Abstract: The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

Abstract: The presently disclosed subject matter relates to a method for characterizing a protein. The method can comprise disposing a protein in a digestion buffer; disposing a hydrolyzing agent inhibitor in the digestion buffer; passing the digestion buffer comprising said protein and said hydrolyzing agent inhibitor through a reaction chamber comprising at least one hydrolyzing agent, wherein said protein contacts said hydrolyzing agent in the presence of said inhibitor and is present in the chamber for a period of time (t) sufficient to produce protein fragments and provide digestion of said protein in the chamber, wherein the passing of the digestion buffer comprising the protein and the hydrolyzing agent inhibitor through the chamber is done at an adjustable flow rate; and performing multi-segment liquid chromatography tandem mass spectrometry (LC MS/MS) to characterize the protein.

Abstract: The present invention describes novel tumor-specific phosphorylated peptides, nucleic acids encoding those peptides, and antibodies generated against said peptides. The genes, peptides, and antibodies described herein may be used as diagnostic indicators of the presence of breast cancer and/or used in therapeutics to treat breast cancer.

Abstract: A set of target peptides are presented by HLA A*0101, A*0201, A*0301, B*4402, B*2705, B*1402, and B*0702 on the surface of disease cells. They are envisioned to among other things (a) stimulate an immune response to the proliferative disease, e.g., cancer, (b) to function as immunotherapeutics in adoptive T cell therapy or as a vaccine, (c) facilitate antibody recognition of tumor boundaries in surgical pathology samples, (d) act as biomarkers for early detection and/or diagnosis of the disease, and (e) act as targets in the generation antibody-like molecules which recognize the target-peptide/MHC complex.

Abstract: The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

Abstract: Compositions that include anti-cancer, anti-tumor, and anti-microbial infection peptides are provided. In some embodiments, the compositions include 1-10 or more synthetic peptides that are between 8 and 50 amino acids long and include an amino acid sequence as disclosed herein.

Abstract: Provided are compositions that include one or more synthetic target peptides, wherein each synthetic target peptide is about or at least 8-50 amino acids long; and has an amino acid sequence as set forth in Table 2 and/or Table 3. Also provided are in vitro populations of dendritic cells that include the disclosed compositions, in vitro population of CD8+ T cells capable of being activated upon being brought into contact with the disclosed populations of dendritic cells, antibodies or antibody-like molecules that specifically binds to a complex of an MHC class I molecule and a peptide having an amino acid sequence as set forth in Table 2 and/or Table 3, methods for treating and/or preventing cancers by administering a therapeutically effective dose of a composition that includes at least one target peptide having an amino acid sequence as set forth in Table 2 and/or Table 3.

Abstract: The present invention describes novel tumor-specific phosphorylated peptides, nucleic acids encoding those peptides, and antibodies generated against said peptides. The genes, peptides, and antibodies described herein may be used as diagnostic indicators of the presence of breast cancer and/or used in therapeutics to treat breast cancer.

Abstract: A set of target peptides are presented by HLA A*0201 on the surface of ovarian cancer cells. They are envisioned to among other things (a) stimulate an immune response to the proliferative disease, e.g., ovarian cancer, (b) function as immunotherapeutics in adoptive T-cell therapy or as a vaccine, (c) facilitate antibody recognition of tumor boundaries in surgical pathology samples, (d) act as biomarkers for early detection and/or diagnosis of the disease, and (e) act as targets in the generation antibody-like molecules which recognize the target-peptide/MHC complex.

Abstract: A set of phosphorylated peptides are presented by HLA A*0101, A*0201, A*0301, B*4402, B*2705, B*1402, and el B*0702 on the surface of melanoma cells. They have the potential to (a) stimulate an immune response to the cancer, (b) to function as immunotherapeutics in adoptive T-cell therapy or as a vaccine, (c) to facilitate antibody recognition of the tumor boundaries in surgical pathology samples, and (d) act as biomarkers for early detection of the disease. Phosphorylated peptides are also presented for other cancers.

Abstract: A set of target peptides are presented by HLA A*0201, B*0301, B*0702 and B*2705 on the surface of disease cells. They are envisioned to, among other things, stimulate an immune response to the proliferative disease, e.g., colorectal cancer, to function as immunotherapeutics in adoptive T cell therapy or as a vaccine, facilitate antibody recognition of tumor boundaries in surgical pathology samples, act as biomarkers for early detection and/or diagnosis of the disease, and/or act as targets in the generation antibody-like molecules which recognize the target-peptide/MHC complex.

Abstract: The present invention describes novel tumor-specific phosphorylated peptides, nucleic acids encoding those peptides, and antibodies generated against said peptides. The genes, peptides, and antibodies described herein may be used as diagnostic indicators of the presence of breast cancer and/or used in therapeutics to treat breast cancer.

Abstract: The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

Abstract: A set of target peptides are presented by HLA A*0201, B*0301, B*0702 and B*2705 on the surface of disease cells. They are envisioned to, among other things, stimulate an immune response to the proliferative disease, e.g., colorectal cancer, to function as immunotherapeutics in adoptive T cell therapy or as a vaccine, facilitate antibody recognition of tumor boundaries in surgical pathology samples, act as biomarkers for early detection and/or diagnosis of the disease, and/or act as targets in the generation antibody-like molecules which recognize the target-peptide/MHC complex.

Abstract: The present invention describes novel tumor-specific phosphorylated peptides, nucleic acids encoding those peptides, and antibodies generated against said peptides. The genes, peptides, and antibodies described herein may be used as diagnostic indicators of the presence of breast cancer and/or used in therapeutics to treat breast cancer.

Abstract: A set of target peptides are presented by HLA class I molecules on the surface of hepatocellular carcinoma (HCC) ceils and/or esophageal cancer cells. They are envisioned to among other things (a) stimulate an immune response to the proliferative disease, e.g., HCC and/or esophageal cancer, (b) function as immunotherapeutics in adoptive T-cell therapy or as a vaccine, (c) facilitate antibody recognition of tumor boundaries in surgical pathology samples, (d) act as biomarkers for early detection and/or diagnosis of the disease, and (e) act as targets in the generation anti-body-like molecules which recognize the target-peptide/MHC complex.

Abstract: The application discloses compositions, methods, systems, and apparatuses for rapid sequence analysis of proteins, including location of post-translational modifications and disulfide bonds. Limited digestion of fully denatured antibody occurs in seconds by flowing sample in 8M urea at constant pressure through a micro column reactor containing immobilized aspergillopepsin I, resulting in a product mixture containing 3-10 kDa peptides, which is then fractionated by capillary column chromatography and analyzed by both electron transfer dissociation (ETD) and collision activated dissociation mass spectrometry. This method provides 95% sequence coverage of a mAb and detects numerous post-translational modifications. For disulfide bond location, native mAb is subjected to longer digestion times. Release of disulfide containing peptides from accessible regions of the folded protein occurs with short digestion times.

Abstract: Provided are compositions that include one or more peptides, wherein each peptide is at least 8 amino acids long and has an amino acid sequence as set forth in any of SEQ ID NOs: 1-45. Also provided are in vitro populations of dendritic cells that include the disclosed compositions, in vitro populations of CD8+ T cells capable of being activated upon being brought into contact with the disclosed populations of dendritic cells, antibodies or antibody-like molecules that specifically bind to complexes of MHC class I molecules and the disclosed peptides, methods for treating and/or preventing cancer such as leukemia using the disclosed compositions and/or populations, methods for making cancer vaccines using the disclosed compositions, methods for screening target peptides for inclusion in an immunotherapy composition, methods for determining a prognosis of a leukemia patient, and kits that include at least one of the disclosed peptides.

Abstract: A set of phosphorylated peptides are presented by HLA A*0101, A*0201, A*0301, B*4402, B*2705, B*1402, and B*0702 on the surface of melanoma cells. They have the potential to (a) stimulate an immune response to the cancer, (b) to function as immunotherapeutics in adoptive T-cell therapy or as a vaccine, (c) to facilitate antibody recognition of the tumor boundaries in surgical pathology samples, and (d) act as biomarkers for early detection of the disease. Phosphorylated peptides are also presented for other cancers.

Abstract: A set of target peptides are presented by HLA A*0101, A*0201, A*0301, B*4402, B*2705, B*1402, and B*0702 on the surface of disease cells. They are envisioned to among other things (a) stimulate an immune response to the proliferative disease, e.g., cancer, (b) to function as immunotherapeutics in adoptive T cell therapy or as a vaccine, (c) facilitate antibody recognition of tumor boundaries in surgical pathology samples, (d) act as biomarkers for early detection and/or diagnosis of the disease, and (e) act as targets in the generation antibody-like molecules which recognize the target-peptide/MHC complex.