# US 8,772,044 B2 · Method of negative-ion MALDI analysis of neutral labeled sugars and screening disease markers > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,772,044 B2 - Document ID: US8772044B2 - Status: Granted - Kind: B2 - Application number: 11/887,365 - Filed: 2006-03-27 - Published: 2009-10-08 - Granted: 2014-07-08 - Earliest claimed: 2005-03-31 - Assignees: The Noguchi Institute; Shimadzu Corporation - Applicants: Junko Amano; Koichi Tanaka - Inventors: Junko Amano; Koichi Tanaka - Web page: https://patentgrep.com/patent/US8772044B2 ## CPC - G01N 33/5308: {for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites} - G01N 33/6851: {Methods of protein analysis involving laser desorption ionisation mass spectrometry} - G01N 33/80: involving blood groups or blood types {or red blood cells (white blood cells G01N33/56972)} - G01N 2400/00: Assays, e.g. immunoassays or enzyme assays, involving carbohydrates - Y10T 436/144444: Glucose - Y10T 436/24: Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION ## Abstract The present invention provides a method for obtaining structural information conveniently and rapidly by generating a negative ion without adding an acidic substance to matrix, thereby improving sensitivity of measurement by a mass spectrometer, and by generating structural specific ions with high reproducibility, and a method for screening disease marker and a method for analyzing a sample containing a biomolecule. A method for mass spectrometry of a sugar chain comprising the steps of: preparing a sample containing a sugar chain; labeling the sugar chain with a labeling compound, to obtain a labeled sugar chain; and subjecting the labeled sugar chain to measurement of negative ions by using a MALDI mass spectrometer, thereby conducting analysis of the sugar chain. A method for screening disease marker comprising the steps of: (1) labeling the biomolecule X derived from a subject affected by a particular disease; subjecting the labeled biomolecule X′ to measurement of negative ions by a MALDI mass spectrometer, (2) separately, labeling the biomolecule Y derived from a subject unaffected by the particular disease; subjecting the labeled biomolecule Y′ to measurement of negative ions by a MALDI mass spectrometer; and (3) comparing mass spectrum of the labeled biomolecule X′ obtained in (1) with mass spectrum of the labeled biomolecule Y′ obtained in (2) to find mass spectrum peaks which are mutually different, thereby ascertaining presence of structure involved in expression of the particular disease. ## Claims ### Claim 1 A method of negative-ion MALDI analysis of neutral labeled sugar chain comprising the steps of: preparing a sample containing a neutral sugar chain; labeling the neutral sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a neutral labeled sugar chain; wherein the neutral sugar chain contains fucose; or preparing a sample containing an acidic sugar chain; neutralizing and labeling the acidic sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine to obtain a neutral labeled sugar chain; wherein the acidic sugar chain contains sialic acid; and subjecting the neutral labeled sugar chain to negative ion MALDI analysis. ### Claim 2 (depends on 1) The method according to claim 1, wherein the sample contains neutral or acidic sugar chains that are mutually structural isomers (A, B, C, . . . ) , wherein subjecting the neutral labeled sugar chains (A′, B′, C′, . . . ) to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using MALDI-QIT-TOF mass spectrometer which produces structurally different ions (a, b, c, . . . ) that are specifically generated from the respective neutral labeled sugar chains (A′, B′, C′, . . . ), thereby distinguishing the sugar chains (A, B, C, . . . ); from one another. ### Claim 3 (depends on 2) The method according to claim 2, wherein by conducting structure analysis for each of the ions (A, B, C, . . . ), an entire structure or a partial structure of the sugar chains (A, B, C, . . . ) is respectively identified. ### Claim 4 (depends on 1) The method according to claim 1, wherein the sample contains plural kinds of structural isomers of neutral or acidic sugar chain in a known mixing ratio, and wherein subjecting the plural kinds of neutral labeled structural isomers to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using MALDI-QIT-TOF mass spectrometer which produces ions specifically generated from the respective plural kinds of neutral labeled structural isomers, thereby analyzing the plural kinds of structural isomers of sugar chain. ### Claim 5 (depends on 4) The method according to claim 4, wherein by conducting structure analysis for the detected specifically generating ions, an entire structure or a partial structure of each of the plural kinds of structural isomers of sugar chain is identified, and/or the detected specifically generating ions are determined as ions for quantification of the plural kinds of structural isomers, and relation between ion intensity of the determined ion and the known mixing ratio is found. ### Claim 6 (depends on 5) The method according to claim 5, wherein the method further comprises performing the same steps, as recited in claim 5, for a second sample, wherein the second sample contains plural kinds of structural isomers of neutral or acidic sugar chain in an unknown mixing ratio, and wherein subjecting the plural kinds of neutral labeled structural isomers to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using MALDI-QIT-TOF mass spectrometer which produces ions specifically generating from the respective plural kinds of neutral labeled structural isomers, thereby analyzing the plural kinds of structural isomers of sugar chain, wherein by conducting structure analysis for the detected specifically generating ions, an entire structure or a partial structure of each of the plural kinds of structural isomers of sugar chain is identified, and/or from ion intensity of detected specifically generating ion, the unknown mixing ratio is calculated based on the relation found for the known sample. ### Claim 7 (depends on 1) The method according to claim 1, wherein the sample contains one kind or plural kinds of neutral or acidic sugar chain having an unknown structure wherein, separately, a sample containing one kind or plural kinds of neutral or acidic sugar chain having a known structure is prepared, and wherein subjecting both of the samples to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using MALD-QIT-TOF mass spectrometer, wherein mass spectrum of the neutral labeled sugar chain having the unknown structure and/or information obtained from the mass spectrum is/are compared with mass spectrum of the neutral labeled sugar chain having the known structure and/or information obtained from the mass spectrum, to analyze the sugar chain having the unknown structure. ### Claim 8 (depends on 7) The method according to claim 7, wherein it is ascertained that an entire mass spectrum peak of the neutral labeled sugar chain having the unknown structure and/or an entire information obtained from the mass spectrum coincides with an entire mass spectrum peak of the neutral labeled sugar chain having the known structure and/or an entire information obtained from the mass spectrum, thereby the sugar chain having the unknown structure is determined to have the same structure as the sugar chain having the known structure. ### Claim 9 (depends on 7) The method according to claim 7, wherein it is ascertained that a particular peak in mass spectrum of the neutral labeled sugar chain having the unknown structure and/or particular information obtained from the mass spectrum coincides with a particular peak in mass spectrum of the neutral labeled sugar chain having the known structure and/or particular information obtained from the mass spectrum, thereby the sugar chain having the unknown structure is determined to have the same structure as the sugar chain having the known structure as a partial structure. ### Claim 10 (depends on 1) The method to claim 1, wherein the labeling compound used for conducting the labeling is selected from the group consisting of pyrenebutanoic acid hydrazide, aminopyrene, 2-aminopyridine, 2-aminobenzene, and amino benzoic acid ester. ### Claim 11 A method for screening disease marker, comprising the steps of: (1) preparing a sample containing a biomolecule X having a neutral sugar chain to be analyzed derived from a subject affected by a particular disease; labeling the neutral sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule X′ having a neutral labeled sugar chain; wherein the neutral sugar chain contains fucose; subjecting the biomolecule X′ having the neutral labeled sugar chain to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using a MALDI-QIT-TOF mass spectrometer, (2) separately, preparing a sample containing a biomolecule Y having the neutral sugar chain to be analyzed derived from a subject unaffected by the particular disease; labeling the neutral sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule Y′ having a neutral labeled sugar chain; wherein the neutral sugar chain contains fucose; subjecting the biomolecule Y′ having the neutral labeled sugar chain to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using a MALDI-QIT-TOF mass spectrometer; or (1) preparing a sample containing a biomolecule X having an acidic sugar chain to be analyzed derived from a subject affected by a particular disease; neutralizing and labeling the acidic sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule X′ having a neutral labeled sugar chain; wherein the acidic sugar chain contains sialic acid; subjecting the biomolecule X′ having the neutral labeled sugar chain to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using a MALDI-QIT-TOF mass spectrometer; (2) separately, preparing a sample containing a biomolecule Y having the acidic sugar chain to be analyzed derived from a subject unaffected by the particular disease; neutralizing and labeling the acidic sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule Y′ having a neutral labeled sugar chain; wherein the acidic sugar chain contains sialic acid; subjecting the biomolecule Y′ having the neutral labeled sugar chain to negative ion MALDI analysis comprises performing MS2 or MS3 measurement by using a MALDI-QIT-TOF mass spectrometer; and (3) comparing mass spectrum of the biomolecule X′ having the neutral labeled sugar chain obtained in (1) and/or information obtained from the mass spectrum, with mass spectrum of the biomolecule Y′ having the neutral labeled sugar chain obtained in (2) and/or information obtained from the mass spectrum, to find mass spectrum peaks and/or information which are mutually different, thereby ascertaining presence of a structure involved in expression of the particular disease. ### Claim 12 (depends on 11) The method for screening disease marker according to claim 11, further comprising, (4) analyzing mass spectrum peaks or information obtained from the mass spectrum peaks found in (3), (5) picking up the following mass spectrum peaks or information (a) or (b), (a) mass spectrum peaks or information having different mass/charge, which are included in mass spectrum of the biomolecule X′ having the neutral labeled sugar chain and/or information obtained from the mass spectrum of the biomolecule X′ but are not included in mass spectrum of the biomolecule Y′ having the neutral labeled sugar chain and/or information obtained from the mass spectrum of the biomolecule Y′, (b) mass spectrum peaks or information having the same mass/charge and different in ion intensities, which are detected at stronger ion intensity, in mass spectrum of the biomolecule X′ having the neutral labeled sugar chain and/or information obtained from the mass spectrum of the biomolecule X′, than in mass spectrum of the biomolecule Y′ having the neutral labeled sugar chain and/or information obtained from the mass spectrum of biomolecule Y′;and (6) determining the structure involved in expression of the particular disease or the structure of the biomolecule X as a structure of disease marker based on the mass spectrum peaks or information picked up in (5). ### Claim 13 (depends on 11) The method for screening disease marker according to claim 11, wherein the biomolecule is a sugar chain. ### Claim 14 (depends on 11) The method for screening disease marker according to claim 11, wherein the particular disease is cancer, and the biomolecule is blood group antigen. ### Claim 15 (depends on 11) The method for screening disease marker according to claim 11, wherein the particular disease is a disease caused by an autoimmune disease and having correlation with blood group, and the biomolecule is blood group antigen. ### Claim 16 (depends on 11) The method for screening disease marker according to claim 11, wherein the particular disease is heart disease or hypercholesterolemia, and the biomolecule is blood group antigen. ### Claim 17 (depends on 11) The method for screening disease marker according to claim 11, wherein the labeling compound used for conducting the labeling is selected from the group consisting of pyrenebutanoic acid hydrazide, aminopyrene, 2-aminopyridine, 2-aminobenzene, and amino benzoic acid ester. ### Claim 18 (depends on 1) The method according to claim 1, wherein the labeling compound is selected from the group consisting of amino pyrene, amino benzene, amino pyridine, pyrene carboxylic acid hydrazide, benzene carboxylic acid hydrazide, and pyridine carboxylic acid hydrazide. ### Claim 19 (depends on 1) The method according to claim 1, wherein the negative ion MALDI analysis is selected from the group consisting of ISD, PSD, and MSn measurement. ### Claim 20 A method for screening disease marker, comprising the steps of: (1) preparing a sample containing a biomolecule X having a neutral sugar chain to be analyzed derived from a subject affected by a particular disease; labeling the neutral sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule X′ having a neutral labeled sugar chain; wherein the neutral sugar chain contains fucose; subjecting the biomolecule X′ having the neutral labeled sugar chain to negative ion MALDI analysis selected from the group consisting of ISD, PSD, and MSn measurement, (2) separately, preparing a sample containing a biomolecule Y having the neutral sugar chain to be analyzed derived from a subject unaffected by the particular disease; labeling the neutral sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule Y′ having a neutral labeled sugar chain; wherein the neutral sugar chain contains fucose; subjecting the biomolecule Y′ having the neutral labeled sugar chain to negative ion MALDI analysis selected from the group consisting of ISD, PSD, and MSn measurement; or (1) preparing a sample containing a biomolecule X having an acidic sugar chain to be analyzed derived from a subject affected by a particular disease; neutralizing and labeling the acidic sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule X′ having a neutral labeled sugar chain; wherein the acidic sugar chain contains sialic acid; subjecting the biomolecule X′ having the neutral labeled sugar chain to negative ion MALDI analysis selected from the group consisting of ISD, PSD, and MSn measurement; (2) separately, preparing a sample containing a biomolecule Y having the acidic sugar chain to be analyzed derived from a subject unaffected by the particular disease; neutralizing and labeling the acidic sugar chain with a labeling compound having a fundamental skeleton of aromatic selected from the group consisting of pyrene, benzene, and pyridine and comprising at least one selected from the group consisting of amino group and carboxylic acid hydrazide group to obtain a biomolecule Y′ having a neutral labeled sugar chain; wherein the acidic sugar chain contains sialic acid; subjecting the biomolecule Y′ having the neutral labeled sugar chain to negative ion MALDI analysis selected from the group consisting of ISD, PSD, and MSn measurement; and (3) comparing mass spectrum of the biomolecule X′ having the neutral labeled sugar chain obtained in (1) and/or information obtained from the mass spectrum, with mass spectrum of the biomolecule Y′ having the neutral labeled sugar chain obtained in (2) and/or information obtained from the mass spectrum, to find mass spectrum peaks and/or information which are mutually different, thereby ascertaining presence of a structure involved in expression of the particular disease.