Abstract: Illustrative embodiments of methods and apparatus for identifying one or more intact glycopeptides in a sample are disclosed. According to one illustrative embodiment, a method may comprise receiving data representing a plurality of mass spectra obtained from mass spectrometry of the sample, scoring data representing each of the plurality of mass spectra against data associated with target glycopeptides, and identifying one or more intact glycopeptides in the sample based at least in part on the scoring of the data representing each of the plurality of mass spectra.

Abstract: Illustrative embodiments of methods and apparatus for identifying one or more intact glycopeptides in a sample are disclosed. According to one illustrative embodiment, a method may comprise receiving data representing a plurality of mass spectra obtained from mass spectrometry of the sample, scoring data representing each of the plurality of mass spectra against data associated with target glycopeptides, and identifying one or more intact glycopeptides in the sample based at least in part on the scoring of the data representing each of the plurality of mass spectra.

Abstract: A solid-phase permethylation procedure is described. For example, solid-phase permethylation can be utilized to prepare permethylated linear and branched, neutral and sialylated oligosaccharides, which can be analyzed by MALDI-MS.

Abstract: A method of analyzing O-linked oligosaccharides in a sample is disclosed. The method comprises the steps of digesting a glycoprotein with a proteolytic enzyme, performing solid-phase permethylation of the oligosaccharide, then analyzing the permethylated and non-reduced O-linked oligosaccharides using MALDI-TOF mass spectrometry.

Abstract: A solid-phase permethylation procedure is described. For example, solid-phase permethylation can be utilized to prepare permethylated linear and branched, neutral and sialylated oligosaccharides, which can be analyzed by MALDI-MS.

Abstract: Specific glycomic profiles derived from human blood sera of breast cancer patients and prostate cancer patients were compared to those of disease-free females and males, respectively. The profiles were acquired using MALDI-MS of permethylated N-glycans released from 10-?l sample aliquots. Quantitative permethylation was attained using solid-phase permethylation. Principal component analysis of the glycomic profiles revealed significant differences among the two sets (diseased vs. non-diseased), allowing their distinct clustering. Several sialylated and fucosylated N-glycan structures were found to be useful as biomarkers for cancer, particularly breast cancer or prostate cancer.

Abstract: A solid-phase permethylation procedure is described. For example, solid-phase permethylation can be utilized to prepare permethylated linear and branched, neutral and sialylated oligosaccharides, which can be analyzed by MALDI-MS.

Abstract: A system and method of incubating a liquid is provided. The system is well-suited for incubating small volumes of liquid at high temperatures. The liquid may be a reaction mixture comprising a glycoprotein. During the incubation process, oligosaccharides may be removed from the glycoprotein.

Abstract: An ammonium-based &bgr;-elimination cleavage of linked oligosaccharides from glycoproteins is described. The method enables the isolation of glycoprotein-derived oligosaccharides having a reducing end which enables subsequent derivatization for chromatographic and/or mass spectral analysis. The described glycoprotein cleavage protocol enables structural investigations using low microgram quantities of glycoproteins.

Abstract: The invention provides a method of cleaving an O-linked oligosaccharide from a glycoprotein. The method comprises the steps of contacting a composition comprising a glycoprotein, wherein the glycoprotein comprises O-linked oligosaccharides, with a solution comprising a borane-ammonia complex to form a mixture comprising the glycoprotein and the borane-ammonia complex, incubating the mixture for a period of time sufficient to cleave the linked oligosaccharides from the glycoprotein, and forming a mixture comprising oligosaccharide alditol products and deglycosylated protein by-products.

Abstract: A system and method of incubating a liquid is provided. The system is well-suited for incubating small volumes of liquid at high temperatures. The liquid may be a reaction mixture comprising a glycoprotein. During the incubation process, oligosaccharides may be removed from the glycoprotein.