Abstract: A diagnostic method for determining the absence or presence of a disease is provided. The method generally includes assaying the amount and/or types of oxidized peptides in a sample from a subject, and comparing these to the amount and types of reference oxidized polypeptides. The method may include the use of stable isotope label, affinity selection, to identify and quantify changes in oxidized peptides or oxidized proteins associated with diseases such as type II diabetes mellitus, breast cancer, and Parkinson's disease, to monitor a patient's response to a therapeutic agent (e.g., an antioxidant), and/or to monitor disease recurrence.

Abstract: The present disclosure provides an automated system and method for protein digestion, recovery, and analysis. The present disclosure also provides a buffer solution for use therein.

Abstract: Reagents and methods are provided that permit simultaneous analysis of multiple diverse small molecule analytes present in a complex mixture. Samples are labeled with chemically identical but isotopically distinct forms of the labeling reagent, and analyzed using mass spectrometry. A single reagent simultaneously derivatizes multiple small molecule analytes having different reactive functional groups.

Abstract: A diagnostic method for determining the absence or presence of a disease is provided. The method includes assaying the amount and/or types of glycopeptides in a sample from a subject, and comparing these to the amount and types of reference glycopeptides. The method may include the use of a stable isotope label, affinity selection, immunoaffinity chromatography, and glycoproteomics techniques, to identify and quantify changes in glycosylated peptides or glycosylated proteins associated with cancers such as malignant lymphoma or breast cancer, to monitor patient's response to therapy, and to monitor disease recurrence.

Abstract: A multi-dimensional method for simultaneously analyzing multiple analytes within a sample solution, comprising adding affinity selectors to a sample solution containing analytes to be measured, the affinity selectors having an affinity for one or more of the analytes within the sample solution; allowing immune complexes to form between the affinity selectors and the analytes; partially or totally resolving the formed immune complexes from non-analyte substances within the sample solution; dissociating the resolved immune complexes; separating the analytes and the affinity selectors of the dissociated immune complexes from one another by capturing the analytes through a surface adsorption process; transferring the captured analytes to a detection means; and resolving the analytes with the detection means in accordance with their mass-to-charge ratios.

Abstract: A diagnostic method for determining the absence or presence of a disease is provided. The method generally includes assaying the amount and/or types of oxidized peptides in a sample from a subject, and comparing these to the amount and types of reference oxidized polypeptides. The method may include the use of stable isotope label, affinity selection, to identify and quantify changes in oxidized peptides or oxidized proteins associated with diseases such as type II diabetes mellitus, breast cancer, and Parkinson's disease, to monitor a patient's response to a therapeutic agent (e.g., an antioxidant), and/or to monitor disease recurrence.

Abstract: A method of probing a plurality of analyzer molecules distributed about a detection platform is disclosed. The method includes contacting a test sample to the plurality of analyzer molecules, scanning the plurality of analyzer molecules at a rate relating to a carrier frequency signal, and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially at a sideband of the carrier frequency signal. A molecule detection platform including a substrate and a plurality of targets positioned about the substrate is also disclosed. Specific analyzer molecules adapted to bind a specific analyte are immobilized about a first set of the targets. Nonspecific analyzer molecules are immobilized about a second set of the targets. The targets positioned about the substrate along at least a segment of a scanning pathway alternate between at least one of the first set and at least one of the second set.

Abstract: A multi-dimensional method for simultaneously analyzing multiple analytes within a sample solution, comprising adding affinity selectors to a sample solution containing analytes to be measured, the affinity selectors having an affinity for one or more of the analytes within the sample solution; allowing immune complexes to form between the affinity selectors and the analytes; partially or totally resolving the formed immune complexes from non-analyte substances within the sample solution; dissociating the resolved immune complexes; separating the analytes and the affinity selectors of the dissociated immune complexes from one another by capturing the analytes through a surface adsorption process; transferring the captured analytes to a detection means; and resolving the analytes with the detection means in accordance with their mass-to-charge ratios.

Abstract: Reagents and methods are provided that permit simultaneous analysis of multiple diverse small molecule analytes present in a complex mixture. Samples are labeled with chemically identical but isotopically distinct forms of the labeling reagent, and analyzed using mass spectrometry. A single reagent simultaneously derivatizes multiple small molecule analytes having different reactive functional groups.

Abstract: A planar array having plurality of biological recognition molecules including at least two types of biological recognition molecules distributed about a substrate is disclosed. A first type of biological recognition molecules is distributed according to a first frequency and a second type of biological recognition molecules is distributed according to a second frequency. Another planar array having a plurality of biological recognition molecules including at least two kinds of biological recognition molecules is disclosed. The recognition molecules are distributed about a substrate with first kind of biological recognition molecules distributed at a first height or depth relative to a surface of the substrate and a second kind of biological recognition molecules distributed at a second height or depth relative to the surface.

Abstract: Compositions and methods for controlling or eliminating isotope effects during fractionation of chemically equivalent but isotopically distinct compounds. Isotope coding agents contain heavy isotopes other than deuterium. The invention facilitates intelligent data acquisition. After sample fractionation, isotope abundance ratios are calculated using mass spectrometry, and analytes of interest are identified in real time.

Abstract: Method and device for detection of analytes, particularly biohazards. A microarray containing immobilized sensing molecules captures complementary analytes on a redundant patterned substrate. Pattern analysis is performed using a computer algorithm.

Abstract: A method for protein identification in complex mixtures that utilizes affinity selection of constituent proteolytic peptide fragments unique to a protein analyte. These “signature peptides” function as analytical surrogates. Mass spectrometric analysis of the proteolyzed mixture permits identification of a protein in a complex sample without purifying the protein or obtaining its composite peptide signature.

Abstract: A phase contrast quadrature interferometric method and apparatus for determining the presence or absence of a target analyte in a sample. The method includes probing a substrate exposed to the sample with a laser beam. The substrate includes a reflecting surface with a first region having recognition molecules specific to the target analyte and a second region without recognition molecules. The method also includes probing the first and second region, and measuring time dependent intensity on a photodetector at one or both of a pair of quadrature angles of a reflected diffraction signal. The apparatus includes a laser source, a platform for receiving the planar array, an objective lens offset from the platform by approximately a focal length, and a split photodetector means for measuring a first quadrature and a second quadrature in a signal resulting from reflection of the laser beam.

Abstract: A method of probing a plurality of analyzer molecules distributed about a detection platform is disclosed. The method includes contacting a test sample to the plurality of analyzer molecules, scanning the plurality of analyzer molecules at a rate relating to a carrier frequency signal, and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially at a sideband of the carrier frequency signal. A molecule detection platform including a substrate and a plurality of targets positioned about the substrate is also disclosed. Specific analyzer molecules adapted to bind a specific analyte are immobilized about a first set of the targets. Nonspecific analyzer molecules are immobilized about a second set of the targets. The targets positioned about the substrate along at least a segment of a scanning pathway alternate between at least one of the first set and at least one of the second set.

Abstract: Compositions and methods for controlling or eliminating isotope effects during fractionation of chemically equivalent but isotopically distinct compounds. Isotope coding agents contain heavy isotopes other than deuterium. The invention facilitates intelligent data acquisition. After sample fractionation, isotope abundance ratios are calculated using mass spectrometry, and analytes of interest are identified in real time.

Abstract: A diagnostic method for determining the absence or presence of a disease is provided. The method includes assaying the amount and/or types of glycopeptides in a sample from a subject, and comparing these to the amount and types of reference glycopeptides. The method may include the use of a stable isotope label, affinity selection, immunoaffinity chromatography, and glycoproteomics techniques, to identify and quantify changes in glycosylated peptides or glycosylated proteins associated with cancers such as malignant lymphoma or breast cancer, to monitor patient's response to therapy, and to monitor disease recurrence.

Abstract: An apparatus for assessing topology of a surface of a target. The apparatus includes an optical source for generating a probe laser beam. The apparatus also includes means for scanning the probe laser beam across at least a portion of the surface of the target. The apparatus further includes a beamsplitter for redirecting a return signal toward means for detecting the return signal in a substantially quadrature condition, the return signal resulting from reflection of the probe laser beam off the surface of the target. A quadrature interferometric method for determining the presence or absence of a target analyte in a sample. The method comprises generating a laser probe beam having a wavelength ? and a waist wo to probe at least a portion of a substrate having a reflecting surface that has been exposed to the sample.

Abstract: Compositions and methods for controlling or eliminating isotope effects during fractionation of chemically equivalent but isotopically distinct compounds. Isotope coding agents contain heavy isotopes other than deuterium. The invention facilitates intelligent data acquisiton. After sample fractionation, isotope abundance ratios are calculated using mass spectrometry, and analytes of interest are identified in real time.

Abstract: An apparatus for assessing topology of a surface of a target including an optical source for generating a probe laser beam. The apparatus also includes a means for scanning the probe laser beam across at least a portion of the surface of the target and a beamsplitter for redirecting a return signal toward the means for detecting the return signal in a substantially quadrature condition. A quadrature interferometric method for determining the presence or absence of a target analyte in a sample comprising a laser probe beam having a wavelength ? and a waist wo to probe at least a portion of a substrate having a reflecting surface that includes at least a first region having a layer of recognition molecules specific to the target analyte and a second region that does not include a layer of recognition molecules specific to the target analyte.