Abstract: Disclosed herein is a method of detecting metastasis of a tumor in a subject, such as metastasis to a lymph node. The method includes directly determining an amount of desmoglein-3 (DSG-3) protein in a sample from the subject (such as a lymph node sample) and comparing the amount of DSG-3 protein to a control, wherein an increase in the amount of DSG-3 protein in the sample relative to the control indicates metastasis of the tumor to the lymph node. The disclosed methods further include selecting a therapy (for example, surgery, lymph node dissection, radiation therapy, chemotherapy, or a combination of two or more thereof) for the subject based on the amount of DSG-3 protein in the sample from the subject.

Abstract: Disclosed herein is a method of identifying a tumor biomarker. In one example, a tumor biomarker is identified by obtaining a peripheral biological fluid sample from a subject with a tumor as well as a tumor sample and an adjacent non-tumor sample from such subject. A protein expression profile is detected in the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample. The protein expression profiles of the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample are then compared, wherein an increase in expression of a specific protein in the tumor sample and peripheral biological fluid sample but not in the adjacent non-tumor sample indicates that the specific protein is a biomarker of the tumor. Also disclosed herein is a gene profiling signature that can be used to diagnosis a subject with renal cell carcinoma (RCC) or to identify agents with therapeutic potential to treat RCC. Thus, methods of diagnosing a subject with RCC are disclosed.

Abstract: Disclosed herein is a method of identifying a tumor biomarker. In one example, a tumor biomarker is identified by obtaining a peripheral biological fluid sample from a subject with a tumor as well as a tumor sample and an adjacent non-tumor sample from such subject. A protein expression profile is detected in the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample. The protein expression profiles of the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample are then compared, wherein an increase in expression of a specific protein in the tumor sample and peripheral biological fluid sample but not in the adjacent non-tumor sample indicates that the specific protein is a biomarker of the tumor. Also disclosed herein is a gene profiling signature that can be used to diagnosis a subject with renal cell carcinoma (RCC) or to identify agents with therapeutic potential to treat RCC. Thus, methods of diagnosing a subject with RCC are disclosed.

Abstract: Disclosed herein is a method of detecting metastasis of a tumor in a subject, such as metastasis to a lymph node. The method includes directly determining an amount of desmoglein-3 (DSG-3) protein in a sample from the subject (such as a lymph node sample) and comparing the amount of DSG-3 protein to a control, wherein an increase in the amount of DSG-3 protein in the sample relative to the control indicates metastasis of the tumor to the lymph node. The disclosed methods further include selecting a therapy (for example, surgery, lymph node dissection, radiation therapy, chemotherapy, or a combination of two or more thereof) for the subject based on the amount of DSG-3 protein in the sample from the subject.

Abstract: Disclosed herein is a method of identifying a tumor biomarker. In one example, a tumor biomarker is identified by obtaining a peripheral biological fluid sample from a subject with a tumor as well as a tumor sample and an adjacent non-tumor sample from such subject. A protein expression profile is detected in the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample. The protein expression profiles of the peripheral biological fluid sample, tumor sample and adjacent non-tumor sample are then compared, wherein an increase in expression of a specific protein in the tumor sample and peripheral biological fluid sample but not in the adjacent non-tumor sample indicates that the specific protein is a biomarker of the tumor. Also disclosed herein is a gene profiling signature that can be used to diagnosis a subject with renal cell carcinoma (RCC) or to identify agents with therapeutic potential to treat RCC. Thus, methods of diagnosing a subject with RCC are disclosed.

Abstract: Mass-spectrometry based methods of analyzing estrogens and other steroids from biological tissue sections samples are disclosed herein. Methods of detecting a disease state or condition or elevated risk of a disease state or condition in a mammal from tissue sections are also disclosed.

Abstract: A novel antiproliferative factor comprising a glycopeptide is disclosed. In specific embodiments, the novel antiproliferative factor is associated with the bladder. Compositions, diagnostic kits and reagents, and methods of using the compounds for identifying and/or treating interstitial cystitis and cancer are disclosed.

Abstract: Contiguous capillaries useful for separating and electrospraying a fluid comprising analyte and electrolyte are provided. The contiguous capillaries have spray tips at one end of the capillaries and electrically conductive portions in proximity to the spray tips. Methods for making the contiguous capillaries and their use as electrospray sources are also disclosed. Apparatus and methods for conveying analyte ions from the capillaries into analytical instruments, such as a mass spectrometer, are also disclosed. The disclosed contiguous capillaries may be used to carryout electrophoresis separation and electrospray ionization of analytes. Methods for obtaining the mass spectra of macromolecular analytes at concentrations lower than previously possibly are provided using the apparatus and procedures described herein.

Abstract: The invention provides reagents and methods for characterizing (i.e., identification and/or quantitation) the phosphorylation states of proteins. Proteins may be post-transcriptionally modified such that they contain phosphate groups at either some or all of their serine, threonine, tyrosine, histidine, and/or lysine amino acid residues. In many cases the extent to which a protein is phosphorylated determines it bioactivity, i.e., its ability to effect cell functions such as differentiation, division, and metabolism. Hence, a powerful tool for diagnosing various diseases and for furthering the understanding of protein—protein interactions is provided.

Abstract: The invention provides reagents and methods for characterizing (i.e., identification and/or quantitation) the phosphorylation states of proteins. Proteins may be post-transcriptionally modified such that they contain phosphate groups at either some or all of their serine, threonine, tyrosine, histidine, and/or lysine amino acid residues. In many cases the extent to which a protein is phosphorylated determines it bioactivity, i.e., its ability to effect cell functions such as differentiation, division, and metabolism. Hence, a powerful tool for diagnosing various diseases and for furthering the understanding of protein-protein interactions is provided.