Abstract: Methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data corresponding to an unidentified chemical compound. By restricting the generation of candidate formulas to those having repeating units and/or end units with specified limitations, the methods and apparatus may more efficiently iteratively search for a chemical formula having matching mass spectrometry output within a threshold tolerance. In another aspect, methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data based at least in part upon neutral loss.

Abstract: Methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data corresponding to an unidentified chemical compound. By restricting the generation of candidate formulas to those having repeating units and/or end units with specified limitations, the methods and apparatus may more efficiently iteratively search for a chemical formula having matching mass spectrometry output within a threshold tolerance. In another aspect, methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data based at least in part upon neutral loss.

Abstract: Methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data corresponding to an unidentified chemical compound. By restricting the generation of candidate formulas to those having repeating units and/or end units with specified limitations, the methods and apparatus may more efficiently iteratively search for a chemical formula having matching mass spectrometry output within a threshold tolerance. In another aspect, methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data based at least in part upon neutral loss.

Abstract: An inventive substrate is provided which includes a substrate compound of formula A-B1-B2-B3-B4: wherein A is a sugar moiety; B1 is a linker moiety allowing the conjugation of moiety A and the remaining structure of the substrate; B2 is a linker moiety with a free reactive amino group so as to be available for reaction with carboxylic acids or detectable tags; B3 contains a permanently charged element such as a quaternary ammonium group so as to increase sensitivity for mass spectrometry analysis; and B4 of various carbon length conferring specificity amongst individual substrates in detection methods. Also provided is a molecule of the formula B1-B2-B3-B4, with similar structural characteristics to an enzymatic product produced by the action of a target enzyme on an inventive substrate. Further provided are methods for using inventive substrates for detecting enzymatic activity.

Abstract: Described herein are methods for determining an amount of an analyte in a test sample. The methods involve preparing a calibration curve using standard samples containing an isotopically-labeled standard in a biological matrix.

Abstract: Methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data corresponding to an unidentified chemical compound. By restricting the generation of candidate formulas to those having repeating units and/or end units with specified limitations, the methods and apparatus may more efficiently iteratively search for a chemical formula having matching mass spectrometry output within a threshold tolerance. In another aspect, methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data based at least in part upon neutral loss.

Abstract: Described herein are methods for determining an amount of an analyte in a test sample. The methods involve preparing a calibration curve using standard samples containing an isotopically-labeled standard in a biological matrix.

Abstract: This invention relates, inter alia, to detecting and/or measuring succinylacetone and one or more additional biological analytes using mass spectrometry, e.g., tandem mass spectrometry, by derivatizing succinylacetone in a sample by contacting the sample with an extraction solution comprising a C1-3 linear or branched chain monoalcohol and a strong base selected from the group consisting of hydrazine, a modified hydrazine, and hydroxylamine.

Abstract: An inventive substrate is provided which includes a substrate compound of formula A—B1—B2—B3: wherein A is a sugar moiety; B1 is a linker moiety allowing the conjugation of moiety A and the remaining structure of the substrate; B2 contains a permanently charged element such as a quaternary ammonium group so as to increase proton affinities and ionization efficiencies for mass spectrometry detection efficiencies analysis; and B3 of various carbon length conferring specificities to targeted enzymes. Also provided is a process to detect lysosomal diseases by contacting a sample with the inventive substrate along with an internal standard which is isotope-labeled analog of the product cleaved by a targeted enzyme upon the substrate.

Abstract: Described herein are methods for determining an amount of an analyte in a test sample. The methods involve preparing a calibration curve using standard samples containing an isotopically-labeled standard in a biological matrix.

Abstract: Provided are methods for detecting a metabolic disorder in an individual using mass spectrometry. One method involves (a) contacting a sample containing (i) a metabolically indicative enzyme and (ii) a metabolic analyte, with a substrate for the enzyme to produce a reaction admixture, under conditions wherein the enzyme is capable of acting on a corresponding substrate to generate a product, and wherein a protease inhibitor is present; (b) contacting the reaction admixture with a reagent that inhibits the ability of the enzyme to act on a corresponding substrate, wherein the metabolic analyte and the product are soluble in the reagent; to produce a test sample and (c) determining the presence or amount of the metabolic analyte and the product contained in the test sample using mass spectrometry, wherein a determined presence or amount of the metabolic analyte and the product correlates with presence or absence of the metabolic disorder.

Abstract: This invention relates, inter alia, to detecting and/or measuring succinylacetone and one or more additional biological analytes using mass spectrometry.

Abstract: Provided are methods for detecting a metabolic disorder in an individual using mass spectrometry. One method involves (a) contacting a sample containing (i) a metabolically indicative enzyme and (ii) a metabolic analyte, with a substrate for the enzyme to produce a reaction admixture, under conditions wherein the enzyme is capable of acting on a corresponding substrate to generate a product, and wherein a protease inhibitor is present; (b) contacting the reaction admixture with a reagent that inhibits the ability of the enzyme to act on a corresponding substrate, wherein the metabolic analyte and the product are soluble in the reagent; to produce a test sample and (c) determining the presence or amount of the metabolic analyte and the product contained in the test sample using mass spectrometry, wherein a determined presence or amount of the metabolic analyte and the product correlates with presence or absence of the metabolic disorder.

Abstract: Described herein are methods for determining an amount of an analyte in a test sample. The methods involve preparing a calibration curve using standard samples containing an isotopically-labeled standard in a biological matrix.

Abstract: Methods of evaluating molecular isomers of branched-chain amino acids are featured. The methods can include: derivatizing one or more molecular isomers of branched-chain amino acids in a sample comprising a branched-chain amino acid labeled with one or more heavy atoms as a first standard; adding, to the sample, after derivatization, a nonderivatized or derivatized branched chain amino acid that is labeled with one or more heavy atoms, as a second standard; evaluating the sample using tandem mass spectrometry; and detecting peaks indicative of derivatized and nonderivatized forms of one or more branched-chain amino acids in the sample.

Abstract: This invention relates, inter alia, to detecting and/or measuring succinylacetone and one or more additional biological analytes using mass spectrometry.

Abstract: Described herein are methods for determining an amount of an analyte in a test sample. The methods involve preparing a calibration curve using standard samples containing an isotopically-labeled standard in a biological matrix.

Abstract: Methods of evaluating molecular isomers of branched-chain amino acids are featured. The methods can include: derivatizing one or more molecular isomers of branched-chain amino acids in a sample comprising a branched-chain amino acid labeled with one or more heavy atoms as a first standard; adding, to the sample, after derivatization, a nonderivatized or derivatized branched chain amino acid that is labeled with one or more heavy atoms, as a second standard; evaluating the sample using tandem mass spectrometry; and detecting peaks indicative of derivatized and nonderivatized forms of one or more branched-chain amino acids in the sample.

Abstract: An inventive substrate is provided which includes a substrate compound of formula A-B1-B2-B3-B4: wherein A is a sugar moiety; B1 is a linker moiety allowing the conjugation of moiety A and the remaining structure of the substrate; B2 is a linker moiety with a free reactive amino group so as to be available for reaction with carboxylic acids or detectable tags; B3 contains a permanently charged element such as a quaternary ammonium group so as to increase sensitivity for mass spectrometry analysis; and B4 of various carbon length conferring specificity amongst individual substrates in detection methods. Also provided is a molecule of the formula B1-B2-B3-B4, with similar structural characteristics to an enzymatic product produced by the action of a target enzyme on an inventive substrate. Further provided are methods for using inventive substrates for detecting enzymatic activity.

Abstract: Provided are methods for detecting a metabolic disorder in an individual using mass spectrometry. One method involves (a) contacting a sample containing (i) a metabolically indicative enzyme and (ii) a metabolic analyte, with a substrate for the enzyme to produce a reaction admixture, under conditions wherein the enzyme is capable of acting on a corresponding substrate to generate a product, and wherein a protease inhibitor is present; (b) contacting the reaction admixture with a reagent that inhibits the ability of the enzyme to act on a corresponding substrate, wherein the metabolic analyte and the product are soluble in the reagent; to produce a test sample and (c) determining the presence or amount of the metabolic analyte and the product contained in the test sample using mass spectrometry, wherein a determined presence or amount of the metabolic analyte and the product correlates with presence or absence of the metabolic disorder.