Abstract: The present invention provides methods for identifying candidate biomarkers in the plasma microparticle proteome. It also provides methods for isolating, identifying, and analyzing microparticles derived from plasma, particularly platelet-poor plasma.

Abstract: A compound that promotes the ubiquitination of a protein comprising the same or substantially the same amino acid sequence as the amino acid sequence shown by SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 or a partial peptide thereof or a salt thereof, or a salt thereof, a compound that promotes the degradation, by proteasome, of the protein or a partial peptide thereof or a salt thereof, or a salt thereof, and the like can be used as, for example, prophylactic/therapeutic agents for neurodegenerative disease. Also, a protein comprising the same or substantially the same amino acid sequence as the amino acid sequence shown by SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 or a partial peptide thereof or a salt thereof and the like are useful for screening for a compound having prophylactic/therapeutic action on neurodegenerative disease and the like or a salt thereof.

Abstract: The present invention relates to a method of peptide sequencing by MALDI (matrix-assisted laser desorption ionization) tandem mass spectrometry, which comprises the steps of chemically modifying a sample peptide with at least one chemical modification method selected from the group consisting of guanidination and esterification in order to change the ionization status of the peptide and performing mass spectrometry using a MALDI tandem mass spectrometer and programmed MALDI tandem mass spectrometry. The peptide sequencing method of the present invention is advantageous in that detection sensitivity of the peptide improves significantly and various daughter ions are detected uniformly, thereby enabling perfect de novo sequencing with tandem mass spectrometry only, without database search.

Abstract: Peptides can be derivatised such that, when ionised and analysed by mass spectrometry, those containing arginine residues give characteristic peak patterns. Peaks corresponding to arginine-containing peptides can therefore be selected from a mass spectrum in order to simplify and improve peptide analysis. Suitable labels give derivatised peptides that have the ability to form both a stabilised ion species ([P]+) and a protonated ion molecular species ([P+H]+) that differ by one average mass unit. A characteristic peak pattern is seen.

Abstract: The present invention provides a method for analyzing the C-terminal amino acid sequence of a peptide by applying reaction technique for successively releasing the C-terminal amino acids therefrom, which method can suppress, when releasing the C-terminal amino acids of the peptide in sequence, such as an undesirable side reaction as cleavage of peptide bond in the intermediate position of the peptide, and allows to carry out the chemical treatment thereof under widely applicable conditions. In the method according to the present invention, an alkanoic acid anhydride and a perfluoroalkanoic acid both of vapor phase, which are supplied from a mixture containing an alkanoic acid anhydride with a small amount of a perfluoroalkanoic acid added thereto, are allowed to act on a dry sample of the peptide to be examined in a dry atmosphere at a temperature chosen in a range of 15 to 60° C.

Abstract: The invention provides compositions and methods for screening individuals for the presence of G-protein coupled receptor (GPCR) variants. The compositions and methods are useful for determining clinical outcome of drug therapy or for tailoring drug therapy for the individual based upon the presence or absence of one or more GPCR variants in the subject.

Abstract: This invention provides for novel methods of identifying covalent modifications of an amino acid residue in a polypeptide chain by detecting mass differences.

Abstract: The present invention concerns methods and kits for diagnosing a disease condition characterized by non-physiological levels of hepcidin, comprising obtaining a tissue or fluid sample from a subject; contacting the sample with an antibody or fragment thereof that specifically binds to a polypeptide corresponding to the mid-portion or C terminus of a hepcidin protein, and quantifying the hepcidin level using an assay based on binding of the antibody and the polypeptide; wherein the non-physiological level of hepcidin is indicative of the disease condition. The present invention also concerns diagnostic methods and kits for applications in genetic technological approaches, such as for overexpressing or downregulating hepcidin. The present invention further concerns therapeutic treatment of certain diseases by treatment of subjects with hepcidin and agonists or antagonists of hepcidin.

Abstract: The invention relates to a composition for the stabilization of sulphur-containing amino acids and/or for the inhibition of the continuous formation of sulphur-containing amino acids in withdrawn blood, to the use of suitable substances and compositions therefor as well as optionally for the determination of sulphur-containing amino acids in blood, to a process for these purposes, as well as to a blood collecting device applied appropriately to these processes.

Abstract: The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS—MS), and/or MS3 analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide.

Abstract: Apparatus, methods, and program products are disclosed that classify spectral peaks in dissociation spectrum data and thereby improves the efficiency of molecular sequencing.

Abstract: Systems and methods of identifying molecules of polymers such as, for example, a nucleic acid, are described. The method involves centering a bias voltage across a pair of nanoelectrodes separated by a channel that corresponds to one of any of the energy differences between any two internal energy levels of a molecule of interest, and modulating the bias voltage with a modulation waveform while the molecule of interest is in the channel. An electrical signal characteristic of the molecule of interest is derived from the tunneling current between the nanoelectrodes, and the characteristic electrical signal is compared with known values of the signal for chemically-known molecules in order to identify the molecule of interest. Multiple pairs of nano-electrodes may be employed to identify more reliably a single molecule or multiple molecules.

Abstract: The present invention relates to a microfluidic system for processing a cell-containing liquid. The system includes a microfabricated substrate having an enrichment channel to prepare an enriched cell sample from the cell-containing liquid. A flow through member is in liquid communication with the enrichment zone. The flow through member substantially prevents cells of the cell-containing fluid from exiting the enrichment zone while allowing liquid of the cell-containing liquid to exit the enrichment zone. A gas actuator associated with the enrichment zone provides a gas pressure sufficient to move the enriched cell sample from the enrichment zone.

Abstract: The invention comprises a preparation of X-S-Cys-X, moiety, BRAUNMYCIN Î>>, where X maybe naturally linked peptide or glycan residues essential for iron-reductase activity, as well as methods of obtaining preparation from an iron-nitriloacetic acid iron binding jaw, BRAUNMYCIN8567, a component of a batch affinity column; and any interpretation derived from this outcome, like, but not limited to, detection of resistance, to iron-containing antibiotics, in DNA synthesizing cells.

Abstract: The present invention is to provide a system for measuring the similarity between protein profile matrices which is suitably used for predicting a protein three-dimensional structure.

Abstract: A compound linked to a solid support (R) through a divalent linker moiety (X) and which is represented by the following formula: is disclosed. In particular, the 1-hydroxybenzotriazole-6-carboxylic acid is directly linked to the support under mild conditions (i.e., in aqueous or organic solvents at neutral pH and at room temperature). The polymer bound 1-hydroxybenzotriazole-6-carboxylic acid can be used for the derivatization of amines as well as for single step amino group modification of proteins, peptides, and amines via acylation or sulfonylation reactions. A flow through device and method for the single step amino group modifications of proteins, peptides, and amines is disclosed. Also disclosed is a flow through device for the detection of amines in a sample. Additionally, a device and method for the detection of amines in a sample using 1-hydroxybenzotriazole-6-carboxylic acid is disclosed. In a preferred embodiment, the device is used to detect the presence of amines in a spoiled meat product.

Abstract: The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS—MS), and/or MS3 analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide.

Abstract: A method is disclosed whereby the concentration of a blood substitute, such as cross-linked hemoglobin, in a serum or plasma specimen is rapidly and accurately identified and quantified. The method further takes the measured concentration of the blood substitute and uses it to correct for its effect, if any, on a measured analyte concentration, e.g., serum/plasma total protein. Further, the method allows for the determination of the concentration of true hemoglobin in the presence of blood substitutes. The method is carried out in respect of samples contained in a primary or secondary labelled tube, or a pipette tip used to dispense serum or plasma in a blood analyzer.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The invention relates to protein-protein interactions and methods for identifying interacting proteins and the amino acid sequence at the site of interaction. Using overlapping hexapeptides that encode for the entire amino acid sequences of the linker domains of human P-glycoprotein gene 1 and 3 (HP-gp1 and HP-gp3), a direct and specific binding between HP-gp1 and 3 linker domains and intracellular proteins was demonstrated. The method of the present invention was further validated with Annexin. The present invention thus demonstrates a novel concept whereby the interactions between two proteins are mediated by strings of few amino acids with high and repulsive binding energies, enabling the identification of high affinity binding sites between any interacting proteins.

Abstract: Provided is a method for characterizing a polypeptide, which method comprises the steps of: (a) optionally reducing cysteine disulphide bridges in the polypeptide to form free thiols, and capping the free thiols; (b) cleaving the polypeptide with a sequence specific cleavage reagent to form peptide fragments; (c) optionally deactivating the cleavage reagent; (d) capping one or more ?-amino groups that are present with a lysine reactive agent; (e) analyzing peptide fragments by mass spectrometry to form a mass fingerprint for the polypeptide; and (f) determining the identity of the polypeptide from the mass fingerprint.

Abstract: In a method for producing a target substance by using a microorganism comprising culturing a microorganism having an ability to produce the target substance in a medium to produce and accumulate the target substance in the medium or cells of the microorganism and collecting the target substance from the medium or the cells of the microorganism, there are used, as the microorganism, a microorganism to which a methanol dehydrogenase gene is introduced, of which activities of hexulose phosphate synthase and phosphohexuloisomerase are enhanced and which is modified so that an ability to utilize methanol should be imparted or enhanced, and there is used a medium containing methanol as a carbon source.

Abstract: The present invention exploits the discovery that amounts of uracil and thymine metabolites, especially ?-aminoisobutyric acid, in various bodily fluids, especially urine, are correlated with the occurrence of epilepsy when compared to matched control subjects. Analytical and diagnostic protocols, including a novel high performance liquid chromatography system, for use in the invention are disclosed.

Abstract: A method of addressing and driving an electrode array includes the step of addressing one or more electrodes within the array using a plurality of row and column lines. In one aspect of the method, a value corresponding to a voltage is stored in a local memory associated with each electrode. The addressed electrodes are then driven at the voltages corresponding to the stored values. In another aspect of the method, a driving element associated with each addressed electrode is selectively coupled with a voltage line so as to charge the electrode with the voltage on the voltage line. The device and methods may be used in the synthesis of biopolymers such as oligonucleotides and peptides.

Abstract: The present invention provides a method for the analysis of a compound with amino group (e.g., an amino acid or peptide) contained in a sample and convenient manner with a high sensitivity. The compound with amino group in a sample containing the compound with amino group is labeled with a specific carbamate compound such as p-trimethylammonium anilyl-N-hydroxysuccinimidyl carbamate iodide to enhance the selectivity and sensitivity. The present invention is preferably used in conjunction with mass spectrometry such as MS/MS method to facilitate quantitative analysis. The present invention further provides labeling reagents for mass spectrometry.

Abstract: In proteomic research, it is often necessary to screen a large number of polypeptides for the presence of stable structure. Described herein are methods (referred to as MALDI MS-HX and SUPREX) for measuring the stability of proteins in a rapid, high-throughput fashion. The method employs hydrogen exchange to estimate the stability of quantities of unpurified protein extracts, using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. A method of quantitatively determining the stability of a test protein under native conditions is disclosed.

Abstract: A method for determining the amount of metal amino acid chelate present in various chelate compositions. FT-IR is used to determine the amount of free amino acid present. The bound amino acids may be in the form of an amino acid complex or an amino acid chelate. A total metal analysis and measurement of ligand quantity is then performed, from which the percent of metal amino acid chelate in the sample is calculated.

Abstract: Methods for determining whether a test agent inhibits a 17?-HSD3, the methods comprising: obtaining a recombinant host cell that expresses the 17?-HSD3; obtaining a reaction mixture comprising the 17?-HSD3, androstenedione, and the test agent; measuring the amount of testosterone in the reaction mixture by a scintillation proximity assay (SPA) using SPA beads conjugated with a testosterone-specific antibody, wherein when the amount of testosterone is lower in the presence of a test agent than in the absence of the test agent, the test agent is identified as an inhibitor of the 17?-HSD3.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: An addressable biologic electrode array includes an array of electrodes disposed on a support, the array of electrodes being selectively addressed and driven using a memory associated with each electrode of the array, the driven electrodes being driven at one of a plurality of stimulus levels by a source of electrical current or voltage external to the array.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time- of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: A biologic electrode array is formed on a semiconductor substrate. A matrix of electrode sites is disposed on the semiconductor substrate. A matrix of optical detectors is disposed beneath the electrode sites in the semiconductor substrate, wherein each electrode site is associated with a corresponding optical detector. The optical detectors are coupled to detection circuitry formed on the semiconductor substrate. The electrode sites may include slitted electrodes, punctuated electrodes, or optically transparent electrodes.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer, predict disease risk assessment, and develop therapeutic avenues against the disease.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer.

Abstract: A method for measuring cystine supersaturation of a patient urine sample as an indicator of the patient's risk for cystine stone formation has been found. A method for collecting a patient urine sample for assessment of cystine concentration and cystine supersaturation has also been found.

Abstract: The present invention relates to novel fluorescent dyes, novel fluorogenic and fluorescent reporter molecules and new enzyme assay processes that can be used to detect the activity of caspases and other enzymes involved in apoptosis in whole cells, cell lines and tissue samples derived from any living organism or organ. The reporter molecules and assay processes can be used in drug screening procedures to identify compounds which act as inhibitors or inducers of the caspase cascade in whole cells or tissues. The reagents and assays described herein are also useful for determining the chemosensitivity of human cancer cells to treatment with chemotherapeutic drugs. The present invention also relates to novel fluorogenic and fluorescent reporter molecules and new enzyme assay processes that can be used to detect the activity of type 2 methionine aminopeptidase, HIV protease, adenovirus protease, HSV-1 protease, HCMV protease and HCV protease.

Abstract: The present invention relates to a therapeutic composition and uses thereof for treatment of damaged tissue, wherein the composition comprises at least one extracellular matrix compound, at least one polar surface active lipid, and a plurality of amino acids having a molar ratio which is characteristic of human breast milk protein; and further comprises a fatty acid, gamma-amino butyric acid or L-carnitine.

Abstract: The object of the present invention is to measure a concentration of protein stably at a temperature not higher than 25° C., which is a possible ambient temperature at home, and further to expand the measurable concentration range while preventing an obstruction due to a suspending particle such as a bubble and the like, using a reagent prepared by mixing an acid in a solution containing tannin, tannic acid and m-galloyl gallic acid. By mixing the reagent in a solution to be detected to opacify the solution, intensities of at least a transmitted light or a scattered light of the solution to be detected is measured, and a protein concentration thereof is determined based on the intensity. The present invention also provides a method for measuring a concentration of a solution and a method of urinalysis, wherein a protein concentration is measured after measuring an angle of rotation.

Abstract: A fully automated, user-independent method is described for computer-mediated interpretation of data derived by mass spectrometry of an experimental peptide to identify and characterize a corresponding peptide sequence in a peptide database. The method identifies the corresponding sequence if it is present in the database, without the need for a skilled observer to choose from amongst a list of possible matches. By using an automated back-read process, the present method can uniquely identify a corresponding peptide sequence in a database based on a single matching peptide sequence. The method also permits mapping of mass spectral data to sequences in peptide or nucleotide databases for unambiguous identification of exons; determining a correct reading frame; identifying artefacts and errors in sequences; identifying mutations and polymorphisms; identifying post-translational modifications; and identifying exon-intron boundaries.

Abstract: A method for producing arrays by spacing a dispenser a distance from a surface of a support, dispensing a volume containing a compound in a single coupling step of less than 5 nl to occupy a localized area of less than 1 cm2 of the surface of the support, allowing the compound to bind directly or indirectly to the support and repeating the steps to produce an array of at least 100 ligands at a density of 1000 per cm2 or greater.

Abstract: The disclosure describes a method for detecting conditions indicative of sepsis. In one embodiment of the invention, an increase in the level of 3-chlorotyrosine or 3-bromotyrosine from the normal level in a sample of body fluid or tissue is indicative of early sepsis or infection. In another embodiment of the invention, the level of 3-chlorotyrosine or 3-bromotyrosine is measured or monitored to determine the response to therapeutic treatment of the infective condition in which a reduction in the level that existed prior to the treatment is an early sign or indication that the treatment is working in vivo. In a preferred embodiment, the method of the invention is illustrated in a clinically relevant mouse model of sepsis.

Abstract: A method for analyzing a plurality of amino acids in a fluid sample by a user is provided comprising the steps of introducing the sample into a buffer solution, passing the sample in the buffer solution through a separation column and setting a lithium ion concentration in the buffer to no more than 0.3 mols/L up to a time before ?-aminoisobutyric acid (?-AiBA) is eluted.

Abstract: A method for locating pattern matches in amino acids by use of various and sequential filters capable of determining inner sample pattern matches, inner group pattern matches, and word matching for purposes of further analysis or data mining. Filters include the use of a scoring scheme, comparison of scan numbers versus sequence of common ions to be MS/MS, and daughter ion subtraction for obtaining pattern match candidates.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of at least one disease state relative to recognition of the presence and/or the absence of the biopolymer.

Abstract: A method of addressing and driving an electrode array includes the step of addressing one or more electrodes within the array using a plurality of row and column lines. In one aspect of the method, a value corresponding to a voltage is stored in a local memory associated with each electrode. The addressed electrodes are then driven at the voltages corresponding to the stored values. In another aspect of the method, a driving element associated with each addressed electrode is selectively coupled with a voltage line so as to charge the electrode with the voltage on the voltage line. The device and methods may be used in the synthesis of biopolymers such as oligonucleotides and peptides.

Abstract: A method for producing polymer arrays by spacing a dispenser a distance from a surface of a support, dispensing a volume containing a monomer in a single coupling step of less than 5 nl to occupy a localized area of less than 1 cm2 of the surface of the support, allowing the monomer to bind directly or indirectly to the support and repeating the steps to produce an array of at least 100 polymer ligands at a density of 1000 per cm2 or greater.