Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Provided are methods for measuring the inherent stability of intrachain disulphide-containing domains (e.g., antibody variable domains) and for optimizing the positioning of intrachain disulphide-containing domains within a protein (e.g., a multispecific binding protein, e.g., a DVD-Ig). Also provided are methods of making multispecific binding proteins (e.g., DVD-Ig molecules) comprising two or more antibody variable domains in which the antibody variable domains are optimally positioned within the multispecific binding proteins to enhance stability of the multispecific binding protein. Multispecific binding proteins optimized using the methods disclosed herein are also provided.

Abstract: The invention relates to novel peptidase substrates of formula (I): wherein R0, R1, R2, R3, R4, R5 and n are as defined in claim 1, and a method for detecting the presence of a catalytically active peptidase, by means of one of these substrates.

Abstract: The present Invention provides a method for diagnosing and/or prognosing Parkinson's disease dementia (PDD) comprising the step of detecting O-glycosylation. in a protein comprising a Ser/Thr motive, in particular Serpin A1, and/or the level of sialic acid on a protein comprising a Ser/Thr motive, in particular Serpin A1. Further, the present invention relates to a molecule for detecting O-linked glycomoieties in a protein comprising a Ser/Thr motive, in particular Serpin A1, and/or glycosylated i so forms of a Ser/Thr motive comprising protein, in particular Serpin A1, for use in the diagnosis and/or prognosis of Parkinson's disease dementia (PDD), Furthermore, the present invention relates to means for diagnosing and/or prognosing Parkinson's disease dementia (PDD) and a kit for diagnosing and/or prognosing Parkinson's disease dementia (PDD).

Abstract: The present invention provides methods for reducing the level of amyloid beta protein in a cell or tissue, the methods generally involving contacting the cell or tissue with an agent that reduces cystatin C levels and/or activity. The present invention provides methods for treating Alzheimer's disease (AD), and methods for treating cerebral angiopathy, in an individual, the methods generally involving administering to an individual having AD a therapeutically effective amount of an agent that reduces cystatin C levels and/or activity. The present invention further provides methods for identifying an agent that reduces cystatin C levels and/or activity.

Abstract: Provided herein is a large immuno-sorbent surface area assay (ALISSA) for the rapid and sensitive detection of botulinum neurotoxins (BoNTs) and anthrax toxin. This assay is designed to capture a low number of toxin molecules and to measure their intrinsic protease activity via conversion of a fluorogenic or luminescent substrate. Also provided herein are novel peptides that can be specifically cleaved by BoNT and novel peptides that are resistant to cleavage by BoNT. The combination of these cleavable and control peptides can be used for implementation of an exemplary ALISSA used to specifically detect BoNT enzymatic activity. Furthermore, the ALISSA as described herein may also be used in a column based format for use in a high-throughput system for testing large quantities of samples.

Abstract: The present invention relates to compositions and methods for testing agents (e.g., Clostridium botulinum neurotoxin (BoNT) detection and analysis). In particular, the present invention relates to the use of Human induced pluripotent stem (hiPS) derived cells for agent detection and analysis.

Abstract: The present invention provides methods of identifying compounds that decrease proline hydroxylation of the alpha subunit of hypoxia inducible factor (HIF?).

Abstract: The present invention provides a compound that can utilize hydrogen isotope and, at the same time, can quantify multiplexed samples at one time, as well as decreasing the cost for synthesis of the labeling agent. In addition, the present invention provides a novel method for quantitatively analyzing protein and peptide analytes having different quantities form each other using the labeling agent, wherein y-type fragment ions having a high mass which comprises the analyte remained after coupling the labeling agent with the analyte and then removing a part of the labeling agent through tandem mass spectrometry are utilized to conduct the quantitative analysis.

Abstract: The invention relates to the field of biotechnology. The method for determining the spatial and temporal distribution of the activity of a proteolytic enzyme in an in vitro heterogeneous system, such as blood or blood plasma, involves the introduction of a luminescent, fluorogenic or chromogenic substrate into a sample with the subsequent release of a detectable tag as the proteolytic enzyme cleaves the substrate, and the recording of the optical characteristics of the sample, which makes it possible to assess the spatial and temporal distribution of the activity of the enzyme. The device for the implementation of the above method comprises an in vitro system, a means for illuminating the sample, a recording means and a control means. A method for diagnosing homeostatic imbalances according to a change in the spatial and temporal distribution of the activity of a proteolytic enzyme in a blood sample is also proposed.

Abstract: A method for measuring an analyte is described that includes the steps of: i) preparing a reagent (D) in which an enzyme (A) and an enzyme (B) coexist in the absence of the analyte; ii) bringing the analyte into contact with the enzyme (A) and the enzyme (B) so that the enzyme (A) acts on the analyte to produce a product (E), on which the enzyme (B) does not substantially act, from the analyte; iii) producing a product (C) by allowing the enzyme (A) or an enzyme (F) that is different from the enzyme (A) that acts on the analyte to produce a product (C) to act on the analyte and/or the product (E); and iv) detecting the product (C) by the enzyme (B).

Abstract: The invention relates to novel compositions and methods for the detection of enzymes using the nuclear reorganization energy, ?, of an electron transfer process.

Abstract: The present invention relates to a method for detecting at least one direct thrombin inhibitor in a sample other than citrate plasma, comprising the step of mixing a sample containing a thrombin inhibitor with a composition containing thrombin under conditions which allow the thrombin to release a detectable substance from a chromogenic substrate.

Abstract: This disclosure is directed to methods and compositions to inhibit MASP protein activity using small molecule inhibitors. In one aspect, the disclosure is directed to methods for identifying inhibitors of MASP protein activity, including methods of screening capable of inhibiting MASP protein activity.

Abstract: Compositions and methods which indicate an increased risk for pancreatic carcinoma in a test subject are disclosed.

Abstract: A method for screening for variant peptides uses mass spectrometry (MS). A system and a kit may be used for performing the method. Proteins in a sample are digested to form a defined series of peptides. The defined series of peptides are ionized. The ionized species are subjected to collision induced dissociation. Species of known mass/charge ratio are detected to confirm the presence of the protein variant in the original sample.

Abstract: The invention relates to the field of disorders of the peripheral or central nervous system, in particular, Alzheimer's disease, and the prevention and/or treatment thereof. In particular, the invention relates to ARF6 and/or ARF6 effector proteins as new targets in Alzheimer's disease, and based thereon, screening methods for compounds that reduce amyloid beta peptide formation in mammalian cells by affecting ARF6-mediated endosomal sorting.

Abstract: The invention relates to variants of plasminogen and plasmin comprising one or more point mutations in the catalytic domain which reduce or prevent autocatalytic destruction of the protease activity of plasmin. Compositions, uses and methods of using said variants of plasminogen and plasmin are also disclosed.

Abstract: Specific peptides, and derived ionization characteristics of those peptides from Death Receptor 5 (DR5) protein are provided that are particularly advantageous for quantifying the DR5 protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.

Abstract: Methods and kits for determining if one or more animals have mastitis and for monitoring animals and the quality of the milk they produce are disclosed. Kits and test assays disclosed are used to determine the quantity of proteasomes and proteins thereof, the activity of proteasome enzymes, the quantity of proteasome bound and regulating proteins, and the quantity of ubiquinated protein. Components and reagents for use in the kits and assays are also disclosed.

Abstract: The invention relates to method for quantification of the absolute amount of allergen in an allergen sample comprising: a) providing a known amount of one or more allergen calibration standard peptide(s) having a sequence of amino acids which is identical with, and optionally unique for, a sequence to be found in the allergen to be quantified and optionally labelling said allergen calibration standard peptide(s), b) degrading the allergen sample to obtain a mixture of peptides, and optionally labelling said peptides with one or more labelling agent(s), wherein at least the peptides in the degraded allergen sample or the calibration standard peptides are labelled, and if both the peptides in the degraded allergen sample and the allergen calibration standard peptide(s) are labelled, the labelling agent(s) used for labelling the allergen calibration standard peptide(s) are different from the labelling agent(s) used for labelling the peptides of the degraded allergen sample, c) quantifying the absolute amount

Abstract: The invention relates to an arrangement, comprising a solid carrier and a matrix arranged on the solid carrier, said matrix comprising at least one enzymatically convertible or modifiable molecule and comprising at least one enzyme that can be released by the conversion or modification of the molecule, said enzyme being capable of converting at least one color-changing substrate located in the matrix and/or on the solid carrier.

Abstract: The current disclosure provides specific peptides, and derived ionization characteristics of the peptides from the estrogen receptor (ER), progesterone receptor (PR), and/or antigen Ki67 (Ki67) proteins that are particularly advantageous for quantifying the ER, PR, and/or Ki67 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.

Abstract: Aspects of the present disclosure include methods for detecting a low abundance protein and methods for identifying a site of N-glycosylation on a protein. In practicing methods according to certain embodiments, a eukaryotic cell is contacted with an isotopic labeling composition and isotopically labeled N-glycosylated peptides obtained from the eukaryotic cell are assessed by liquid chromatography-tandem mass spectrometry. A predetermined isotopic pattern in the mass spectrum is identified and amino acid sequences of the peptides containing the predetermined isotopic pattern are determined. Systems for identifying a predetermined isotopic pattern in mass spectra and determining amino acid sequences of peptides containing the predetermined isotopic pattern are also described.

Abstract: The present invention relates to methods of diagnosing, monitoring, and assessing treatment effects for neurological and neurodegenerative diseases and disorders, such as Alzheimer's Disease, early in the course of clinical disease or prior to the onset of brain damage and clinical symptoms. Methods of measuring the in vivo metabolism of biomolecules produced in the CNS in a subject are provided.

Abstract: The present invention relates to methods and compositions for monitoring, diagnosis, prognosis, and determination of treatment regimens in subjects suffering from or suspected of having a renal injury.

Abstract: A clickable cross-linker compound provides an easily scanned reporter ion for effective and efficient cross-linking and identification of intermolecular and intramolecular interactions of proteins and peptides.

Abstract: Enzyme substrates and associated technology of the present invention are provided. An enzyme substrate of the invention may comprise a biologically functional fluorescent dye and an enzyme-specific substrate moiety attached in such a way that the functionality of the functional dye is diminished. An enzymatic reaction may cleave at least a portion of the substrate moiety from the enzyme substrate to provide a more functional product dye. This product dye may be nonfluorescent or weakly fluorescent, in general, and relatively fluorescent, in a particular condition, such as when bound to a partner biological molecule or an assembly of partner biological molecules. An enzyme substrate of the present invention may thus be useful in fluorescence detection, and/or in any of a variety of useful applications, such as the detection of enzymatic activity in a cell-free system or in a living cell, the screening of drugs, or the diagnosis of disease.

Abstract: According to some embodiments, a method selects one or more inflammatory markers to evaluate. The one or more inflammatory markers selected from the group consisting of iNOS, COX-2, TNF-alpha, NO, PGE2, IL-6, and IL-1?. The method determines a first expression level and a second expression level of the one or more inflammatory markers. The first expression level is associated with a positive control sample comprising a type of human macrophages. The second expression level is associated with a test sample obtained by exposing a food product to a digest, the type of human macrophages, and a pro-inflammatory compound. The method performs a comparison between the first expression level and the second expression level and designates the food product according to an anti-inflammatory standard based on the comparison.

Abstract: The inventors have identified several proteases and a protease inhibitor that are overexpressed in ovarian cancer tumors. They have developed monoclonal antibodies against the proteins and shown that they can be detected in serum and the levels of the proteins in serum fluctuate during cancer treatment. They have shown that serum assays for the proteases and protease inhibitor can be used for early detection of ovarian cancer, and for monitoring cancer treatment.

Abstract: The methods described herein enable the evaluation of compounds on subjects to assess their therapeutic efficacy or toxic effects. The target of analysis is the underlying biochemical process or processes (i.e., metabolic process) thought to be involved in disease pathogenesis. Molecular flux rates within the one or more biochemical processes serve as biomarkers and are quantitated and compared with the molecular flux rates (i.e., biomarker) from control subjects (i.e., subjects not exposed to the compounds). Any change in the biomarker in the subject relative to the biomarker in the control subject provides the necessary information to evaluate therapeutic efficacy of an administered drug or a toxic effect and to develop the compound further if desired. In one aspect of the invention, stable isotope-labeled substrate molecules are administered to a subject and the label is incorporated into targeted molecules in a manner that reveals molecular flux rates through one or more metabolic pathways of interest.

Abstract: System and method for detecting and measuring chemical perturbations in a sample. The system and method are useful for non-invasive pH monitoring of blood or blood products sealed in storage bags.

Abstract: The stabilization of a hydrolytic enzyme in a liquid preparation is to be improved through a component that stabilizes the hydrolytic enzyme. This is accomplished by a method for adapting a hydrolytic enzyme to a component that stabilizes the hydrolytic enzyme, comprising the following method steps: a) providing a hydrolytic enzyme (starting enzyme) and a component that stabilizes the hydrolytic enzyme and that comprises a reversible inhibitor of the hydrolytic enzyme; b) changing the amino acid sequence of the hydrolytic enzyme in at least one position, by substitution, deletion or insertion; c) determining the relative activity of the hydrolytic enzyme from step b) and the relative activity of the starting enzyme in a liquid preparation; d) selecting the hydrolytic enzyme that has a reduced relative activity by comparison with the relative activity of the starting enzyme.

Abstract: The invention disclosed herein generally relates to methods and compositions for inhibiting proteasome activity comprising a syrbactin compound having the structure of Formula I or II:

Abstract: This invention relates, e.g., to a method for determining if a subject has myocardial ischemia, comprising (a) providing a blood sample obtained from a subject suspected of having myocardial ischemia; (b) determining in the sample the amount of one or more of the following proteins: (i) Lumican and/or (ii) Extracellular matrix protein 1 and/or (iii) Carboxypeptidase N; and (c) comparing the amount(s) of the protein(s) to a baseline value that is indicative of the amount of the protein in a subject that does not have myocardial ischemia, wherein a statistically significantly increased amount of the protein(s) compared to the baseline value is indicative of myocardial ischemia. Other proteins indicative of myocardial ischemia are also described, as are methods for treating a subject based on a diagnostic procedure of the invention, and kits for carrying out a method of the invention.

Abstract: The present disclosure relates to biomarkers of preterm birth, biomarkers of term birth, and methods of use thereof. In particular, the present disclosure provides methods of determining whether a pregnant woman is at an increased risk for premature delivery. The present disclosure further provides methods for decreasing a pregnant woman's risk for premature delivery.

Abstract: This method for inhibiting protease in a biological sample containing pancreatic juice components inhibits protease enzyme activity in the biological sample by adding at least one type of protease inhibitor having a sulfonyl fluoride group to the biological sample containing pancreatic juice components. In addition, this protease inhibitor for a biological sample containing pancreatic juice components is a compound having a sulfonyl fluoride group, has protease inhibitory activity, and is added to a biological sample containing pancreatic juice components in order to inhibit protease present in the biological sample. Moreover, this kit for preserving a biological sample containing pancreatic juice components contains at least one type of protease inhibitory having a sulfonyl fluoride group, and is used to store a biological sample containing pancreatic juice components.

Abstract: Embodiments of the present invention are directed to articles of manufacture, devices, methods and apparatus for performing liquid chromatography featuring a chromatographic sorbent having one or more pentafluorophenyl groups, wherein said one or more pentafluorophenyl groups are a bonded phase on a sorbent selected from the group comprising silica, organic polymers or hybrid organic silane material and said pentafluorophenyl groups are in a mono-, bi-, and tridentate forms.

Abstract: The present invention provides a method for determining the amino acid polymorphisms of heavy gamma chain of immunoglobulins G by a proteomic approach. This method distinguishes the immunoglobulins of the mother and those of the newborn in a blood sample obtained during the first months of the child's life. The invention also relates to the use of this method in the early diagnosis of vertically transmitted diseases in the neonate. The invention also provides peptides distinctive of G3m and IGHG3 alleles, and a kit comprising said peptides.

Abstract: A method for determining the activity of proteases is provided. Fluorogenic substrates from which the fluorogen 7-amino-4-trifluoromethylcoumarin is eliminated proved to be particularly advantageous for the activity measurement. These substrates make it possible for measurement in microtiter plates with a fluorescence reader and thus for the fluorimetric determination of such enzyme activities in blood serum.

Abstract: A diagnostic test kit for detecting the presence or quantity of an enzyme or enzyme inhibitor is provided. The diagnostic kit utilizes substrate conjugates to facilitate the detection of the enzyme or enzyme inhibitor via direct detection of the substrate and/or a product formed in an enzyme-catalyzed reaction of the substrate. The substrate conjugates include a substrate joined (e.g., covalently bonded, physically adsorbed, etc.) to a reporter. In one embodiment, for example, a peptide, protein, or glycoprotein substrate is joined to a reporter (e.g., dyed latex particle). In this embodiment, the substrate provides a cleavage target for an enzyme. Specifically, upon contacting the substrate conjugate, the enzyme catalyzes a reaction with the substrate and forms a product conjugate that includes the product of the enzyme catalyzed reaction joined to the reporter. The signal exhibited by the reporters may then be used to indicate the presence or quantity of an enzyme or enzyme inhibitor within the test sample.

Abstract: Methods for multiplexed delivery of agents to a solid tissue in vivo followed by assessment of efficacy with mass spectrometry are described.

Abstract: An immobilized enzymatic reactor can include a wall defining a chamber having an inlet and an outlet; a solid stationary phase covalently linked to an enzyme and disposed within the chamber; and a pressure modulator in fluid communication with the chamber and adapted to support continuous flow of a liquid sample comprising a polymer analyte through the inlet, over the solid stationary phase, and out of the outlet under a pressure between about 2,500 and 35,000 psi. In one example, the solid stationary phase includes inorganic/organic hybrid particles in an ultra performance liquid chromatography system, the enzyme is a protease, and the polymer analyte is a polypeptide. The immobilized enzymatic reactor can prepare an analyte for applications such as for hydrogen deuterium exchange mass spectrometry.

Abstract: Assay methods and systems use enzymatic cleavage resulting from protein-protein interaction to modulate (activate or inactivate) a reporter.

Abstract: The present invention relates to a method for determining the presence or absence of a microorganism, said method including the steps of: 1) providing an enclosure containing a liquid or semi-solid phase consisting of a biological medium capable of containing a living form of said microorganism, nutritional elements, and an enzymatic substrate which is specific to said microorganism and which can be metabolised into at least one VOC metabolite, and a gaseous phase adjacent to said liquid or semi-solid phase; 2) exposing at least said liquid or semi-solid phase to conditions that are propitious for said microorganism to metabolise said enzymatic substrate into a molecule of said VOC metabolite; and 3) determining, by optical transduction, the presence or absence of said VOC metabolite, characterised in that the latter interacts with a nanoporous matrix, said matrix being implemented in a form that is separate from said enzymatic substrate, and in that the detection, by optical transduction, of a change in the

Abstract: A method and a biomarker for detecting of acute kidney injury is provided, wherein the method of the present comprises the following steps: detecting a soluble form of hemojuvelin in a sample obtained from a subject, wherein when the soluble form of hemojuvelin is present in the sample, the subject is identified as having acute kidney injury.

Abstract: A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

Abstract: Compositions comprising hydroxytyrosol-containing formulations and treatment regiments comprising hydroxytyrosol and/or oleuropein and chemotherapeutic agents are disclosed. Compositions and/or regiments may optionally include the administration of vitamins, minerals, and anti-oxidants. Methods for using these compositions and treatment regimens for treating subjects for diseases, such as a malignancy, and for inducing or enhancing angiogenesis, treating or preventing oxidative stress, for treating or preventing high glucose-induced dysfunction, treating or preventing chemotherapy-induced dysfunction, and for improving cell viability are provided. Various methods for use of the hydroxytyrosol compositions for inhibition of lysine specific demethylase 1 (LSD1) in various cancers are also provided.

Abstract: Peptides from the Insulin-Like Growth Factor 1 Receptor (IGF-1R) protein are provided that are particularly advantageous for quantifying the IGF-1 R protein directly in biological samples, such as samples fixed in formalin. The ionization characteristics of the peptides also are disclosed. The peptides may be used in Selected Reaction Monitoring (SRM) mass spectrometry methods, also referred to Multiple Reaction Monitoring (MRM) mass spectrometry methods. The samples are chemically preserved and fixed, such as tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample may be prepared from the biological sample and the IGF-IR protein is quantitated by the method of SRM/MRM mass spectrometry by quantitating one or more of the described peptides.

Abstract: The present invention provides a method of pretreating a sample containing a glycated amine as an analyte, thereby enabling highly reliable measurement of a glycated amine. A glycated amino acid in the sample is degraded by causing a fructosyl amino acid oxidase (FAOD) to act thereon, and thereafter, a FAOD further is caused to act on the glycated amine as the analyte in the sample to cause a redox reaction. The amount of the glycated amine is determined by measuring the redox reaction. The substrate specificity of the FAOD caused to act on the glycated amino acid may be either the same as or different from that of the FAOD caused to act on the glycated amine. When using the same FAOD, a FAOD is caused to act on the glycated amino acid to degrade it, and thereafter, the sample is treated with a protease to inactivate the FAOD and also to degrade the glycated amine.