Abstract: The invention relates to a method for the spectrometric characterization of microorganisms, comprising: providing a test microorganism; acquiring spectrometric measurement data from the test microorganism under potential exposure to variance that is not based on taxonomic classification; selecting a classifier which is trained to determine the identity of a microorganism on a second taxonomic level; and applying the classifier to the measurement data in order to determine the identity of the test microorganism on the second taxonomic level, wherein the classifier is variance-conditioned in such a way that it largely or completely masks out the effect of variance in the characterization of the test microorganism on the second taxonomic level.

Abstract: The invention provides a method that gives direct information about the intervention of a potential drug on the secondary structure distribution of a targetbiomolecule, i.e., for a disease with misfolded protein, such as neurodegenerative diseases in a complex body fluid. The secondary structural change is monitored by vibrational spectroscopy. The method can be applied for prescreening of drug candidates for targeting of specific biomolecules. The effect of the drug on the secondary structure distribution is monitored label-free in real time and provides thereby direct information about the efficacy of the potential drug.

Abstract: The present disclosure is to provide a measurement chip, a measuring device, and a measuring method which can accurately estimate an analyte concentration with a simple configuration. A measurement chip may include a propagation layer, an introductory part, a drawn-out part and a reaction part. Through the propagation layer, light may propagate. The introductory part may introduce the light into the propagation layer. The drawn-out part may draw the light from the propagation layer. The reaction part may have, in a surface of the propagation layer where a reactant that reacts to a substance to be detected is formed, an area where a content of the reactant changes monotonously in a perpendicular direction perpendicular to a propagating direction of the light, over a given length in the propagating direction.

Abstract: One mode is a method for the structural analysis of an organic compound by MALDI mass spectrometry, including: a sample preparation process (S1) which includes preparing a sample by mixing a specimen containing an organic compound to be analyzed with a predetermined matrix at a mixture ratio within a range from 1:5 to 1:5000 in molar ratio; a mass spectrometry process (S3) which includes irradiating the prepared sample with a laser beam having a spot size equal to or smaller than 15 ?m to generate ions originating from a component of the specimen in the sample, and performing a mass spectrometric analysis of the generated ions; and an analyzing process (S4) which includes detecting, from a mass spectrum acquired in the mass spectrometry process, ions including product ions resulting from in-source decay, and estimating the structure of the organic compound to be analyzed based on information concerning the ions.

Abstract: Individual biological cells can be selected in a micro-fluidic device and moved into isolation pens in the device. The cells can then be lysed in the pens, releasing nucleic acid material, which can be captured by one or more capture objects in the pens. The capture objects with the captured nucleic acid material can then be removed from the pens. The capture objects can include unique identifiers, allowing each capture object to be correlated to the individual cell from which the nucleic acid material captured by the object originated.

Abstract: A method to detect transient binding of a substrate molecule of interest in solution to a molecular target includes selecting the substrate molecule of interest and the molecular target such that the substrate molecule of interest can transiently bind to the molecular target; placing one of a sample or a subject of interest in a magnetic resonance (MR) apparatus, the sample or the subject of interest containing the substrate molecule of interest so as to be in contact with the molecular target; providing magnetic labelling of non-exchangeable or slowly exchangeable MR sensitive nuclei of the substrate molecule of interest; receiving an MR signal from the MR sensitive nuclei of the solvent molecules using the MR apparatus; and analyzing the MR signal to obtain a quantity associated with the transient binding of the substrate molecule of interest to the molecular target.

Abstract: The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices.

Abstract: A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.

Abstract: In an example, a method for preparing a nucleotide solution includes flowing an aqueous solution from an initial solution storage of a sequencing instrument continuously through a container fluidically coupled to the sequencing instrument, the container comprising a nucleotide concentrate; and collecting the aqueous solution with nucleotide in a storage container.

Abstract: Described are compositions and methods for diagnosing acute exacerbations of chronic obstructive pulmonary disease (AECOPD). Multiple reaction monitoring mass spectrometry (MRM-MS) was used to quantify the amount of protein biomarkers in plasma samples from human subjects. The amount of the biomarkers in the sample can distinguish AECOPD from a stable or convalescent state of COPD, or from a subject without COPD.

Abstract: The present disclosure provides a method for sequencing nucleic acids. The method can include polymerase catalyzed incorporation of nucleotides into a nascent nucleic acid strand against a nucleic acid template, wherein the polymerase is attached to a charge sensor that detects nucleotide incorporation events. One or more non-natural nucleotide types that each produce a unique signatures at the charge sensor can be used to uniquely identify different nucleotides in the template nucleic acid.

Abstract: Provided herein are methods, kits, and compositions for use in the diagnosis and treatment of diseases. Peptoids recognized by Alzheimers disease specific antibodies are identified.

Abstract: Various embodiments are described herein for a system and a method for identifying a region of interest in tissue using mass spectrometry. An agent administration component can be provided to administer an exogenous agent to the tissue. A sampling unit can also be provided to acquire a sample from the tissue. The sample can then be provided to a high sensitivity analysis platform, such as a mass analyzer, to analyze the sample and determine a distribution of the exogenous agent or a by-product of the exogenous agent within the tissue based on the analysis. The analysis platform can then identify the region of interest based on the distribution of the exogenous agent or the distribution of the by-product.

Abstract: At least an embodiment addresses the problem of providing a SPR (surface plasmon resonance) or SPFS (surface plasmon-field enhanced fluorescence spectroscopy) immunoassay, which enables the measurement of whole blood, undergoes little fluctuations in measurement values, and can measure whole blood, serum and plasma in a single apparatus. At least an embodiment solves the above-mentioned problem by a SPR or SPFS immunoassay, which is an immunoassay utilizing SPR or SPFS, including an absorbance measurement step of measuring an absorbance of a sample, a mode setting step of setting a mode that corresponds to the result of the absorbance measured in the absorbance measurement step, and one or multiple step(s) for which treatment condition(s) has/have been set in accordance with the mode set in the mode setting step.

Abstract: Viruses and other bioagents are of high medical and biodefense concern and their detection at concentrations well below the threshold necessary to cause health hazards continues to be a challenge with respect to sensitivity, specificity, and selectivity. Ideally, assays for accurate and real time detection of viral agents and other bioagents would not necessitate any pre-processing of the analyte, which would make them applicable for example to bodily fluids (blood, sputum) and man-made as well as naturally occurring bodies of water (pools, rivers). We describe herein a robust biosensor that combines the sensitivity of surface acoustic waves (SAW) generated at a frequency of 325 MHz with the specificity provided by antibodies and other ligands for the detection of viral agents.

Abstract: Provided herein are methods for a novel bead-based next-generation “X-aptamer” selection scheme that extends aptamer technology to include X-modified bases, thus resulting in X-aptamers, at any position along the sequence because the aptamers are chemically synthesized via a split-pool scheme on individual beads. Also provides are application to a wide range of commonly used DNA modifications, including, but not limited to, monothioate and dithioate backbone substitutions. This new class of aptamer allows chemical modifications introduced to any of the bases in the aptamer sequence as well as the phosphate backbones and can be extended to other carbohydrate-based systems.

Abstract: Disclosed herein are methods and compositions for detection of target small molecules in a mixed sample by performing a competition assay between the target and a surrogate and subsequently detecting the complex types in a nanopore device. Disclosed herein are competition assays for detection of small molecules using a nanopore. Target molecules of a sufficient size (>20 kDa) when passed through a solid-state nanopore cause a change in the current impedance, translocation time, or other measurable parameter. In the event the target molecule is not sufficiently big, and thus does not cause a noticeable change, an additional molecule/reagent can be used to aid in detection. This detection reagent would bind to the small molecule or to the “capture ligand-molecule complex” (e.g. peptide detection is aided by a monoclonal antibody (mAb) that recognizes a peptide/aptamer complex).

Abstract: Provided herein are products and processes for the amplification, detection and sequencing of short-stranded nucleic acid in the presence of a high background of long-stranded genomic material (e.g., host or maternal nucleic acids). The methods rely on the use of inside and outside primers introduced at varying concentrations, as well as universal amplification reactions that preferentially amplify short, low copy number nucleic acid.

Abstract: Disclosed herein are systems and methods for mass spectrometry using laserspray ionization (LSI). LSI can create multiply-charged ions at atmospheric pressure for analysis and allows for analysis of high molecular weight molecules including molecules over 4000 Daltons. The analysis can be solvent-based or solvent-free. Solvent-free analysis following LSI allows for improved spatial resolution beneficial in surface and/or tissue imaging.

Abstract: The present invention provides a new method for recombinantly expressing a protein of interest, such as the human BRCA2 protein, BLM protein, CtIP protein, or EXOI protein, by expressing the protein in the form of a fusion protein comprising two maltose-binding protein (MBP) or glutathione-S-transferase (GST) tags. The expression cassette useful for this method and the fusion protein produced by this method are also described.

Abstract: The present invention relates to a method of measuring polysorbates, such as polysorbate 80, using Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR).

Abstract: A method for analyzing water toxicity, the method including: exposure experiment, sample collection, transcriptome detection, metabolome detection, screening of differentially expressed genes, screening of differentially expressed metabolites, and identification of commonly changed biological pathways in both the transcriptome and the metabolome.

Abstract: The invention provides a method for preparing a compound or a product having one or more characteristics that meet or exceed a user specification, the process comprising the step of selecting a first combination of chemical inputs, optionally together with physical inputs, and supplying those inputs to a reaction space, thereby to generate a first product; analysing one or more characteristics of the product generated; comparing the one or more characteristics against a user specification; using a genetic algorithm selecting a second combination of chemical inputs, optionally together with physical inputs, wherein the second combination differs from the first combination, and supplying those inputs to the reaction space, thereby to generate a second product; analysing one or more characteristics of the second product generated; comparing the one or more characteristics generated against the user specification; repeating the selecting and analysing steps for further individual combinations of chemical and/or p

Abstract: A method of comparative ligand mapping to identify peptide ligands presented by MHC positive cells that distinguish an infected/transfected cell from an uninfected/non-transfected cell is disclosed.

Abstract: Techniques for characterizing a molecule are described herein. In one example, a portion of the molecule is trapped in a nanopore, a variable voltage is applied across the nanopore until the trapped portion of molecule is moved within the nanopore, and the molecule is characterized based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore.

Abstract: The present disclosure provides technologies for achieving cell patterning, as well as patterned cell arrays achieved with such technologies. Provided apparatus and methods are useful in a variety of contexts and provide particular advantages with respect to assessing living cell arrays and/or their responsiveness to stimuli, including identifying and/or characterizing complex cellular responses.

Abstract: A method for the parallel identification of one or more metabolite species within a biological sample is provided. The method comprises producing a first spectrum by subjecting the sample to a nuclear magnetic resonance analysis, the first spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; producing a second spectrum by subjecting the sample to a mass spectrometry analysis, the spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; subjecting each of the individual spectral peaks to a statistical pattern recognition analysis to identify the one or more metabolite species contained within the sample; and identifying the one or more metabolite species contained within the sample by analyzing the individual spectral peaks of the mass and nuclear magnetic resonance spectra.

Abstract: A method for assaying phenotypic similarity or dissimilarity between organisms is disclosed in which a composite sample of admixed first and second samples is provided. The first, standard sample contains average concentrations of compounds of molecular mass less than about 1000 AMU present in the organism species. The second, assay sample contains compounds of having a similar molecular mass present in the organism whose phenotype is to be assayed. The constituents of both samples are (i) in a liquid medium and (ii) each compound of a sample has the same, first and second respective amounts of first and second stable isotopes of a first atom. The composite sample is mass spectroscopically analyzed for analytes, with the ratio of first to second isotope being determined for each analyte, along with a composite sample median ratio. The ratios for each analyte are compared to the median, with outlying ratios indicating dissimilarity.

Abstract: Disclosed here is a method for measuring the kinetics (i.e., the molecular flux rates-synthesis and breakdown or removal rates) of a plurality of proteins or organic metabolites in living systems. The methods may be accomplished in a high-throughput, large-scale automated manner, by using existing mass spectrometric profiling techniques and art well known in the fields of static proteomics and static organeomics, without the need for additional biochemical preparative steps or analytic/instrumental devices.

Abstract: The present invention provides a method for assessing the presence and risk of developing type 2 diabetes, cancer of all sites, or cardiovascular disease in a subject by detecting sequence variation in one or more genes such as carboxypeptidase E (CPE) and insulin degradation enzyme (IDE). A kit, array, and device useful for such a method are also provided. In addition, the present invention provides a method for treating type 2 diabetes, cancer of all sites, or cardiovascular disease in patients who have been tested and shown to have the pertinent genetic variations.

Abstract: The invention relates to an additive which can be added to buffers used in nucleotide detection processes and improved methods of nucleic acid sequencing using this additive. In particular the invention relates to use of the additive to improve the efficiency of fluorescence-based multiple cycle nucleic acid sequencing reactions.

Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes compositions and methods of nucleic acid sequencing using a single polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid attached proximal to a nanopore, and nucleotide analogs in solution comprising charge blockade label that are attached to the polyphosphate portion of the nucleotide analog such that the charge blockade labels are cleaved when the nucleotide analog is incorporated into a growing nucleic acid and the charge blockade label is detected by the nanopore to determine the presence and identity of the incorporated nucleotide and thereby determine the sequence of a template nucleic acid.

Abstract: A peptide is cleaved at various bonding sites into oligopeptides or similar fragments by digestion using proteinase K (S3). The obtained fragments are separated according to their kinds by reversed-phase chromatography and fractionated (S4), and each fragment is subjected to mass spectrometry to determine its mass (S6). For each peptide fragment, an amino-acid composition is calculated from the measured mass, and amino-acid sequence candidates are deduced from that composition. The amino-acid sequence candidates of the other peptide fragments are searched for a fragment having an overlapping portion available for combining two peptide fragments to obtain amino-acid sequence candidates of the original peptide (S7). The masses of the amino-acid sequence candidates are compared with a measured mass derived from a result of mass spectrometry of the original peptide to select a correct sequence (S6 and S8).

Abstract: In a first location of a mass spectrometer, a plurality of ionized molecules of an ion source are selected that have mass-to-charge ratios within a mass-to-charge ratio window width. The plurality of selected ionized molecules are transmitted from a first to a second location. Reagent ions are transmitted to the second location to reduce a charge state of one or more of the plurality of selected ionized molecules. A mass analyzer is used to analyze the plurality of reduced ionized molecules and produce a mass spectrum. A compound is identified from a peak of the spectrum that has a mass-to-charge ratio less than or equal to the highest mass-to-charge ratio in the window width if the noise is multiply charged and greater than the highest mass-to-charge ratio in the window width if the noise is singly charged.

Abstract: The present disclosure relates to systems and methods for high efficiency electronic sequencing of nucleic acids and molecular detection. In an example embodiment of the instant disclosure, the NanoNeedle may be utilized to detect a change in impedance resulting from the modulation of the counter ion concentration or Debye length associated with a biomolecule of interest, such as DNA or protein, for an application of interest, such as DNA sequencing, DNA hybridization, or protein detection.

Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.

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: The present disclosure provides methods an compositions for the detection of plant exposure to plant pathogens. The methods relate to determining the identity of peptides isolated from the surface of plant starch granules.

Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: The invention relates to a spatially encoded polymer matrix in the form of a bead or a granule for combinatorial solid phase synthesis, assaying, functional proteomics and diagnostic use. Compositions of such beads or granules are also provided. Each beaded polymer matrix of the composition comprises a plurality of spatially immobilized particles. The spatial immobilization of the particles confers on each beaded polymer matrix a “fingerprint” which enables identification of unique beads in a population of beads. The unique identification of individual beads makes it possible to perform combinatorial chemistry strategies while logging individual chemical transformation. Also provided are methods for detection of relative positions in space of particles, methods for generating matrices, methods for distance matrix determination, methods for identifying individual matrices and devices for recording and storing images of matrices.

Abstract: Nanochannel arrays that enable high-throughput macromolecular analysis are disclosed. Also disclosed are methods of preparing nanochannel arrays and nanofluidic chips. Methods of analyzing macromolecules, such as entire strands of genomic DNA, are also disclosed, as well as systems for carrying out these methods.

Abstract: The present invention provides copolymers that facilitate nucleic acid analysis, compositions that comprise such copolymers, and methods for making or using such copolymers.

Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.

Abstract: The present invention provides a method for detecting modified LDL, abnormal cells or bacteria using an intermolecular interaction analysis method, in which a region involved in ligand recognition by a receptor is expressed, without modification or as a biotinylated protein, in cells or in a test tube, and thereafter, the expressed region or the expressed biotinylated protein is immobilized via avidin or streptavidin to a solid phase while the orientation thereof is maintained, and the immobilized protein is utilized; and a kit for detecting the modified LDL or the like.

Abstract: An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed.

Abstract: The present invention relates to methods of screening for expression of a soluble candidate protein within an expression library of candidate proteins. The method involves fusing each candidate protein in the library to a peptide substrate and identifying cells that express soluble candidate protein by detecting enzymatic modification of the peptide 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.