Abstract: The invention provides methods for preparing a peptide as an immunogen to generate an antibody specific for the deglycosylated form of a glycopolypeptide by preparing a peptide that includes an N-linked glycosylation site of said glycopolypeptide and identifying a peptide sequence that includes said glycosylated site and preparing said peptide wherein N of said site is converted to D.

Abstract: The invention provides methods for preparing a peptide useful in generating an antibody specific for the glycosylated form of a glycopolypeptide wherein the glycosylated portion is isolated and a peptide corresponding to amino acids adjacent to a glycosylated N-linked glycosylation site is prepared.

Abstract: The invention provides a method for diagnosing or predicting susceptibility to a prostate neoplastic condition in an individual. The method involves (a) determining a level of RDC1 in a sample from the individual, and (b) comparing the level of RDC1 in the sample to a reference level of RDC1, wherein a level of RDC1 in the sample 2-fold or more higher than the reference level indicates the presence of, or susceptibility to, a prostate neoplastic condition in the individual.

Abstract: The invention provides methods for preparing a peptide useful in generating an antibody specific for the glycosylated form of a glycopolypeptide wherein the glycosylated portion is isolated and a peptide corresponding to amino acids adjacent to a glycosylated N-linked glycosylation site is prepared.

Abstract: The invention provides methods for preparing a peptide as an immunogen to generate an antibody specific for the deglycosylated form of a glycopolypeptide by preparing a peptide that includes an N-linked glycosylation site of said glycopolypeptide and identifying a peptide sequence that includes said glycosylated site and preparing said peptide wherein N of said site is converted to D.

Abstract: The invention provides methods for generating an antibody specific for the deglycosylated form of a glycopolypeptide using a peptide corresponding to an N-linked glycosylation site of a glycopolypeptide. The invention additionally provides methods for generating an antibody specific for a glycopolypeptide using a peptide corresponding to amino acids adjacent to an authentic N-linked glycosylation site.

Abstract: The invention provides compositions and methods for identifying and/or quantifying glycopolypeptides from human serum or plasma. The compositions and methods include a plurality of standard peptides containing glycosylation sites determined for human serum/plasma proteins.

Abstract: The invention provides methods for identifying and quantifying polypeptides in a sample. The methods include the steps of labeling peptides in a polypeptide sample with an isotope tag; adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag; resolving the labeled sample and standard peptides into a plurality of fractions; analyzing the resolved fractions using mass spectrometry; identifying an isotope-tagged sample peptide in an analyzed fraction; and determining the amount of the identified isotope-tagged sample peptide in the analyzed fraction by comparison to the amount of isotope tagged standard peptide in the same fraction.

Abstract: The invention provides methods of detecting polypeptides in a sample. The method can include the steps of cleaving polypeptides in a test sample to generate peptides; adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, wherein the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; washing the array to remove unbound peptides, thereby retaining affinity captured sample peptides and standard peptides; analyzing the affinity captured peptides using mass spectrometry; and determining the presence of bound test peptides and standard peptides. The method can further include the step of quantifying the amount of the test peptides by comparing the ratio of test peptide to corresponding standard peptide.

Abstract: The invention provides a method for diagnosing or predicting susceptibility to a prostate neoplastic condition in an individual. The method involves (a) determining a level of RDC1 in a sample from the individual, and (b) comparing the level of RDC1 in the sample to a reference level of RDC1, wherein a level of RDC1 in the sample 2-fold or more higher than the reference level indicates the presence of, or susceptibility to, a prostate neoplastic condition in the individual.

Abstract: The invention provides methods for identifying and quantifying polypeptides in a sample. The methods include the steps of labeling peptides in a polypeptide sample with an isotope tag; adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag; resolving the labeled sample and standard peptides into a plurality of fractions; analyzing the resolved fractions using mass spectrometry; identifying an isotope-tagged sample peptide in an analyzed fraction; and determining the amount of the identified isotope-tagged sample peptide in the analyzed fraction by comparison to the amount of isotope tagged standard peptide in the same fraction.

Abstract: The invention provides a reagent comprising an affinity tag, a detectable moiety, a linker, an isotope tag and a reactive group. The invention also provides methods of using a reagent of the invention. The methods can be used to label a polypeptide in a sample by contacting a sample with a reagent of the invention under conditions allowing the reactive group to bind to one or more polypeptides in the sample. The invention additionally provides methods of isolating, identifying and quantifying a polypeptide in a sample. The invention further provides methods of diagnosing a disease using a reagent of the invention.

Abstract: The invention provides a reagent comprising an affinity tag, a detectable moiety, a linker, an isotope tag and a reactive group. The invention also provides methods of using a reagent of the invention. The methods can be used to label a polypeptide in a sample by contacting a sample with a reagent of the invention under conditions allowing the reactive group to bind to one or more polypeptides in the sample. The invention additionally provides methods of isolating, identifying and quantifying a polypeptide in a sample. The invention further provides methods of diagnosing a disease using a reagent of the invention.

Abstract: The invention provides methods for labeling a molecule by contacting a sample molecule with a solid support coupled to a chemical group comprising a cleavable functional group, one or more functional groups, and a reactive group for the sample molecule, under conditions allowing the sample molecule to covalently bind to the reactive group; and cleaving the cleavable functional group, thereby releasing the sample molecule comprising the one or more functional groups, which can be a tag. The invention also provides a solid support covalently coupled to a chemical group comprising a cleavable functional group, a mass spectrometry tag and a reactive group for covalently attaching a sample molecule, wherein the cleavable functional group, the tag and the reactive group are positioned relative to each other to allow transfer of the tag to the sample molecule upon cleavage of the cleavable functional group.

Abstract: The invention provides methods for labeling a molecule by contacting a sample molecule with a solid support coupled to a chemical group comprising a cleavable functional group, one or more functional groups, and a reactive group for the sample molecule, under conditions allowing the sample molecule to covalently bind to the reactive group; and cleaving the cleavable functional group, thereby releasing the sample molecule comprising the one or more functional groups, which can be a tag. The invention also provides a solid support covalently coupled to a chemical group comprising a cleavable functional group, a mass spectrometry tag and a reactive group for covalently attaching a sample molecule, wherein the cleavable functional group, the tag and the reactive group are positioned relative to each other to allow transfer of the tag to the sample molecule upon cleavage of the cleavable functional group.

Abstract: The invention provides a method for identifying and quantifying polyglycopeptides in a sample. The method can include the steps of immobilizing glycopolypeptides to a solid support; cleaving the immobilized glycopolypeptides, thereby releasing non-glycosylated peptides and retaining immobilized glycopeptides; releasing the glycopeptides from the solid support; and analyzing the released glycopeptides. The method can further include the step of identifying one or more glycopeptides, for example, using mass spectrometry.

Abstract: Methods using gel electrophoresis and mass spectrometry for the rapid, quantitative analysis of proteins or protein function in mixtures of proteins derived from two or more samples in one unit operation are disclosed.

Abstract: The invention provides methods for labeling a molecule by contacting a sample molecule with a solid support coupled to a chemical group comprising a cleavable functional group, one or more functional groups, and a reactive group for the sample molecule, under conditions allowing the sample molecule to covalently bind to the reactive group; and cleaving the cleavable functional group, thereby releasing the sample molecule comprising the one or more functional groups, which can be a tag. The invention also provides a solid support covalently coupled to a chemical group comprising a cleavable functional group, a mass spectrometry tag and a reactive group for covalently attaching a sample molecule, wherein the cleavable functional group, the tag and the reactive group are positioned relative to each other to allow transfer of the tag to the sample molecule upon cleavage of the cleavable functional group.

Abstract: The invention provides a method for diagnosing or predicting susceptibility to a prostate neoplastic condition in an individual. The method involves (a) determining a level of RDC1 in a sample from the individual, and (b) comparing the level of RDC1 in the sample to a reference level of RDC1, wherein a level of RDC1 in the sample 2-fold or more higher than the reference level indicates the presence of, or susceptibility to, a prostate neoplastic condition in the individual.

Abstract: The invention provides methods for labeling a molecule by contacting a sample molecule with a solid support coupled to a chemical group comprising a cleavable functional group, one or more functional groups, and a reactive group for the sample molecule, under conditions allowing the sample molecule to covalently bind to the reactive group; and cleaving the cleavable functional group, thereby releasing the sample molecule comprising the one or more functional groups, which can be a tag. The invention also provides a solid support covalently coupled to a chemical group comprising a cleavable functional group, a mass spectrometry tag and a reactive group for covalently attaching a sample molecule, wherein the cleavable functional group, the tag and the reactive group are positioned relative to each other to allow transfer of the tag to the sample molecule upon cleavage of the cleavable functional group.