article suitable to enclose a solid or liquid. In some embodiments, when there is more than one component, the kit can contain a second vial and/or other container, which allows for separate dosing. The kit can in some embodiments also contain another container for a pharmaceutically acceptable liquid. In some embodiments, a therapeutic kit contains an apparatus (e.g., one or more needles, syringes, eye droppers, pipette, etc.) that facilitates administration of the agents of the disclosure that are components of the present kit. 
     VII.E Markers for Efficacy 
     When administered to a patient, the vaccine compositions of the presently disclosed subject matter are envisioned to have certain physiological effects, including but not limited to the induction of a T cell mediated immune response. 
     VIII.E.1 Immunohistochemistry, Immunofluorescence, Western Blots, and Flow Cytometry 
     Validation and testing of antibodies for characterization of cellular and molecular features of lymphoid neogenesis has been performed. Commercially available antibodies for use in immunohistochemistry (IHC), immunofluorescence (IF), flow cytometry (FC), and western blot (WB) can in some embodiments be employed. In some embodiments, such techniques can be employed to analyze patient samples, e.g., formalin-fixed, paraffin-embedded tissue samples, for CD1a, S100, CD83, DC-LAMP, CD3, CD4, CD8, CD20, CD45, CD79a, PNAd, TNFalpha, LIGHT, CCL19, CCL21, CXCL12, TLR4, TLR7, FoxP3, PD-1 and Ki67 expression. In some embodiments, flow cytometry is used to determine CD3, CD4, CD8, CD13, CD14, CD16, CCL19, CD45RA, CD45RO, CD56, CD62L, CD27, CD28, CCR7, FoxP3 (intracellular), and MHC-peptide tetramers for I MHC associated (phospho)-peptides. In some embodiments, positive control tissue selected from among normal human peripheral blood lymphocytes (PBL), PBL activated with CD3/CD28 beads (activated PBL), human lymph node tissue from non-ovarian cancer patients (LN), and inflamed human tissue from a surgical specimen of Crohn&#39;s disease (Crohn&#39;s) can be employed. 
     VII.E.2. ELISpot Assay 
     In some embodiments, vaccination site infiltrating lymphocytes and lymphocytes from the sentinel immunized nod (SIN) and vaccine site can be evaluated by ELISpot. ELISpot permits the direct counting of T-cells reacting to antigen by production of INFγ. Peripheral blood lymphocytes can be evaluated by ELISpot assay for the number of peptide-reactive T-cells. Vaccine site infiltrating lymphocytes and SIN lymphocytes can be compared to those in peripheral blood. It is envisioned that positive results of the ELISpot assay correlate with increased patient progression free survival. Progression free survival is in some embodiments defined as the time from start of treatment until death from any cause or date of last follow up. 
     VII.E.3. Tetramer Assay 
     Peripheral blood lymphocytes and lymphocytes from the SIN and vaccine site can be evaluated by flow cytometry after incubation with MHC-peptide tetramers for the number of peptide-reactive T-cells. 
     VII.E.4. Proliferation Assay/Cytokine Analysis 
     Peripheral blood mononuclear cells (PBMC), vaccine-site inflammatory cells, and lymphocytes from the SIN from patients can in some embodiments be evaluated for CD4 T cell reactivity to, e.g., tetanus helper peptide mixture, using a  3 H-thymidine uptake assay. Additionally, Th1 (IL-2, IFN-gamma, TNFa), Th2 (IL-4, IL-5, IL-10), Th17 (IL-17, and IL23), and T-reg (TGF-beta) cytokines in media from 48 hours in that proliferation assay can be employed to determine if the microenvironment supports generation of Tb1, Th2, Th17, and/or T-reg responses. In some embodiments, two peptides are used as negative controls: a tetanus peptide and the PADRE peptide (AK(X)VAAWTLKAA; SEQ ID NO: 243). 
     VII.E.5. Evaluation of Tumors 
     In some embodiments tumor tissue collected prior to treatment or at the time of progression can be evaluated by routine histology and immunohistochemistry. Alternatively or in addition, in vitro evaluations of tumor tissue and tumor infiltrating lymphocytes can be completed. 
     VII.E.6. Studies of Homing Receptor Expression 
     Patient samples can in some embodiments be studied for T cell homing receptors induced by vaccination the compositions of the invention. These include, but are not limited to, integrins (including alphaE-beta7, alpha1-beta1, alpha4-beta1), chemokine receptors (including CXCR3), and selectin ligands (including (CLA, PSL) on lymphocytes, and their ligands in the vaccine sites and SIN. These can be assayed by immunohistochemistry, flow cytometry or other techniques. 
     VII.E.7. Studies of Gene and Protein Expression 
     Differences in gene expression and/or for differences in panels of proteins can in some embodiments be assayed by high-throughput screening assays (e.g. nucleic acid chips, protein arrays, etc.) in the vaccine sites and sentinel immunized nodes. 
     VIII. Antibodies Including Antibody-Like Molecules 
     Antibodies and antibody-like molecules (e.g. T cell receptors) specific for target peptides or target peptide/MHC complexes are, for example, useful, inter alia, for analyzing tissue to determine the pathological nature of tumor margins and/or can be employed in some embodiments as therapeutics. Alternatively, such molecules can in some embodiments be employed as therapeutics targeting cells, e.g., tumor cells, which display target peptides on their surface. In some embodiments, the antibodies and antibody-like molecules bind the target peptides or target peptide-MHC complex specifically and do not substantially cross react with non-phosphorylated native peptides. 
     As used herein, “antibody” and “antibody peptide(s)” refer to intact antibodies, antibody-like molecules, and binding fragments thereof that compete with intact antibodies for specific binding. Binding fragments are in some embodiments produced by recombinant DNA techniques or in some embodiments by enzymatic or chemical cleavage of intact antibodies. Binding fragments include Fab, Fab′, F(ab′) 2 , Fv, and single-chain antibodies. An antibody other than a “bispecific” or “bifunctional” antibody is understood to have each of its binding sites identical. An antibody in some embodiments substantially inhibits adhesion of a receptor to a counterreceptor when an excess of antibody reduces the quantity of receptor bound to counterreceptor by at least about 20%, 40%, 60%, 80%, 85%, 90%, 91% 92% 93%, 94% 95% 96%, 97%, 98%, 99%, or greater than 99% as measured, for example, in an in vitro competitive binding assay. 
     The term “MHC” as used herein refers to the Major Histocompability Complex, which is defined as a set of gene loci specifying major histocompatibility antigens. The term “HLA” as used herein refers to Human Leukocyte Antigens, which are defined as the histocompatibility antigens found in humans. As used herein, “HLA” is the human form of “MHC”. 
     The terms “MHC light chain” and “MHC heavy chain” as used herein refer to portions of MHC molecules. Structurally, class I molecules are heterodimers comprised of two non-covalently bound polypeptide chains, a larger “heavy” chain (a) and a smaller “light” chain β-2-microglobulin or β2m). The polymorphic, polygenic heavy chain (45 kDa), encoded within the MHC on chromosome six, is subdivided into three extracellular domains (designated 1, 2, and 3), one intracellular domain, and one transmembrane domain. The two outermost extracellular domains, 1 and 2, together form the groove that binds antigenic peptide. Thus, interaction with the TCR occurs at this region of the protein. The 3 domain of the molecule contains the recognition site for the CD8 protein on the CTL; this interaction serves to stabilize the contact between the T cell and the APC. The invariant light chain (12 kDa), encoded outside the MHC on chromosome 15, consists of a single, extracellular polypeptide. The terms “MHC light chain”, “β2-microglobulin”, and “β2m” are used interchangeably herein. 
     The term “epitope” includes any protein determinant capable of specific binding to an immunoglobulin or T-cell receptor. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics. An antibody or antibody like molecule is said to “specifically” bind an antigen when the dissociation constant is in some embodiments less than 1 μM, in some embodiments less than 100 nM, and in some embodiments less than 10 nM. 
     The term “antibody” is used in the broadest sense, and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments (e.g., Fab, F(ab′) 2  and Fv), as well as “antibody-like molecules” so long as they exhibit the desired biological activity. Antibodies (Abs) and immunoglobulins (Igs) are glycoproteins having the same structural characteristics. The term is also meant to encompass “antibody like molecules” and other members of the immunoglobulin superfamily, e.g., T-cell receptors, MHC molecules, containing e.g., an antigen-binding regions and/or variable regions, e.g., complementary determining regions (CDRs) which specifically bind the target peptides disclosed herein. 
     In some embodiments, antibodies and antibody-like molecules bind to the target peptides of the presently disclosed subject matter but do not substantially and/or specifically cross react with the same peptide in a modified form. See e.g., U.S. Patent Application Publication No. 2009/0226474, which is incorporated by reference. 
     The presently disclosed subject matter also includes antibodies that recognize target peptides associated with a tumorigenic or disease state, wherein the peptides are displayed in the context of HLA molecules. These antibodies typically mimic the specificity of a T cell receptor (TCR) but can in some embodiments have higher binding affinity such that the molecules can be employed as therapeutic, diagnostic, and/or research reagents. Methods of producing a T-cell receptor mimic of the presently disclosed subject matter include identifying a target peptide of interest, wherein the target peptide of interest comprises an amino acid sequence as set forth in any of SEQ ID NOs: 1-193. Then, an immunogen comprising at least one target peptide/MHC complex is formed. An effective amount of the immunogen is then administered to a host for eliciting an immune response, and serum collected from the host is assayed to determine if desired antibodies that recognize a three-dimensional presentation of the target peptide in the binding groove of the MHC molecule are being produced. The desired antibodies can differentiate the target peptide/MHC complex from the MHC molecule alone, the target peptide alone, and a complex of MHC and irrelevant target peptide. Finally, in some embodiments the desired antibodies are isolated. 
     The term “antibody” also encompasses soluble T cell receptors (TCR) cytoplasmic domains which are stable at low concentrations and which can recognize MHC-peptide complexes. See e.g., U.S. Patent Application Publication No. 2002/0119149, which is incorporated by reference. Such soluble TCRs might for example be conjugated to immunostimulatory peptides and/or proteins or moieties, such as CD3 agonists (anti-CD3 antibody), for example. The CD3 antigen is present on mature human T cells, thymocytes, and a subset of natural killer cells. It is associated with the TCR and is responsible for the signal transduction of the TCR. 
     Antibodies specific for the human CD3 antigen are well-known. One such antibody is the murine monoclonal antibody OKT3 which was the first monoclonal antibody approved by the FDA, OKT3 is reported to be a potent T cell mitogen (Van Wauve (1980)  J Immunol  124:2708-2718; see also U.S. Pat. No. 4,361,539) and a potent T cell killer (Wong (1990)  Transpliantaion  50:683-389). Other antibodies specific for the CD3 antigen have also been reported. (see PCT International Patent Application Publication No. WO 2004/0106380; U.S. Patent Application Publication No. 2004/0202657; U.S. Pat. Nos. 6,750,325, 6,706,265; GB 2249310A; Clark et al. (1989)  Eur J Immunol  19:381-388; U S. Pat. No. 5,968,509; and U.S. Patent Application Publication No. 2009/0117102). ImmTACs (Immunocore Limited, Milton Park, Abington, Oxon, United Kingdom) are innovative bifunctional proteins that combine high-affinity monoclonal T cell receptor (mTCR) targeting technology with a clinically-validated, highly potent therapeutic mechanism of action (Anti-CD3 scFv). 
     Native antibodies and immunoglobulins are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond. The number of disulfide linkages varies between the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (VL) and a constant domain at its other end. The constant domain of the light chain is aligned with the first constant domain of the heavy chain, and the light chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light and heavy chain variable domains (Clothia et al. (1985)  J Mol Biol  186:651-66; Novotny &amp; Haber (1985)  Proc Natl Acad Sci USA  82:4592-4596). 
     An “isolated” antibody is one which has been separated, identified, and/or recovered from a component of the environment in which it was produced. Contaminant components of its production environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and can include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In some embodiments, the antibody is purified as measurable by at least one of the following three different methods: 1) to in some embodiments greater than 50% by weight of antibody as determined by the Lowry method, such as but not limited to in some embodiments greater than 75% by weight, in some embodiments greater than 85% by weight, in some embodiments greater than 95% by weight, in some embodiments greater than 99% by weight; 2) to a degree sufficient to obtain at least 10 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequentator, such as at least 15 residues of sequence; or 3) to homogeneity by SDS-PAGE under reducing or non-reducing conditions using Coomasie blue or, in some embodiments, silver stain. Isolated antibodies include the antibody in situ within recombinant cells since at least one component of the antibody&#39;s natural environment is not present. In some embodiments, however, isolated antibodies are prepared by a method that includes at least one purification step. 
     The terms “antibody mutant”, “antibody variant”, and “antibody derivative” refer to an amino acid sequence variant of an antibody wherein one or more of the amino acid residues of a reference antibody has been modified (e.g., substituted, deleted, chemically modified, etc.). Such mutants necessarily have less than 100% sequence identity or similarity with the amino acid sequence of either the heavy or light chain variable domain of the reference antibody. The resultant sequence identity or similarity between the modified antibody and the reference antibody is thus in some embodiments at least 80%, in some embodiments at least 85%, in some embodiments at least 90%, in some embodiments at least 95%, in some embodiments at least 97%, and in some embodiments at least 99%. 
     The term “variable” in the context of variable domain of antibodies, refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen(s). However, the variability is not evenly distributed through the variable domains of antibodies. It is concentrated in three segments called complementarity determining regions (CDRs) also known as hypervariable regions both in the light chain and the heavy chain variable domains. There are at least two techniques for determining CDRs: (1) an approach based on cross-species sequence variability (i.e., Kabat et al. (1987) Sequences of Proteins of Immunological Interest National institute of Health, Bethesda, Md., United States of America); and (2) an approach based on crystallographic studies of antigen-antibody complexes (Chothia et al. (1989)  Nature  342:877-883). The more highly conserved portions of variable domains are called the framework (FR) regions. The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a β-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen binding site of antibodies (see Kabat et al., 1987, op. cit.). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector function, such as participation of the antibody in antibody-dependent cellular toxicity. The term “antibody fragment” refers to a portion of a full-length antibody, generally the antigen binding or variable region. Examples of antibody fragments include Fab, Fab′, F(ab′)2 and Fv fragments. Papain digestion of antibodies produces two identical antigen binding fragments, called the Fab fragment, each with a single antigen binding site, and a residual “Fe” fragment, so-called for its ability to crystallize readily. Pepsin treatment yields an F(ab′)2 fragment that has two antigen binding fragments which are capable of cross-linking antigen, and a residual other fragment (which is termed pFc′). As used herein, “functional fragment” with respect to antibodies, refers to Fv, F(ab) and F(ab′)2 fragments. 
     An “Fv” fragment is the minimum antibody fragment which contains a complete antigen recognition and binding site. This region consists of a dimer of one heavy and one light chain variable domain in a tight, non-covalent association (V H -V L  dimer). It is in this configuration that the three CDRs of each variable domain interact to define an antigen binding site on the surface of the V H -V L  dimer. Collectively, the six CDRs confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site. 
     The Fab fragment, also designated as F(ab), also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain. Fab′ fragments differ from Fab fragments by the addition of a few residues at the carboxyl terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains have a free thiol group. F(ab′) fragments are produced by cleavage of the disulfide bond at the hinge cysteines of the F(ab′)2 pepsin digestion product. Additional chemical couplings of antibody fragments are known to those of ordinary skill in the art. 
     The light chains of antibodies (immunoglobulin) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino sequences of their constant domain. 
     Depending on the amino acid sequences of the constant domain of their heavy chains, immunoglobulins can be assigned to different classes. There are at least five (5) major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these can be further divided into subclasses (isotypes), e.g., IgG 1 , IgG 2 , IgG 3 , and IgG 4 ; IgA 1  and IgA 2 . The heavy chains constant domains that correspond to the different classes of immunoglobulins are called alpha (α), delta (Δ), epsilon (ε), gamma (γ), and mu (μ), respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well-known. 
     The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that can be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, monoclonal antibodies can be advantageous in that they can be synthesized in hybridoma culture, uncontaminated by other immunoglobulins. 
     The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the presently disclosed subject matter can in some embodiments be made by the hybridoma method first described by Kohler &amp; Milstein (1975)  Nature  256:495, or can in some embodiments be made by recombinant methods, e.g., as described in U.S. Pat. No. 4,816,567. The monoclonal antibodies for use with the presently disclosed subject matter can in some embodiments also be isolated from phage antibody libraries using the techniques described in Clackson et al. (1991)  Nature  352:624-628 or in Marks et a. (1991)  J Mol Biol  222:581-597. 
     Utilization of the monoclonal antibodies of the presently disclosed subject matter can in some embodiments require administration of such or similar monoclonal antibody to a subject, such as a human. However, when the monoclonal antibodies are produced in a non-human animal, such as a rodent, administration of such antibodies to a human patient will normally elicit an immune response, wherein the immune response is directed towards the antibodies themselves. Such reactions limit the duration and effectiveness of such a therapy. In order to overcome such problem, the monoclonal antibodies of the presently disclosed subject matter can be “humanized”: that is, the antibodies can be engineered such that antigenic portions thereof are removed and like portions of a human antibody are substituted therefor, while the antibodies&#39; affinity for specific peptide/MHC complexes is retained. This engineering can in some embodiments only involve a few amino acids, or can in some embodiments include entire framework regions of the antibody, leaving only the complementarity determining regions of the antibody intact. Several methods for humanizing antibodies are known in the art and are disclosed, for example, in U.S. Pat. No. 6,180,370 to Queen et al; U.S. Pat. No. 6,054,927 to Brickell; U.S. Pat. No. 5,869,619 to Studnicka; U.S. Pat. No. 5,861,155 to Lin; U.S. Pat. No. 5,712,120 to Rodriguez et al; and U.S. Pat. No. 4,816,567 to Cabilly et al, the entire content of each of which is hereby expressly incorporated herein by reference in its entirety. 
     Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains, or fragments thereof (such as Fv, Fab, Fab′, F(ab′) 2  or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. In some embodiments, humanization can be performed following the method of Winter and co-workers (see e.g., Jones et al. (1986)  Nature  321:522-525; Riechmann el al. (1988)  Nature  332:323-327; Verhoeyen et at (1988)  Science  239:1534-1536) by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. See also U.S. Pat. No. 5,225,539. In some embodiments, F, framework residues of a human immunoglobulin are replaced by corresponding non-human residues. 
     Humanized antibodies can also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, a humanized antibody comprises substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally can in some embodiments also comprise at least a portion of an immunoglobulin constant region (Fe), typically that of a human immunoglobulin. See e.g., Jones et al. (1986)  Nature  321:522-525; Riechmann et al. (1988)  Nature  332:323-327; Presta (1992)  Proc Natl Acad Sci USA  89:4285-4289. 
     Many articles relating to the generation or use of humanized antibodies teach useful examples of protocols that can be utilized with the presently disclosed subject matter, such as but not limited to Sandborn et al (2001)  Gastroenterology  120:1330-1338; Mihara et al. (2001)  Clin Immunol  98:319; Yenari et al. (200)  Neurol Res  23:72: Morales et al. (2000), Nucl Med Biol 27:199; Richards et al. (1999)  Cancer Res  59:2096; Yenari et al. (1998)  Exp Neurol  153:223; and Shinkura et al. (1998)  Anticancer Res  18:121, all of which are expressly incorporated in their entireties by reference. For example, a treatment protocol that can be utilized in such a method includes a single dose, generally administered intravenously, of 10-20 mg of humanized mAb per kg (Sandborn, et al. (2001)  Gastroenterology  120:1330-1338). In some embodiments, alternative dosing patterns can be appropriate, such as but not limited to the use of three infusions, administered once every two weeks, of 800 to 1600 mg or even higher amounts of humanized mAb (Richards et al., 1999, op. cit.). However, it is to be understood that the presently disclosed subject matter is not limited to the treatment protocols described above, and other treatment protocols that are known to a person of ordinary skill in the art can be utilized in the methods of the presently disclosed subject matter. 
     The presently disclosed and claimed subject matter further includes in some embodiments fully human monoclonal antibodies against specific target peptide/MHC complexes. Fully human antibodies essentially relate to antibody molecules in which the entire sequence of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are referred to herein as “human antibodies” or “fully human antibodies”. Human monoclonal antibodies can be prepared by the trioma technique; the human B-cell hybridoma technique (see Kozbor et al. (1983)  Hybridoma,  2:7), and the EBV hybridoma technique to produce human monoclonal antibodies (see Cole et al. (1985)  Proc Natl Acad Sci USA  82:859). Human monoclonal antibodies can in some embodiments be utilized in the practice of the presently disclosed subject matter and can in some embodiments be produced by using human hybridomas (see Cote et al. (1983)  Proc Natl Acad Sci USA  80:2026) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole el al., 1985, op. cit.). 
     In addition, human antibodies can also be produced using additional techniques, including but not limited to phage display libraries (Hoogenboom e al. (1991)  Nucleic Acids Res  19:4133; Marks et al. (1991)  J Mol Biol  222:581). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; and 5,661,016; and in Marks et at (1992)  J Biol Chem  267:16007: Lonberg et al. (1994)  Nature  368:856; Fishwild et al. (1996)  Nature Biotechnol  14:845; Neuberger (1996)  Nature Biotechnol  14:826; and Lonberg &amp; Huszar (1995)  Intl Rev Immunol  13:65. 
     Human antibodies can in some embodiments additionally be produced using transgenic nonhuman animals which are modified so as to produce fully human antibodies rather than the animal&#39;s endogenous antibodies in response to challenge by an antigen. See PCT International Patent Application Publication No. WO 1994/02602). Typically, the endogenous genes encoding the heavy and light immunoglobulin chains in the non-human host are incapacitated, and active loci encoding human heavy and light chain immunoglobulins are inserted into the host&#39;s genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal that provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. 
     A non-limiting example of such a nonhuman animal is a mouse, and is termed the XENOMOUSE™ as disclosed in PCT International Patent Application Publication Nos. WO 1996/33735 and WO 1996/34096. This animal produces B cells which secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B cells derived from the animal, such as hybridomas producing monoclonal antibodies. Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules. 
     An example of a method of producing a non-human host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S. Pat. No. 5,939,598 to Kucherlapati et al. (incorporated herein by reference). It can be obtained by a method including deleting the J segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker. 
     An exemplary method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Pat. No. 5,916,771 to Hori et al. (incorporated herein by reference). It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain. 
     The antigen target peptides are known to be expressed on a variety of cancer cell types. Thus, antibodies and antibody-like molecules can be used where appropriate, in treating, diagnosing, vaccinating, preventing, retarding, and/or attenuating melanoma, ovarian cancer, breast cancer, colorectal cancer, squamous carcinoma of the lung, sarcoma, renal cell carcinoma, pancreatic carcinomas, squamous tumors of the head and neck, leukemia, brain cancer, liver cancer, prostate cancer, ovarian cancer, and cervical cancer. 
     Antibodies generated with specificity for the antigen target peptides can be used to detect the corresponding target peptides in biological samples. The biological sample could come from an individual who is suspected of having cancer and thus detection would serve to diagnose the cancer. Alternatively, the biological sample can in some embodiments come from an individual known to have cancer, and detection of the antigen target peptides would serve as an indicator of disease prognosis, cancer characterization, or treatment efficacy. Appropriate immunoassays are well-known in the art and include, but are not limited to, immunohistochemistry, flow cytometry, radioimmunoassay, western blotting, and ELISA. Biological samples suitable for such testing include, but are not limited to, cells, tissue biopsy specimens, whole blood, plasma, serum, sputum, cerebrospinal fluid, pleural fluid, and urine. Antigens recognized by T cells, whether helper T lymphocytes or CTL, are not recognized as intact proteins, but rather as small peptides that associate with class I or class II IHC proteins on the surface of cells. During the course of a naturally occurring immune response antigens that are recognized in association with class II MHC molecules on antigen presenting cells are acquired from outside the cell, internalized, and processed into small peptides that associate with the class II MHC molecules. Conversely, the antigens that give rise to proteins that are recognized in association with class I MHC molecules are generally proteins made within the cells, and these antigens are processed and associate with class I MHC molecules. It is now well-known that the peptides that associate with a given class I or class II MHC molecule are characterized as having a common binding motif, and the binding motifs for a large number of different class I and II MHC molecules have been determined. It is also well-known that synthetic peptides can be made which correspond to the sequence of a given antigen and which contain the binding motif for a given class I or II MHC molecule. These peptides can then be added to appropriate antigen presenting cells, and the antigen presenting cells can be used to stimulate a T helper cell or CTL response either in vitro or in vivo. The binding motifs, methods for synthesizing the peptides, and methods for stimulating a T helper cell or CTL response are all well-known and readily available. 
     Kits can in some embodiments be composed for help in diagnosis, monitoring, and/or prognosis. The kits are to facilitate the detecting and/or measuring of cancer-specific target peptides or proteins. Such kits can in some embodiments contain in a single or divided container, a molecule comprising an antigen-binding region. Such molecules can in some embodiments be antibodies and/or antibody-like molecules. Additional components that can be included in the kit include, for example, solid supports, detection reagents, secondary antibodies, instructions for practicing, vessels for running assays, gels, control samples, and the like. The antibody and/or antibody-like molecules can in some embodiments be directly or indirectly labeled, as an option. 
     Alternatively or in addition, the antibody or antibody-like molecules specific for target peptides and/or target peptide/MIC complexes can in some embodiments be conjugated to therapeutic agents. Exemplary therapeutic agents include: 
     Alkylating Agents: Alkylating agents are drugs that directly interact with genomic DNA to prevent cells from proliferating. This category of chemotherapeutic drugs represents agents that affect all phases of the cell cycle, that is, they are not phase-specific. An alkylating agent can in some embodiments include, but is not limited to, a nitrogen mustard, an ethylenimene, a methylmelamine, an alkyl sulfonate, a nitrosourea or a triazines. They include but are not limited to busulfan, chlorambucil, cisplatin, cyclophosphamide (cytoxan), dacarbazine, ifosfamide, mechlorethamine (mustargen), and melphalan. 
     Antimetabolites: Antimetabolites disrupt DNA and RNA synthesis. Unlike alkylating agents, they specifically influence the cell cycle during S phase. Antimetabolites can be differentiated into various categories, such as folic acid analogs, pyrimidine analogs and purine analogs and related inhibitory compounds. Antimetabolites include but are not limited to 5-fluorouracil (5-FU), cytarabine (Ara-C), fludarabine, gemcitabine, and methotrexate. 
     Natural Products: Natural products generally refer to compounds originally isolated from a natural source, and identified as having a pharmacological activity. Such compounds, as well as analogs and derivatives thereof, can in some embodiments be isolated from a natural source, chemically synthesized or recombinantly produced by any technique known to those of skill in the art. Natural products include such categories as mitotic inhibitors, antitumor antibiotics, enzymes and biological response modifiers. 
     Mitotic inhibitors include plant alkaloids and other natural agents that can inhibit either protein synthesis required for cell division or mitosis. They operate during a specific phase during the cell cycle. Mitotic inhibitors include, for example, docetaxel, etoposide (VP16), teniposide, paclitaxel, taxol, vinblastine, vincristine, and vinorelbine. 
     Taxoids are a class of related compounds isolated from the bark of the ash tree,  Taxus brevifolia . Taxoids include, but are not limited to, compounds such as docetaxel and paclitaxel. Paclitaxel binds to tubulin (at a site distinct from that used by the  vinca  alkaloids) and promotes the assembly of microtubules. 
       Vinca  alkaloids are a type of plant alkaloid identified to have pharmaceutical activity. They include such compounds as vinblastine (VLB) and vincristine. 
     Antibiotics: Certain antibiotics have both antimicrobial and cytotoxic activity. These drugs can also interfere with DNA by chemically inhibiting enzymes and mitosis or altering cellular membranes. These agents are typically not phase-specific so they work in all phases of the cell cycle. Examples of cytotoxic antibiotics include but are not limited to bleomycin, dactinomycin, daunorubicin, doxorubicin (Adriamycin), plicamycin (mithramycin), and idarubicin. 
     Miscellaneous Agents: Miscellaneous cytotoxic agents that do not fall into the previous categories include but are not limited to platinum coordination complexes, anthracenediones, substituted ureas, methyl hydrazine derivatives, amsacrine, L-asparaginase, and tretinoin. Platinum coordination complexes include such compounds as carboplatin and cisplatin (cis-DDP). An exemplary anthracenedione is mitoxantrone. An exemplary substituted urea is hydroxyurea. An exemplary methyl hydrazine derivative is procarbazine (N-methylhydrazine, MIH). These examples are not limiting and it is contemplated that any known cytotoxic, cytostatic, and/or cytocidal agent can be conjugated or otherwise attached to targeting peptides and administered to a targeted organ, tissue, and/or cell type within the scope of the presently disclosed subject matter. 
     Chemotherapeutic (cytotoxic) agents include but are not limited to 5-fluorouracil, bleomycin, busulfan, camptothecin, carboplatin, chlorambucil, cisplatin (CDDP), cyclophosphamide, dactinomycin, daunorubicin, doxorubicin, estrogen receptor binding agents, etoposide (VP16), farnesyl-protein transferase inhibitors, gemcitabine, ifosfamide, mechlorethamine, melphalan, mitomycin, navelbine, nitrosurea, plicomycin, procarbazine, raioxifene, tamoxifen, taxol, temazolomide (an aqueous form of DTIC), transplatinum, vinblastine and methotrexate, vincristine, or any analog or derivative variant of the foregoing. Most chemotherapeutic agents fall into the categories of alkylating agents, antimetabolites, antitumor antibiotics, corticosteroid hormones, mitotic inhibitors, and nitrosoureas, hormone agents, miscellaneous agents, and any analog or derivative variant thereof. 
     The peptides identified and tested thus far in peptide-based vaccine approaches have generally fallen into one of three categories: 1) mutated on individual tumors, and thus not displayed on a broad cross section of tumors from different patients; 2) derived from unmutated tissue-specific proteins, and thus compromised by mechanisms of self-tolerance; and 3) expressed in subsets of cancer cells and normal testes. 
     Antigens linked to transformation or oncogenic processes are of primary interest for immunotherapeutic development based on the hypothesis that tumor escape through mutation of these proteins can be more difficult without compromising tumor growth or metastatic potential. 
     The target peptides of the presently disclosed subject matter are unique in that the identified target peptides are modified by intracellular modification. This modification is of particular relevance because it is associated with a variety of cellular control processes, some of which are dysregulated in cancer cells. For example, the source proteins for class I MHC-associated phosphopeptides are often known phosphoproteins, supporting the idea that the phosphopeptides are processed from folded proteins participating in signaling pathways. 
     Although not wishing to be bound by any particular theory, it is envisioned that the target peptides of the presently disclosed subject matter are unexpectedly superior to known tumor-associated antigen-derived peptides for use in immunotherapy because: 1) they only displayed on the surface of cells in which intracellular phosphorylation is dysregulated, i.e., cancer cells, and not normal thymus cells, and thus they are not are not compromised by self-tolerance (as opposed to TAA which are associated with overexpression or otherwise expressed on non-mutated cells); and/or 2) they identify a cell displaying them on their surface as having dysregulated phosphorylation. Thus, post-translationally-modified phosphopeptides that are differentially displayed on cancer cells and derived from source proteins objectively linked to cellular transformation and metastasis allow for more extensive anti-tumor responses to be elicited following vaccination. Target peptides are, therefore, better immunogens in peptide-based vaccines, as target peptides are derived from proteins involved with cellular growth control, survival, or metastasis and alterations in these proteins as a mechanism of immune escape can interfere with the malignant phenotype of tumors. 
     As such, the presently disclosed subject matter also relates in some embodiments to methods for identifying target peptides for use in immunotherapy which are displayed on transformed cells but are not substantially expressed on normal tissue in general or in the thymus in particular. In some embodiments, target peptides bind the MHC class I molecule more tightly than their non-phosphorylated native counterparts. Moreover, such target peptides can in some embodiments have additional binding strength by having amino acid substitutions at certain anchor positions. In some embodiments, such modified target peptides can remain cross-reactive with TCRs specific for native target peptide MHC complexes. Additionally, it is envisioned that the target peptides associated with proteins involved in intracellular signaling cascades or cycle regulation are of particular interest for use in immunotherapy. In some cases, the TCR binding can specifically react with the phosphate groups on the target peptide being displayed on an MHC class I molecule. 
     In some embodiments, the method of screening target peptides for use in immunotherapy, e.g., in adaptive cell therapy or in a vaccine, involves determining whether the candidate target peptides are capable of inducing a memory T cell response. The contemplated screening methods can include providing target peptides, e.g., those disclosed herein or those to be identified in the future, to a healthy volunteer and determining the extent to which a target peptide-specific T cell response is observed. In some embodiments, the extent to which the T cell response is a memory T cell response is also determined. In some embodiments, it is determined the extent to which a T CM  response is elicited, e.g., relative to other T cell types. In some embodiments, those target peptides which are capable of inducing a memory T cell response in health and/or diseased patients are selected for inclusion in the therapeutic compositions of the presently disclosed subject matter. 
     In some embodiments, the presently disclosed subject matter provides methods for inducing a target peptide-specific memory T cell response (e.g., T CM ) response in a patient by providing the patient with a composition comprising the target peptides disclosed herein. In some embodiments, the compositions are those disclosed herein and are provided in a dosing regimen disclosed herein. 
     In some embodiments, the presently disclosed subject matter relates to methods for determining a cancer disease prognosis. These methods involve providing a patient with target peptide compositions and determining the extent to which the patient is able to mount a target peptide specific T cell response. In some embodiments, the target peptide composition contains target peptides selected in the same substantially the same manner that one would select target peptides for inclusion in a therapeutic composition. If a patient is able to mount a significant target peptide-specific T cell response, then the patient is likely to have a better prognosis than a patient with the similar disease and therapeutic regimen that is not able to mount a target peptide-specific T cell response. In some embodiments, the methods involve determining whether the target peptide specific T cell response is a T CM  response. In some embodiments, the presence of a target peptide-specific T cell response as a result of the presently disclosed diagnostic methods correlates with an at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 250, 300, 400, 500, or more percent increase in progression free survival over standard of care. 
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(1994) The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes.  J Immunol  153:5586-5592.   Slawson et al. (2005) Perturbations in O-linked β-N-acetylglucosamine protein modification cause severe defects in mitotic progression and cytokinesis.  J Biol Chem  280:32944-32956.   Slawson et al. (2008) A mitotic GlcN Acylation/phosphorylation signaling complex alters the posttranslational state of the cytoskeletal protein vimentin.  Mol Biol. Cell  19:4130-4140.   Slingluff et al. (2000) Melanomas with concordant loss of multiple melanocytic differentiation proteins: immune escape that may be overcome by targeting unique or undefined antigens.  Cancer Immunol Immunother  48:661-672.   Sun et alt (2005) Infrequent mutation of APC, AXIN1, and GSK3B in human pituitary adenomas with abnormal accumulation of CTNNB1 . J Neurooncol  73:131-134.   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(2005) Epigenetic profiling of cutaneous T cell lymphoma: promoter hypermethylation of multiple tumor suppressor genes including BCL7a, PTPRG, and p 73 . J Clin Oncol  23:3886-3896.   Wang el al. (2007) Dynamic interplay between O-linked N-acetylglucosaminylation and glyocen synthase kinase-3-dependent phosphorylation.  Mol Cell Proteomics  6:1365-1379.   Wang et al. (2010) Extensive Crosstalk Between O-GlcNAcylation and Phosphorylation Regulates Cytokinesis,  Sci Signal  3(104):ra2, including Supplemental Materials.   Waun Ki Hong et al.  Holland - Frei Cancer Medicine  10 A.D. McGraw-Hill Medical. Ref Type: Edited Book   Worm et al. (2004) Genetic and epigenetic alterations of the APC gene in malignant melanoma.  Oncogene  23:5215-5226.   Wuttge et al. (1999) T cell recognition of lipid peroxidation products breaks tolerance to self proteins.  Immunol  98:273-279.   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     It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the presently disclosed subject matter. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 HLA A*0201 Phosphopeptides on Transformed Ovarian Cells (FHIOSE and/or SKOV3) 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 SEQ 
                   
                   
                   
                   
                 UniProt/ 
                   
               
               
                 ID 
                 Peptide 
                   
                   
                   
                 GENBANK ® 
                   
               
               
                 NO. 
                 Sequence 
                 F/S 
                 Start 
                 Stop 
                 Acc. No. 
                 Source Protein 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 1 
                 AILsPAFKV 
                 F 
                 381 
                 389 
                 P34932 
                 Heat shock 70 kDa protein 4 
               
               
                   
               
               
                 2 
                 AIMRsPQMV 
                 F 
                 187 
                 195 
                 P35222 
                 Catenin beta-1 
               
               
                   
               
               
                 3 
                 ALDsGASLLHL 
                 S 
                 482 
                 492 
                 P57078 
                 Receptor-interacting serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                   
                 kinase 4 
               
               
                   
               
               
                 4 
                 ALGNtPPFL 
                 S 
                 111 
                 119 
                 Q7Z739 
                 YTH domain family protein 3 
               
               
                   
               
               
                 5 
                 ALLsLLKRV 
                 S 
                 25 
                 33 
                 Q9UPU9 
                 Protein Smaug homolog 1 
               
               
                   
               
               
                 6 
                 AMAAsPHAV 
                 S 
                 64 
                 72 
                 Q13151 
                 Heterogeneous nuclear ribonucleoprotein A0 
               
               
                   
               
               
                 7 
                 AMLGSKsPDPYRL 
                 F/S 
                 904 
                 916 
                 P18583 
                 Protein SON 
               
               
                   
               
               
                 8 
                 ATWsGSEFEV 
                 S 
                 356 
                 368 
                 Q9BQQ3 
                 Golgi reassembly-stacking protein 1 
               
               
                   
               
               
                 9 
                 AVVsPPALHNA 
                 S 
                 855 
                 865 
                 O60885 
                 Bromodomain-containing protein 4 
               
               
                   
               
               
                 10 
                 DLRtVEKEL 
                 F 
                 240 
                 248 
                 P35237 
                 Serpin B6 
               
               
                   
               
               
                 11 
                 DLWKItKVMD 
                 S 
                 430 
                 439 
                 O96005 
                 Cleft lip and palate transmembrane protein 1 
               
               
                   
               
               
                 12 
                 ELFSsPPAV 
                 F 
                 953 
                 961 
                 O94916 
                 Nuclear factor of activated T-cells 5 
               
               
                   
               
               
                 13 
                 ELRISGsVQL 
                 F 
                 322 
                 331 
                 Q96DT0 
                 Galectin-12 
               
               
                   
               
               
                 14 
                 FIGsPTTPAGL 
                 S 
                 2125 
                 2135 
                 O14686 
                 Histone-lysine N-methyltransferase MLL2 
               
               
                   
               
               
                 15 
                 FLDNsFEKV 
                 F 
                 576 
                 584 
                 O43303 
                 Centriolar coiled-coil protein of 110 kDa 
               
               
                   
               
               
                 16 
                 FLDRPPtPLFI 
                 S 
                 280 
                 290 
                 Q86UC2 
                 Radial spoke head protein 3 homolog 
               
               
                   
               
               
                 17 
                 FLDsLRDLI 
                 F 
                 161 
                 169 
                 P63010 
                 AP-2 complex subunit beta 
               
               
                   
               
               
                 18 
                 FLFDKPVsPLLL 
                 S 
                 192 
                 203 
                 P06732 
                 Creatine kinase M-type 
               
               
                   
               
               
                 19 
                 FLGVRPKsA 
                 S 
                 1283 
                 1291 
                 Q9BZ95 
                 Histone-lysine N-methyltransferase NSD3 
               
               
                   
               
               
                 20 
                 FLITGGGKGsGFSL 
                 S 
                 246 
                 259 
                 O43166 
                 Signal-induced proliferation-associated 1-like 
               
               
                   
                   
                   
                   
                   
                   
                 protein 1 
               
               
                   
               
               
                 21 
                 FLLsQNFDDE 
                 S 
                 354 
                 363 
                 P54725 
                 UV excision repair protein RAD23 homolog A 
               
               
                   
               
               
                 22 
                 GALsPSLLHSL 
                 F 
                 1527 
                 1537 
                 P10070 
                 Zinc finger protein GLI2 
               
               
                   
               
               
                 23 
                 GLAPtPPSM 
                 S 
                 1197 
                 1205 
                 Q99700 
                 Ataxin-2 
               
               
                   
               
               
                 24 
                 GLDsLDQVEI 
                 S 
                 109 
                 118 
                 O14561 
                 Acyl carrier protein, mitochondrial 
               
               
                   
               
               
                 25 
                 GLGELLRsL 
                 F 
                 110 
                 118 
                 P50454 
                 Serpin H1 
               
               
                   
               
               
                 26 
                 GLIsPELRHL 
                 F 
                 86 
                 95 
                 Q147X3 
                 N-alpha-acetyltransferase 30 
               
               
                   
               
               
                 27 
                 GLIsPNVQL 
                 F 
                 742 
                 750 
                 A0AVK6 
                 Transcription factor E2F8 
               
               
                   
               
               
                 28 
                 GLIsPVWGA 
                 F/S 
                 50 
                 58 
                 Q76N32 
                 Centrosomal protein of 68 kDa 
               
               
                   
               
               
                 29 
                 GLItPGGFSSV 
                 S 
                 744 
                 754 
                 Q13435 
                 Splicing factor 3B subunit 2 
               
               
                   
               
               
                 30 
                 GLLDsPTSI 
                 F 
                 218 
                 226 
                 Q07352 
                 Zinc finger protein 36, C3H1 type-like 1 
               
               
                   
               
               
                 31 
                 GLLGsPARL 
                 F 
                 232 
                 240 
                 Q6UXB0 
                 Protein FAM131A 
               
               
                   
               
               
                 32 
                 GLLGsPVRA 
                 F/S 
                 38 
                 46 
                 P30305 
                 M-phase inducer phosphatase 2 
               
               
                   
               
               
                 33 
                 GLLsPRFVDV 
                 S 
                 525 
                 534 
                 Q8WYP5 
                 Protein ELYS 
               
               
                   
               
               
                 34 
                 GLLsPRHSL 
                 F 
                 913 
                 921 
                 Q9Y2K2 
                 Serine/threonine-protein kinase SIK3 
               
               
                   
               
               
                 35 
                 GMLsPGKSIEV 
                 S 
                 4474 
                 4484 
                 Q8IVF2 
                 Protein AHNAK2 
               
               
                   
               
               
                 36 
                 GsQLAVMMYL 
                 S 
                 17 
                 26 
                 O60512 
                 Beta-1,4-galactosyltransferase 3 
               
               
                   
               
               
                 37 
                 GVAsPTITV 
                 F 
                 626 
                 634 
                 P46379 
                 Large proline-rich protein BAG6 
               
               
                   
               
               
                 38 
                 GVVsPTFEL 
                 F 
                 447 
                 455 
                 B4DIR9 
                 TGF-beta-activated kinase 1 and MAP3K7-binding 
               
               
                   
                   
                   
                   
                   
                   
                 protein 2 
               
               
                   
               
               
                 39 
                 HLHsPQHKL 
                 S 
                 547 
                 555 
                 Q6T4R5 
                 Nance-Horan syndrome protein 
               
               
                   
               
               
                 40 
                 ILQtPQFQM 
                 F/S 
                 208 
                 216 
                 Q14980 
                 Nuclear mitotic apparatus protein 1 
               
               
                   
               
               
                 41 
                 ILQVsIPSL 
                 S 
                 404 
                 412 
                 Q86W92 
                 Liprin-beta-1 
               
               
                   
               
               
                 42 
                 IVLsDSEVIQL 
                 S 
                 75 
                 85 
                 Q8N3Z6 
                 Zinc finger CCHC domain-containing protein 7 
               
               
                   
               
               
                 43 
                 KAFsPVRSV 
                 F/S 
                 2 
                 10 
                 Q02363 
                 DNA-binding protein inhibitor ID-2 
               
               
                   
               
               
                 44 
                 KIAsEIAQL 
                 F 
                 541 
                 549 
                 Q8WXE0 
                 Caskin-2 
               
               
                   
               
               
                 45 
                 KIEsLENLYL 
                 F 
                 385 
                 394 
                 Q659A1 
                 NMDA receptor-regulated protein 2 
               
               
                   
               
               
                 46 
                 KIGsIIFQV 
                 F/S 
                 1223 
                 1231 
                 Q460N5 
                 Poly [ADP-ribose] polymerase 14 
               
               
                   
               
               
                 47 
                 KLAsLEREASV 
                 S 
                 368 
                 378 
                 Q8WYA0 
                 Intraflagellar transport protein 81 homolog 
               
               
                   
               
               
                 48 
                 KLAsPEKLAGL 
                 F/S 
                 987 
                 997 
                 Q6T4R5 
                 Nance-Horan syndrome protein 
               
               
                   
               
               
                 49 
                 KLAsPELERL 
                 F/S 
                 70 
                 79 
                 P05412 
                 Transcription factor AP-1 
               
               
                   
               
               
                 50 
                 KLFPDtPLAL 
                 F/S 
                 587 
                 596 
                 Q12906 
                 Interleukin enhancer-binding factor 3 
               
               
                   
               
               
                 51 
                 KLFsPSKEAEL 
                 F 
                 845 
                 855 
                 Q96RY5 
                 Protein cramped-like 
               
               
                   
               
               
                 52 
                 KLIDIVsSQKV 
                 S 
                 461 
                 471 
                 O14757 
                 Serine/threonine-protein kinase Chk1 
               
               
                   
               
               
                 53 
                 KLKsQEIFL 
                 F 
                 416 
                 424 
                 Q9BZD4 
                 Kinetochore protein Nuf2 
               
               
                   
               
               
                 54 
                 KLLsPSDEKL 
                 F 
                 544 
                 553 
                 Q14694 
                 Ubiquitin carboxyl-terminal hydrolase 10 
               
               
                   
               
               
                 55 
                 KLLsPSNEKL 
                 F 
                 544 
                 553 
                 Q14694 
                 Ubiquitin carboxyl-terminal hydrolase 10 
               
               
                   
               
               
                 56 
                 KLMAPDIsL 
                 F 
                 52 
                 60 
                 Q12982 
                 BCL2/adenovirus E1B 19 kDa protein-interacting 
               
               
                   
                   
                   
                   
                   
                   
                 protein 2 
               
               
                   
               
               
                 57 
                 KLMsPKADV 
                 F/S 
                 44 
                 52 
                 Q86T90 
                 Uncharacterized protein KIAA1328 
               
               
                   
               
               
                 58 
                 KLMsPKADVKL 
                 F/S 
                 44 
                 54 
                 Q86T90 
                 Uncharacterized protein KIAA1328 
               
               
                   
               
               
                 59 
                 KLQEFLQtL 
                 F 
                 16 
                 24 
                 Q9NVI1 
                 Fanconi anemia group I protein 
               
               
                   
               
               
                 60 
                 KQDsLVINL 
                 F 
                 647 
                 655 
                 Q9Y5B9 
                 FACT complex subunit SPT16 
               
               
                   
               
               
                 61 
                 KRLsTSPVRL 
                 S 
                 757 
                 766 
                 Q9Y2J2 
                 Band 4.1-like protein 3 
               
               
                   
               
               
                 62 
                 KTMsGTFLL 
                 F 
                 592 
                 600 
                 P52630 
                 Signal transducer and activator of transcrip- 
               
               
                   
                   
                   
                   
                   
                   
                 tion 2 
               
               
                   
               
               
                 63 
                 KTWKGsIGL 
                 F/S 
                 822 
                 831 
                 Q8IY63 
                 Angiomotin-like protein 1 
               
               
                   
               
               
                 64 
                 KVLsKEFHL 
                 S 
                 150 
                 158 
                 Q01105 
                 Protein SET 
               
               
                   
               
               
                 65 
                 KVLsTEEMEL 
                 F 
                 31 
                 40 
                 Q6P582 
                 Mitotic-spindle organizing protein 2A 
               
               
                   
               
               
                 66 
                 KVLStEEMEL 
                 F 
                 31 
                 40 
                 Q6P582 
                 Mitotic-spindle organizing protein 2A 
               
               
                   
               
               
                 67 
                 LLAsPGHISV 
                 S 
                 740 
                 749 
                 A0FGR8 
                 Extended synaptotagmin-2 
               
               
                   
               
               
                 68 
                 LQLsPLKGLSL 
                 F/S 
                 17 
                 27 
                 P31350 
                 Ribonucleoside-diphosphate reductase subunit M2 
               
               
                   
               
               
                 69 
                 LQNItENQL 
                 S 
                 86 
                 94 
                 Q8N5J4 
                 Transcription factor Spi-C 
               
               
                   
               
               
                 70 
                 NLGsRNHVHQL 
                 S 
                 1398 
                 1408 
                 Q9HAR2 
                 Latrophilin-3 
               
               
                   
               
               
                 71 
                 NLLsPDGKMISV 
                 S 
                 395 
                 405 
                 P35680 
                 Hepatocyte nuclear factor 1-beta 
               
               
                   
               
               
                 72 
                 RASsLSITV 
                 F 
                 839 
                 847 
                 Q6ZS17 
                 Protein FAM65A-isoform 2 
               
               
                   
               
               
                 73 
                 REDsTPGKVFL 
                 S 
                 61 
                 71 
                 P13056 
                 Nuclear receptor subfamily 2 group C member 1 
               
               
                   
               
               
                 74 
                 RIDsKDSASEL 
                 S 
                 602 
                 612 
                 Q96S38 
                 Ribosomal protein S6 kinase delta-1 
               
               
                   
               
               
                 75 
                 RINsFEEHV 
                 S 
                 475 
                 483 
                 Q16875 
                 6-phosphofructo-2-kinase/fructose-2,6-bis- 
               
               
                   
                   
                   
                   
                   
                   
                 phosphatase 3 
               
               
                   
               
               
                 76 
                 RIQsKLYRA 
                 F 
                 483 
                 491 
                 O75643 
                 U5 small nuclear ribonucleoprotein 200 kDa 
               
               
                   
                   
                   
                   
                   
                   
                 helicase 
               
               
                   
               
               
                 77 
                 RITsLIVHV 
                 F 
                 315 
                 323 
                 Q3ZCT1 
                 Zinc finger protein 260 
               
               
                   
               
               
                 78 
                 RLAsASRAL 
                 F 
                   
                   
                   
                 No database hit 
               
               
                   
               
               
                 79 
                 RLAsLNAEAL 
                 F 
                 118 
                 127 
                 Q8TBE0 
                 Bromo adjacent homology domain-containing 1 
               
               
                   
                   
                   
                   
                   
                   
                 protein 
               
               
                   
               
               
                 80 
                 RLAsRPLLL 
                 F 
                 3 
                 11 
                 Q9P2B2 
                 Prostaglandin F2 receptor negative regulator 
               
               
                   
               
               
                 81 
                 RLDsYLRAP 
                 S 
                 137 
                 145 
                 O95833 
                 Chloride intracellular channel protein 3 
               
               
                   
               
               
                 82 
                 RLDsYVR 
                 F 
                 129 
                 135 
                 Q9Y5R8 
                 Trafficking protein particle complex subunit 1 
               
               
                   
               
               
                 83 
                 RLDsYVRSL 
                 F/S 
                 129 
                 137 
                 Q9Y5R8 
                 Trafficking protein particle complex subunit 1 
               
               
                   
               
               
                 84 
                 RLDtGPQSL 
                 S 
                 424 
                 432 
                 P35269 
                 General transcription factor IIF subunit 1 
               
               
                   
               
               
                 85 
                 RLEsANRRL 
                 S 
                 397 
                 405 
                 Q9Y2J4 
                 Angiomotin-like protein 2 
               
               
                   
               
               
                 86 
                 RLFsKELRC* 
                 F/S 
                 30 
                 38 
                 Q15543 
                 Transcription initiation factor TFIID subunit 13 
               
               
                   
               
               
                 87 
                 RLFSLsNPSL 
                 F 
                 365 
                 374 
                 Q6UUV7 
                 CREB-regulated transcription coactivator 3 
               
               
                   
               
               
                 88 
                 RLFsQGQDV 
                 S 
                 1796 
                 1804 
                 P55196 
                 Afadin 
               
               
                   
               
               
                 89 
                 RLGsFHELLL 
                 F/S 
                 312 
                 321 
                 Q5H9R7 
                 Serine/threonine-protein phosphatase 6 regulatory 
               
               
                   
                   
                   
                   
                   
                   
                 subunit 3 
               
               
                   
               
               
                 90 
                 RLKsDERPVHI 
                 S 
                 1116 
                 1126 
                 Q9UPN9 
                 E3 ubiquitin-protein ligase TRIM33 
               
               
                   
               
               
                 91 
                 RLLsDGQQHL 
                 F 
                 2080 
                 2089 
                 Q02224 
                 Centromere-associated protein E 
               
               
                   
               
               
                 92 
                 RLLsDLEEL 
                 F 
                 245 
                 253 
                 Q8IWP9 
                 Coiled-coil domain-containing protein 28A 
               
               
                   
               
               
                 93 
                 RLLsDQTRL 
                 F 
                 232 
                 240 
                 Q8TDM6 
                 Disks large homolog 5 
               
               
                   
               
               
                 94 
                 RLLsFQRYL 
                 F 
                 110 
                 118 
                 Q13946 
                 High affinity cAMP-specific 3′,5′-cyclic phospho- 
               
               
                   
                   
                   
                   
                   
                   
                 diesterase 7A 
               
               
                   
               
               
                 95 
                 RLLsPLSSA 
                 F 
                 581 
                 589 
                 E9PAU2 
                 Ribonucleoprotein PTB-binding 1 
               
               
                   
               
               
                 96 
                 RLLsPLSSARL 
                 F 
                 581 
                 589 
                 E9PAU2 
                 Ribonucleoprotein PTB-binding 1 
               
               
                   
               
               
                 97 
                 RLLsPRPSL 
                 F 
                 936 
                 944 
                 Q9Y618 
                 Nuclear receptor corepressor 2 
               
               
                   
               
               
                 98 
                 RLLsPRPSLL 
                 F 
                 936 
                 945 
                 Q9Y618 
                 Nuclear receptor corepressor 2 
               
               
                   
               
               
                 99 
                 RLLsVHDFDF 
                 F 
                 188 
                 197 
                 Q9BV36 
                 Melanophilin 
               
               
                   
               
               
                 100 
                 RLNtSDFQKL 
                 S 
                 243 
                 252 
                 Q96B36 
                 Proline-rich AKT1 substrate 1 
               
               
                   
               
               
                 101 
                 RLPNRIPsL 
                 F 
                 640 
                 648 
                 Q9P227 
                 Rho GTPase-activating protein 23 
               
               
                   
               
               
                 102 
                 RLQsLIKNI 
                 F/S 
                 632 
                 640 
                 Q14527 
                 Helicase-like transcription factor 
               
               
                   
               
               
                 103 
                 RLQsTSERL 
                 F 
                 217 
                 225 
                 Q96TA2 
                 ATP-dependent zinc metalloprotease YME1L1   
               
               
                   
               
               
                 104 
                 RLRsYEDMI 
                 F/S 
                 317 
                 325 
                 O60716 
                 Catenin delta-1 
               
               
                   
               
               
                 105 
                 RLSsPLHFV 
                 F/S 
                 400 
                 408 
                 Q8NC44 
                 Protein FAM134A 
               
               
                   
               
               
                 106 
                 RMFPtPPSL 
                 F 
                 863 
                 871 
                 Q71F56 
                 Mediator of RNA polymerase II transcription 
               
               
                   
                   
                   
                   
                   
                   
                 subunit 13-like 
               
               
                   
               
               
                 107 
                 RMFsPMEEKELL 
                 F 
                 691 
                 702 
                 Q9UHB7 
                 AF4/FMR2 family member 4 
               
               
                   
               
               
                 108 
                 RMIsTGSEL 
                 F 
                 207 
                 215 
                 Q86T82 
                 Ubiquitin carboxyl-terminal hydrolase 37 
               
               
                   
               
               
                 109 
                 RMLsLRDQRL 
                 F 
                 15 
                 24 
                 Q9Y324 
                 rRNA-processing protein FCF1 homolog 
               
               
                   
               
               
                 110 
                 RMYsFDDVL 
                 F 
                 802 
                 810 
                 Q8WWI1 
                 LIM domain only protein 7 
               
               
                   
               
               
                 111 
                 RMYsPIIYQA 
                 S 
                 200 
                 209 
                 Q49A88 
                 Coiled-coil domain-containing protein 14 
               
               
                   
               
               
                 112 
                 RQDsTPGKVFL 
                 F/S 
                 61 
                 71 
                 P13056 
                 Nuclear receptor subfamily 2 group C member 1 
               
               
                   
               
               
                 113 
                 RQIsFKAEV 
                 F 
                 181 
                 189 
                 Q9Y385 
                 Ubiquitin-conjugating enzyme E2 J1 
               
               
                   
               
               
                 114 
                 RQIsQDVKL 
                 F 
                 165 
                 173 
                 Q01433 
                 AMP deaminase 2 
               
               
                   
               
               
                 115 
                 RQLsALHRA 
                 F/S 
                 31 
                 39 
                 P61313 
                 60S ribosomal protein L15 
               
               
                   
               
               
                 116 
                 RQLsLEGSGLGV 
                 S 
                 749 
                 760 
                 Q9UMZ2 
                 Synergin gamma 
               
               
                   
               
               
                 117 
                 RQLsSGVSEI 
                 S 
                 79 
                 88 
                 P04792 
                 Heat shock protein beta-1 
               
               
                   
               
               
                 118 
                 RQSsSRFNL 
                 F 
                 86 
                 94 
                 Q14738 
                 Serine/threonine-protein phosphatase 2A 56 kDa 
               
               
                   
                   
                   
                   
                   
                   
                 regulatory subunit 
               
               
                   
               
               
                 119 
                 RRLsERETR 
                 S 
                 148 
                 156 
                 O60285 
                 NUAK family SNF1-like kinase 1 
               
               
                   
               
               
                 120 
                 RSAsPDDDLGSSN 
                 S 
                 14 
                 26 
                 O00193 
                 Small acidic protein 
               
               
                   
               
               
                 121 
                 RSFsPTMKV 
                 F/S 
                 211 
                 219 
                 A3KN83 
                 Protein strawberry notch homolog 1 
               
               
                   
               
               
                 122 
                 RSLsQELVGV 
                 S 
                 333 
                 342 
                 Q5VUA4 
                 Zinc finger protein 318 
               
               
                   
               
               
                 123 
                 RTAsLIIKV 
                 F 
                 2707 
                 2715 
                 Q7Z7G8 
                 Vacuolar protein sorting-associated protein 13B 
               
               
                   
               
               
                 124 
                 RTFsLDTIL 
                 F 
                 88 
                 96 
                 Q9C073 
                 Protein FAM117A 
               
               
                   
               
               
                 125 
                 RTFsPTYGL 
                 F/S 
                 426 
                 434 
                 O15061 
                 Synemin 
               
               
                   
               
               
                 126 
                 RTHsLLLLL 
                 F/S 
                 5 
                 13 
                 P34096 
                 Ribonuclease 4 
               
               
                   
               
               
                 127 
                 RTLsHISEA 
                 F 
                 450 
                 458 
                 Q6ZS17 
                 Protein FAM65A 
               
               
                   
               
               
                 128 
                 RTSsFTEQL 
                 F 
                 38 
                 46 
                 Q13439 
                 Golgin subfamily A member 4 
               
               
                   
               
               
                 129 
                 RVAsPTSGV 
                 F 
                 1097 
                 1105 
                 Q9Y4H2 
                 Insulin receptor substrate 2 
               
               
                   
               
               
                 130 
                 RVDsPSHGL 
                 F 
                 685 
                 693 
                 Q9UER7 
                 Death domain-associated protein 6 
               
               
                   
               
               
                 131 
                 RVGsLVLNL 
                 F 
                   
                   
                   
                 No database hit 
               
               
                   
               
               
                 132 
                 RVIsGVLQL 
                 F 
                 341 
                 349 
                 P35579 
                 Myosin-9 
               
               
                   
               
               
                 133 
                 RVLHsPPAV 
                 F 
                 1212 
                 1220 
                 A8MQ54 
                 Protein SOGA2 
               
               
                   
               
               
                 134 
                 RVPsLLVLL 
                 F 
                 4 
                 12 
                 P19021 
                 Peptidyl-glycine alpha-amidating monooxygenase 
               
               
                   
               
               
                 135 
                 RVTsAEIKL 
                 F 
                 648 
                 656 
                 Q8N4X5 
                 Actin filament-associated protein 1-like 2 
               
               
                   
               
               
                 136 
                 RVWsPPRVHKV 
                 S 
                 613 
                 623 
                 O15209 
                 Zinc finger and BTB domain-containing protein 22 
               
               
                   
               
               
                 137 
                 SARGsPTRPNPPVR 
                 F 
                 518 
                 531 
                 Q14195 
                 Dihydropyrimidinase-related protein 3 
               
               
                   
               
               
                 138 
                 SILsFVSGL 
                 S 
                 1715 
                 1724 
                 O95996 
                 Adenomatous polyposis coli protein 2 
               
               
                   
               
               
                 139 
                 SIMsFHIDL 
                 F/S 
                 204 
                 213 
                 Q9H3Q1 
                 Cdc42 effector protein 4 
               
               
                   
               
               
                 140 
                 SIMsPEIQL 
                 F/S 
                 153 
                 162 
                 Q96RK0 
                 Protein capicua homolog 
               
               
                   
               
               
                 141 
                 SISStPPAV 
                 S 
                 260 
                 268 
                 Q9H8Y8 
                 Golgi reassembly-stacking protein 2 
               
               
                   
               
               
                 142 
                 SKtVATFIL 
                 F 
                 178 
                 186 
                 Q92600 
                 Cell differentiation protein RCD1 homolog 
               
               
                   
               
               
                 143 
                 SLAsLTEKI 
                 F 
                 369 
                 377 
                 Q5M775 
                 Cytospin-B 
               
               
                   
               
               
                 144 
                 SLDSEDYsL 
                 F 
                 253 
                 261 
                 Q00987 
                 E3 ubiquitin-protein ligase Mdm2 
               
               
                   
               
               
                 145 
                 SLDsLGDVFL 
                 F/S 
                 1789 
                 1798 
                 Q14980 
                 Nuclear mitotic apparatus protein 1 
               
               
                   
               
               
                 146 
                 SLFGGsVKL 
                 F 
                 103 
                 111 
                 Q8WUM4 
                 Programmed cell death 6-interacting protein 
               
               
                   
               
               
                 147 
                 SLFKRLYsL 
                 F 
                 1058 
                 1066 
                 P78527 
                 DNA-dependent protein kinase catalytic subunit 
               
               
                   
               
               
                 148 
                 SLFsSEESNLGA 
                 F 
                 403 
                 414 
                 P04004 
                 Vitronectin 
               
               
                   
               
               
                 149 
                 SLFsGDEENA 
                 S 
                 22 
                 31 
                 Q53EL6 
                 Programmed cell death protein 4 
               
               
                   
               
               
                 150 
                 SLFsGSYSSL 
                 S 
                 147 
                 156 
                 Q13490 
                 Baculoviral IAP repeat-containing protein 2 
               
               
                   
               
               
                 151 
                 SLLAsPGHISV 
                 S 
                 739 
                 749 
                 A0FGR8 
                 Extended synaptotagmin-2 
               
               
                   
               
               
                 152 
                 SLLHTSRsL 
                 F 
                 1240 
                 1248 
                 Q6P0Q8 
                 Microtubule-associated serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                   
                 kinase 2 
               
               
                   
               
               
                 153 
                 SLLsLHVDL 
                 F 
                 179 
                 187 
                 O14613 
                 Cdc42 effector protein 2 
               
               
                   
               
               
                 154 
                 SLMsGTLESL 
                 F/S 
                 274 
                 283 
                 Q4KMP7 
                 TBC1 domain family member 10B 
               
               
                   
               
               
                 155 
                 SLQPRSHsV 
                 S 
                 448 
                 456 
                 Q9Y2H5 
                 Pleckstrin homology domain-containing family A 
               
               
                   
                   
                   
                   
                   
                   
                 member 6 
               
               
                   
               
               
                 156 
                 SLQsLETSV 
                 S 
                 1233 
                 1241 
                 P23634 
                 Plasma membrane calcium-transporting ATPase 4 
               
               
                   
               
               
                 157 
                 SLSsLLVKL 
                 S 
                 1636 
                 1644 
                 O15078 
                 Centrosomal protein of 290 kDa 
               
               
                   
               
               
                 158 
                 SLVDGyFRL 
                 F 
                 407 
                 415 
                 P23458 
                 Tyrosine-protein kinase JAK1 
               
               
                   
               
               
                 159 
                 SMLsQEIQTL 
                 S 
                 192 
                 201 
                 Q9UHY8 
                 Fasciculation and elongation protein zeta-2 
               
               
                   
               
               
                 160 
                 SMSsLSREV 
                 S 
                 2117 
                 2125 
                 O15027 
                 Protein transport protein Sec16A 
               
               
                   
               
               
                 161 
                 SMTRsPPRV 
                 F/S 
                 248 
                 256 
                 Q9BRL6 
                 Serine/arginine-rich splicing factor 8 
               
               
                   
               
               
                 162 
                 SPRssQLV 
                 F 
                 538 
                 545 
                 P32519 
                 ETS-related transcription factor Elf-1 
               
               
                   
               
               
                 163 
                 sPTRPNPPVRNLH 
                 F 
                 522 
                 534 
                 Q14195 
                 Dihydropyrimidinase-related protein 3 
               
               
                   
               
               
                 164 
                 SQIsPKSWGV 
                 S 
                 563 
                 571 
                 Q6IMN6 
                 Caprin-2 
               
               
                   
               
               
                 165 
                 STMsLNIITV 
                 S 
                 243 
                 252 
                 P54792 
                 Segment polarity protein dishevelled homolog 
               
               
                   
                   
                   
                   
                   
                   
                 DVL-1-like 
               
               
                   
               
               
                 166 
                 sTMSLNIITV 
                 S 
                 243 
                 252 
                 P54792 
                 Segment polarity protein dishevelled homolog 
               
               
                   
                   
                   
                   
                   
                   
                 DVL-1-like 
               
               
                   
               
               
                 167 
                 SVFsPSFGL 
                 F/S 
                 1473 
                 1481 
                 Q02880 
                 DNA topoisomerase 2-beta 
               
               
                   
               
               
                 168 
                 SVGsDYYIQL 
                 S 
                 546 
                 555 
                 Q8IWU2 
                 Serine/threonine-protein kinase LMTK2 
               
               
                   
               
               
                 169 
                 SVLsPSFQL 
                 F 
                 72 
                 80 
                 Q12968 
                 Nuclear factor of activated T-cells, cyto- 
               
               
                   
                   
                   
                   
                   
                   
                 plasmic 3 
               
               
                   
               
               
                 170 
                 SVMDsPKKL 
                 F 
                 143 
                 151 
                 Q8TBB0 
                 THAP domain-containing protein 6 
               
               
                   
               
               
                 171 
                 SVYsGDFGNLEV 
                 S 
                 617 
                 628 
                 Q9HCH5 
                 Synaptotagmin-like protein 2 
               
               
                   
               
               
                 172 
                 TLSsPPPGL 
                 S 
                 2324 
                 2332 
                 O95613 
                 Pericentrin 
               
               
                   
               
               
                 173 
                 TMMsPSQFL 
                 F 
                 520 
                 528 
                 Q9ULH7 
                 MKL/myocardin-like protein 2 
               
               
                   
               
               
                 174 
                 TVMsNSSVIHL 
                 S 
                 389 
                 399 
                 Q7L7X3 
                 Serine/threonine-protein kinase TAO1 
               
               
                   
               
               
                 175 
                 VIDsQELSKV 
                 S 
                 260 
                 269 
                 P10451 
                 Osteopontin 
               
               
                   
               
               
                 176 
                 VLFsSPPQM 
                 F 
                 67 
                 75 
                 P33991 
                 DNA replication licensing factor MCM4 
               
               
                   
               
               
                 177 
                 VLFSsPPQM 
                 F 
                 67 
                 75 
                 P33991 
                 DNA replication licensing factor MCM4 
               
               
                   
               
               
                 178 
                 VLSSLtPAKV 
                 S 
                 559 
                 568 
                 Q13330 
                 Metastasis-associated protein MTA1 
               
               
                   
               
               
                 179 
                 VMFRtPLASV 
                 S 
                 319 
                 328 
                 Q9UKT4 
                 F-box only protein 5 
               
               
                   
               
               
                 180 
                 VMIGsPKKV 
                 F/S 
                 1437 
                 1445 
                 Q68CZ2 
                 Tensin-3 
               
               
                   
               
               
                 181 
                 YAYDGKDyI 
                 S 
                 140 
                 148 
                 P18464 
                 HLA class I histocompatibility antigen, B-51 
               
               
                   
                   
                   
                   
                   
                   
                 alpha chain 
               
               
                   
               
               
                 182 
                 YLAsLEKKL 
                 F 
                 77 
                 85 
                 Q9BV29 
                 Uncharacterized protein C15orf57 
               
               
                   
               
               
                 183 
                 YLDsGIHSG 
                 S 
                 30 
                 38 
                 P35222 
                 Catenin beta-1 
               
               
                   
               
               
                 184 
                 YLDsGIHSGA 
                 S 
                 30 
                 39 
                 P35222 
                 Catenin beta-1 
               
               
                   
               
               
                 185 
                 yLGLDVPV 
                 S 
                 1248 
                 1255 
                 P04626 
                 Receptor tyrosine-protein kinase erbB-2 
               
               
                   
               
               
                 186 
                 YLGsISTLVTL 
                 S 
                 498 
                 508 
                 Q76N32 
                 Centrosomal protein of 68 kDa 
               
               
                   
               
               
                 187 
                 YLIHsPMSL 
                 S 
                 114 
                 122 
                 P42330 
                 Aldo-keto reductase family 1 member C3 
               
               
                   
               
               
                 188 
                 YLLsPLNTL 
                 F 
                 442 
                 450 
                 Q8TF76 
                 Serine/threonine-protein kinase haspin 
               
               
                   
               
               
                 189 
                 yLQSRYYRA 
                 F 
                 359 
                 367 
                 Q9H422 
                 Homeodomain-interacting protein kinase 3 
               
               
                   
               
               
                 190 
                 YLQsRYYRA 
                 F/S 
                 359 
                 367 
                 Q9H422 
                 Homeodomain-interacting protein kinase 3 
               
               
                   
               
               
                 191 
                 YLSDsDTEAKL 
                 S 
                 1708 
                 1718 
                 Q92614 
                 Unconventional myosin-XVIIIa 
               
               
                   
               
               
                 192 
                 YQLsPTKLPSI 
                 S 
                 429 
                 439 
                 O60934 
                 Nibrin 
               
               
                   
               
               
                 193 
                 YTAGtPYKV 
                 S 
                 103 
                 111 
                 Q92567 
                 Protein FAM168A 
               
               
                   
               
               
                 Column 2: Phosphopeptide sequences; pSer, pThr and pTyr are specified by s, t, and y, respectively. * = Cysteinylated 
               
               
                 Column 3: S = SKOV3 Cells: F = FHIOSE Cells 
               
               
                 Column 4 &amp; 5: Entries define the location of the phosphopeptides within the sequence of the parent protein. 
               
               
                 Column 6: Protein identifier in the UniProt biosequence database available on the World Wide Wide at the website uniprot&lt;&lt;dot&gt;&gt;org 
               
               
                 Column 7: Name of the protein in the UniProt biosequence database.