Abstract: Aspects of the present invention relate to a method for the preparation of samples for MALDI MS imaging. Certain embodiments relate to a method of matrix deposition for samples, wherein tissue sections are prepared via a synergistic combination of fixation with matrix. In certain embodiments, tissue is fixed with cold solvent, according to well-established histology protocols, and in the presence of matrix, allowing for high resolution spatial mapping of protein, lipid, sugar, and/or nucleic acid distribution. In certain embodiments, the present invention relates to fixation with matrix of whole organisms. In certain embodiments, animals are perfused with fixation and matrix mixtures, which allows for direct mass spectrometry analysis.

Abstract: The present invention provides liquid chromatography-mass spectrometry methods and kits for the specific, sensitive and rapid detection as well as quantitation of free amino acids in samples following High Pressure Liquid Chromatography (HPLC) separation.

Abstract: Provided is a set of mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalization moiety, each mass label in the set having a common mass; wherein the set comprises a plurality of groups of mass labels, the mass of the mass marker moiety being the same for mass labels within a group, the mass of the mass marker moiety being different between groups; the mass marker moiety is capable of fragmentation into two or three fragments; and the mass of at least one fragment of the mass marker moiety differs between mass labels within a group.

Abstract: The present invention provides variable mass labeling reagents, a set of the variable mass labeling reagents, and a multiplexed set of variable mass labeling reagents.

Abstract: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: A method for screening a drug for cytochrome P450 (CYP) induction is provided and can include incubating the drug with a microsome-containing biological sample and then quantitating at least one cytochrome P450 isoform. The isoforms can be selected from 2B6, 3A4, 1A2, and 3A5 isoforms. In some embodiments, the method uses liquid chromatography tandem mass spectrometry (LC-MSMS). A quantitated value can be compared to a threshold value and the drug can be determined to exhibit an acceptable CYP induction potential when the quantitated value does not exceed the threshold value. Isolated peptides are also provided.

Abstract: A gas chromatography-mass spectrometry (GC-MS) method that includes performing a first GC-MS run on a sample using a gas chromatography-mass spectrometry system. Performing the first GC-MS nm includes i) passing a first flow of a carrier gas carrying a first portion of the sample through a gas chromatograph to provide a first effluent; ii) generating first ions under protonation conditions by passing the first effluent through an atmospheric pressure ionization source; iii) passing the first ions through a mass spectrometer; and iv) recording first GC-MS data for the first ions. The method also include performing a second GC-MS run on the sample using the gas chromatography-mass spectrometry system.

Abstract: Provided are methods of detecting the presence or amount of a vitamin D metabolite in a sample using mass spectrometry. The methods generally comprise ionizing a vitamin D metabolite in a sample and detecting the amount of the ion to determine the presence or amount of the vitamin D metabolite in the sample. Also provided are methods to detect the presence or amount of two or more vitamin D metabolites in a single assay.

Abstract: The invention generally relates to systems and methods for sample analysis. In certain embodiments, the invention provides a system for analyzing a sample that includes a probe including a material connected to a high voltage source, a device for generating a heated gas, and a mass analyzer.

Abstract: Methods for evaluating a fuel are provided. In one embodiment, a method of evaluating a fuel includes providing a testing specimen of the fuel. Also, the method includes analyzing the testing specimen and identifying a compound in the testing specimen. The method also provides for determining the fuel is biologically-sourced based on the identified trace compound.

Abstract: The present invention pertains to the field of diagnostics for kidney toxicity and toxicological assessments for risk stratification of chemical compounds. Specifically, it relates to a method for diagnosing kidney toxicity. It also relates to a method for determining whether a compound is capable of inducing such kidney toxicity in a subject and to a method of identifying a drug for treating kidney toxicity. Furthermore, the present invention relates to a device and a kit for diagnosing kidney toxicity.

Abstract: The presently disclosed subject matter provides methods for evaluating and characterizing peptides, peptide mixtures, and polypeptide mixtures. More particularly, the presently disclosed subject matter provides methods for evaluating or characterizing complex peptide or polypeptide mixtures comprising glutamic acid, alanine, tyrosine, and lysine, e.g., Copolymer-1 or glatiramer acetate, including, but not limited to, methods of identifying, isolating, quantifying, and purifying amino acids, peptides, polypeptides, and combinations thereof having a diethylamide group instead of a carboxyl group present on the C-terminus. The presently disclosed methods can be used to determine the mole percent of polypeptides having a diethylamide group at a C-terminus thereof and can be used to evaluate one or more properties of a sample of one polypeptide mixture as compared to one or more properties of a different sample of a polypeptide mixture.

Abstract: An apparatus and method for a sample using a mass spectrometer is described, including, generating ions of a first polarity from an analyte using electrospray ionization; generating ions of a second polarity from a reagent; injecting the ions of the first polarity and ions of the second polarity in sequence into a chamber of the mass spectrometer such that the ions of the first polarity and the ions of the second polarity interact in the chamber to form analyte ions having the second polarity; and, analyzing the mass spectrum of the analyte ions of the second polarity. A reagent such as a polyamidomine is selected to preferentially yield analyte ions of the second polarity having a desired mass-to-charge ratio.

Abstract: Reagents and methods are disclosed for detection of oxidizers and inorganic salts and other analytes of interest. The reagents can interact with their target analytes, especially oxidizer compositions or oxidizer-based explosives, to selectively enhance their ionization yield, interacting by chemical reaction or by forming an associative adduct which facilitates their detection. For example, the reagents can adduct with the counter-ion of the intended analyte for improved direct detection and/or react chemically via acid-base reactions to produce a new product for detection. In another aspect of the invention, reactive reagents and methods are also disclosed that facilitate indirect detection of the analyte at lower temperatures based on reduction-oxidation (redox) chemistry. These reagents are particularly useful in detecting oxidizer analytes.

Abstract: The presently disclosed subject matter provides methods for evaluating and characterizing peptides, peptide mixtures, and polypeptide mixtures. More particularly, the presently disclosed subject matter provides methods for evaluating or characterizing complex peptide or polypeptide mixtures comprising glutamic acid, alanine, tyrosine, and lysine, e.g., Copolymer-1 or glatiramer acetate, including, but not limited to, methods of identifying, isolating, quantifying, and purifying amino acids, peptides, polypeptides, and combinations thereof having a diethylamide group instead of a carboxyl group present on the C-terminus. The presently disclosed methods can be used to determine the mole percent of polypeptides having a diethylamide group at a C-terminus thereof and can be used to evaluate one or more properties of a sample of one polypeptide mixture as compared to one or more properties of a different sample of a polypeptide mixture.

Abstract: Methods are provided for the prevention, treatment and diagnosis of Alzheimer's disease, based on the glycosylation pattern of amyloid-beta peptides in body fluids and tissues.

Abstract: A method of detecting and sequencing post translationally modified peptides is disclosed wherein a negative ion precursor scan is performed. A negative ion high resolution MS scan is then performed and then MRM channels in positive ion mode are determined and monitored. A positive ion MS/MS scan is then performed.

Abstract: Provided are methods for determining the amount of estrone in a sample using mass spectrometry. The methods generally involve ionizing estrone in a sample and detecting and quantifying the amount of the ion to determine the amount of estrone in the sample.

Abstract: Methods and apparatus for obtaining a mass spectrum of a sample and determining a concentration of a component of the sample by utilizing a model of chemical and electron ionization and the obtained mass spectrum.

Abstract: In general, the present disclosure is directed toward a novel hybrid spintronic device for converting chemical absorption into a change in magnetoresistance. This device uses a novel magnetic material which depends on the attachment of an organic structure to a metallic film for its magnetism. Changes in the chemical environment lead to absorption on the surface of this organometallic bilayer and thus modify its magnetic properties. The change in magnetic properties, in turn, leads to a change in the resistance of a magnetoresistive structure or a spin transistor structure, allowing a standard electrical detection of the chemical change in the sensor surface.

Abstract: A method for analyzing a binding ability of protein to a compound, comprising the steps of (a) fractionating a first group of isotope-labeled proteins into plural fractions using a carrier having the compound immobilized thereon; (b) fractionating a second group of proteins into one or plural fractions using a carrier having the compound immobilized thereon; (c) adding an amount of at least one fraction obtained in step (b) to each of the fractions obtained in step (a); (d) analyzing the fractions obtained in step (c) with mass spectrometry; and (e) based on the mass spectrometry information, obtaining, regarding each fraction, an intensity ratio between a peak derived from a protein in the fraction obtained in step (a) and a peak derived from a protein in the fraction obtained in step (b), and comparing degrees of the binding ability of the plural kinds of proteins to the compound.

Abstract: Provided herein are methods for measuring molecular flux rates of molecules of interest in a tissue sample in spatially-organized manner and generating output (e.g., an image, a heat map, a contour map, a table or a database) representing the molecular flux rates of each spatially-defined location of the sample. Provided herein are also the output, as well as systems and computer-readable medium with computer-executable instructions for determining molecular flux rates of molecules of interest in the sample.

Abstract: A mass spectrometer is disclosed comprising an Electron Transfer Dissociation cell. Positive analyte ions are fragmented into fragment ions upon colliding with singly charged negative reagent ions with the cell. The cell comprises a plurality of ring electrodes which form a spherical trapping volume. Ions experience negligible RF heating over the majority of the trapping volume which enables the kinetic energy of the analyte and reagent ions to be reduced to just above thermal temperatures. An Electron Transfer Dissociation cell having an enhanced sensitivity is thereby provided. Fragment ions created within the cell may be cooled and may be transmitted onwardly to an orthogonal acceleration Time of Flight mass analyser enabling a significant improvement in the resolution of the mass analyser to be obtained.

Abstract: The invention provides a mechanism for semi-quantitatively measuring individual isotopomer species of a molecule using gas chromatograph mass spectrometry. The method allows for semi-quantitatively tracking the movement of ions by measuring the individual isotopomer species of a molecule.

Abstract: The presence of hydrogen peroxide vapor is detected with high sensitivity. Oxygen molecules in the air are ionized by electrons generated by a discharge plasma, thereby producing an oxygen molecule negative ion O2?. The oxygen molecule negative ion O2? produced is supplied to a space in which a hydrogen peroxide molecule H2O2 is to be detected. If a hydrogen peroxide molecule H2O2 is present, a cluster ion O2?(H2O2) of the oxygen molecule negative ion O2? and hydrogen peroxide molecule H2O2 is produced. The hydrogen peroxide molecule H2O2, therefore, can be detected by mass spectrometry. Other gas-phase negative ions such as chloride ion Cl? can be used besides the oxygen molecule negative ion O2?.

Abstract: According to the present invention, there is provided a device for transferring an analyte from a reaction chamber to a detector, which detector is capable of detecting said analyte. The device comprises a tubular member having a first end adapted to receive a sample containing said analyte within said reaction chamber and a second end adapted to communicate with a sample inlet of said detector; and a jacket for regulating the temperature of sample passing through the tubular member, wherein said jacket is disposed about at least a portion of the tubular member. Methods of using the device, and apparatus comprising the device, are also provided. The device may be used to transfer an analyte from a reaction chamber to a detector during the course of a chemical reaction, such that the reaction can be monitored in situ.

Abstract: The invention provides methods for isolating a target molecule from a sample. In an embodiment, the method involves contacting a sample with a capture agent, the agent comprising a siderophore and a transition metal cation, under conditions wherein the agent is capable of binding a target molecule to form a target molecule-capture agent complex, wherein the target molecule is selected from the group consisting of a phosphorylated molecule, a nitrotyrosine-containing molecule and a sulfated molecule, and separating the target molecule-capture agent complex from the sample, thereby isolating the target molecule from the sample. Also provided are methods for determining the presence of a target molecule in a sample, that involve contacting a sample with a capture agent, the agent comprising a siderophore and a transition metal cation.

Abstract: Disclosed herein is a method for discriminating sitosterolemia by simultaneously measuring relative concentrations of phytosterol and cholesterol metabolism-related compounds in a blood spot on the paper. According to the present disclosure, sitosterolemia may be quickly discriminated with high accuracy by simple sample collecting using a trace amount of blood spot stained on a paper, and it may be used for newborn screening and preschool children, particularly patients with xanthoma.

Abstract: Properties, such as concentrations, of gas phase bases or acids of a gas sample are determined by providing a sample gas flow, which includes the bases or acids to be determined as sample constituents, as well as also interfering constituents, which are other constituents than the sample constituents. Reagent ions are provided and introduced into the sample gas flow to arrange proton transfer reaction and thereby forming sample ions. Also a dopant is introduced into the sample gas flow to arrange proton transfer reaction between the dopant and the interfering ions thereby forming dopant ions and electrically neutral interfering constituents. For determination the gas flow with the sample ions to be determined is introduced together with the dopant ions to a mass spectrometer in order to determine the properties of the gas phase bases or acids.

Abstract: Disclosed herein is a method for identifying the compounds contributing to urine odor emitting from an air conditioner, a method for artificially reproducing the detected urine odor, and preparing a corresponding urine odor composition. Through the analysis method of the present invention, the compounds contributing to the urine odor emitted from an air conditioner may be identified and quantified. The detected urine odor may be reproduced from a combination of the compounds identified by the analysis method of the present invention. The reproduced urine odor may provide meaningful data required for development of an apparatus and a method for removing specific odor.

Abstract: Provided are methods of detecting the presence or amount of a dihydroxyvitamin D metabolite in a sample using mass spectrometry. The methods generally comprise ionizing a dihydroxyvitamin D metabolite in a sample and detecting the amount of the ion to determine the presence or amount of the vitamin D metabolite in the sample. In certain preferred embodiments the methods include immunopurifying the dihydroxyvitamin D metabolites prior to mass spectrometry. Also provided are methods to detect the presence or amount of two or more dihydroxyvitamin D metabolites in a single assay.

Abstract: Disclosed herein is a method for identifying compounds contributing to a sour odor emitting from an air conditioner, a method for artificially reproducing the detected sour odor and preparing a corresponding sour odor composition. Through the analysis method of the present invention, the compounds contributing to the sour odor emitted from an air conditioner may be identified and quantified. The detected sour odor may be reproduced from a combination of the compounds identified by the analysis method of the present invention. The reproduced sour odor may provide meaningful data required for development of an apparatus and a method for removing specific odors.

Abstract: A detecting method using an IMS apparatus with a preconcentrator outside its inlet aperture. Analyte vapor is adsorbed during a first phase when substantially no gas is admitted to the reaction region. The preconcentrator is then energized to desorb the analyte molecules and create a volume of desorbed molecules outside the IMS housing. Next, a pressure pulser is energized momentarily to drop pressure in the housing and draw in a small sip of the analyte molecules from the desorbed volume through the aperture. This is repeated until the concentration of analyte molecules in the desorbed volume is too low for accurate analysis, following which the apparatus enters another adsorption phase.

Abstract: The present invention provides various biomarkers of amyotrophic lateral sclerosis (ALS). The present invention also provides various methods of using the biomarkers, including methods for diagnosis of ALS, methods of determining predisposition to ALS, methods of monitoring progression/regression of ALS, methods of assessing efficacy of compositions for treating ALS, methods of screening compositions for activity in modulating biomarkers of ALS, methods of treating ALS, as well as other methods based on biomarkers of ALS.

Abstract: The present invention comprises methods for determining the presence, amount, or concentration of analytes of interest including Vitamin D and other secosteroids from biological samples, through derivatization, with improved speed and ease of analysis and improved sensitivity to mass spectrometry. In a preferred embodiment, the present invention comprises methods for determining the presence, amount, or concentration of analytes of interest, including Vitamin D and other secosteroids from whole human blood, through derivatization, and using a plasma collection device to facilitate collection, separation, and preparation of the sample for derivatization and analysis.

Abstract: Featured are a new class of reporter genes including reporter compositions as well as methods, MRI systems and MRI imaging kits related thereto. The genes according to the present invention provide MR contrast when the sample/subject is irradiated at a specific off-resonance radio-frequency (RF frequency), where the contrast mechanism utilizes chemical exchange saturation transfer (CEST) technique for imaging.

Abstract: Methods and systems for processing samples fixed to a porous substrate generally comprising, a compressor defining one or more fluid isolation areas, a support, for the porous substrate, having an opening corresponding to one or more of the fluid isolation areas of the compressor, an actuator that causes at least a portion of the compressor to press against the porous substrate, a fluid inlet having access to the fluid isolation area at least when the compressor is pressed against the porous substrate, and a fluid outlet to receive fluid, through the opening in the support corresponding to the fluid isolation area of the compressor, at least when the compressor is pressed against the porous substrate.

Abstract: In order to provide an analysis method that is capable of determining a glycan structure with high detection sensitivity, a method of the present invention includes the steps of: carrying out triple quadrupole mass spectrometry at various values of CID energy; creating an energy-resolved profile including yield curves representing relationships between (i) a value of the CID energy and (ii) measured amounts of specific types of product ions; preparing a reference profile, and identifying a glycan structure of a test material by comparing the energy-resolved profile with the reference profile.

Abstract: Processes and methods for creating a database of genomic samples from healthy human donors, methods that use the database to identify and correlate polymorphic genetic markers and other markers with diseases and conditions are provided.

Abstract: A method for analyzing a minute quantity of a material included in a different material is performed in short extraction treatment without taking a long time and the minute content is rapidly analyzed. The method of analyzing a minute content includes mounting on a sample table a sample piece of a material having a minute content of a different material to be analyzed; dropping onto the sample table a solvent for extracting the minute content from the sample piece, so that the solvent is disposed between the sample table and the sample piece; maintaining at room temperature the solvent between the sample table and the sample piece, and, with the solvent maintained between the sample table and the sample piece, extracting the material of the minute content from the sample piece; and analyzing the content extracted from the sample piece.

Abstract: Materials and methods for studying and modulating the interaction of carbohydrate-containing moieties with other species are described, in particular, small particles, e.g. clusters of metal or semiconductor atoms, which can be employed as a substrate for immobilising a plurality of ligands comprising carbohydrate groups. These “nanoparticles” can then be used to study carbohydrate mediated interactions, e.g. with other carbohydrates or proteins, and as therapeutics and diagnostic reagents.

Abstract: The present invention relates generally a method and apparatus for measuring multiple parameters in-situ in a sample collected from an environmental system via a single device. In one embodiment, the method includes collecting the sample from said environmental system via the single device, measuring a first parameter of the sample in-situ via the single device, adding a reagent tot the sample within the single device to create a reagent infused sample and measuring a second parameter of the sample in-situ via the single device using the reagent infused sample.

Abstract: Methods and apparatuses for analyzing proteins and other biological materials and xenobiotics within a sample. A specimen is generated, which may include an energy absorbent matrix. The specimen is struck with laser beams such that the specimen releases proteins. The atomic mass of the released proteins over a range of atomic masses is measured. An atomic mass window of interest within the range of atomic masses is analyzed to determine the spatial arrangement of specific proteins within the sample, and those specific proteins are identified as a function of the spatial arrangement. By analyzing the proteins, one may monitor and classify disease within a sample.

Abstract: We disclose the synthesis and use of chiral ionic liquids based on a substituted pentose, furanose, hexose, or pyranose sugar. The compounds and processes to make or use them are provided.

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.

Abstract: A method of differentiating among the presence of ductal carcinoma in situ in the breast, benign fibroadenoma of the breast, and non-cancerous breast tissue in a subject is disclosed. The method involves measuring the concentration of at least one protein biomarker selected from a group of forty-nine differentially expressed proteins in the saliva of persons with DCIS, or benign fibroadenoma, or in persons who are cancer-free. The resulting test data is compared to a reference panel. From the comparison the presence in the subject of either ductal carcinoma in situ of the breast, or benign fibroadenoma of the breast is determined.

Abstract: A method for matching each of a plurality of progenitor ion types to respective product or fragment ion types, comprising: generating the plurality of progenitor ion types over a time range by ionizing compounds eluting during the time range using an atmospheric pressure ion source; generating the product or fragment ion types within a pressure range of 750 mTorr to atmospheric pressure in an ionization chamber or first vacuum chamber; detecting abundances of the plurality of progenitor ion types and the product or fragment ion types using a mass analyzer; calculating a plurality of extracted ion chromatograms (XICs) relating to the detected abundances; automatically detecting and characterizing chromatogram peaks within each XIC; automatically generating synthetic analytical fit peaks; performing cross-correlation score calculations between each pair of synthetic analytical fit peaks; and recognizing matches based on the cross correlation scores.

Abstract: An apparatus for chemical separations includes a microfluidic substrate having an outlet aperture for outputting an eluent of a sample, a spray unit having an inlet to receive the eluent and an outlet to emit a spray of the eluent, and a force-applying unit. The spray unit has a deformable portion defining the inlet and having an elastic modulus that is lower than an elastic modulus of the microfluidic substrate. The force-applying unit, such as a spring, is disposed to urge the deformable portion in contact with the substrate to form a substantially fluid-tight seal.

Abstract: Methods are disclosed for using stable isotopes of carbon and nitrogen in hair and feces to predict disease in animals such as predicting the susceptibility of dairy cows to periparturient production-related metabolic diseases (PRMDs). Other methods that are disclosed are for using stable isotopes of carbon and nitrogen in blood components, erythrocytes and plasma proteins, to predict dairy cow susceptibility to PRMDS; yet other disclosed methods are for using stable isotopes of carbon and nitrogen in hair and feces of horses as a prognostic indicator after surgical or medical correction of gastrointestinal colic. Other methods that are disclosed also include using stable isotopes of carbon and nitrogen in blood components, erythrocytes and plasma proteins, of horses as a prognostic indicator before or after surgical or medical correction of gastrointestinal colic.

Abstract: This invention relates generally to methods and apparatus for desorption and ionization of analytes for the purpose of subsequent scientific analysis by such methods, for example, as mass spectrometry or biosensors. More specifically, this invention relates to the field of mass spectrometry, especially to the type of matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry used to analyze macromolecules, such as proteins or biomolecules. Most specifically, this invention relates to the sample probe geometry, sample probe composition, and sample probe surface chemistries that enable the selective capture and desorption of analytes, including intact macromolecules, directly from the probe surface into the gas (vapor) phase without added chemical matrix.