Abstract: A data analysis method for a component separation/tandem mass spectrometer system, including first and second MS steps which data therefrom includes respective sample components (MS1-SC, MS2-SC), includes analyzing per sample a data set for MS2-SC to determine mass-to-charge ratio and retention index (m/z-RI) for each MS2-SC. m/z-RI for each MS2-SC is compared to a known compound library and matching MS2-SC removed from the data set, the remaining MS2-SC being candidate MS2-SC. Clusters are formed across the candidate MS2-SC, each having m/z-RI within respective ranges per cluster. For each sample within each cluster, MS1-SC within the cluster ranges are retrieved. For each cluster, at most one consensus MS1-SC represents each sample, with corresponding consensus MS2-SC and m/z-RI, and designated as a molecular ion or derivative thereof. Clusters are grouped by consensus RI and candidate clusters from each group are selected and correlated by consensus parameters with an unknown compound.

Abstract: A method for determining in a sample, by liquid chromatography/mass spectrometry, the presence, absence, or amount of one or more or a plurality of analytes is described. The method comprises subjecting the sample to an ionization source under conditions suitable to produce one or more ions detectable by mass spectrometry from each of the one or more of the analytes; measuring, by liquid chromatography/mass spectrometry, the amount of the one or more ions from each of the one or more analytes; and using the measured amount of the one or more ions to determine the presence, absence, or amount of each of the one or more or plurality of analytes in the sample.

Abstract: The present invention provides a method for diagnosing a disease or disorder selected from the group consisting of insulin resistance, a metabolic disorder, diabetes and pre-diabetes in a subject. The method comprises the step of determining the level of a compound represented by structural formula (VI): or a salt thereof. Compositions and method of making thereof are also described.

Abstract: The present invention provides a compound of formula (I) or a salt thereof and their use as a biomarker in assessing or monitoring kidney function in a subject, determining predisposition to developing reduced kidney function, classifying a subject according to level of kidney function, diagnosing or monitoring chronic kidney disease. Compositions and method of making of the compound of formula (I) are also described.

Abstract: The present invention provides a method for diagnosing a disease or disorder selected from the group consisting of insulin resistance, a metabolic disorder, diabetes and pre-diabetes in a subject. The method comprises the step of determining the level of a compound represented by structural formula (VI): or a salt thereof. Compositions and method of making thereof are also described.

Abstract: A method for determining in a sample, by mass spectrometry, the presence, absence or amount of one or more lipid species from one or more lipid classes is described herein. The one or more lipid classes are selected from the group consisting of wax esters (WE), squalene (SQ), triacylglycerols (TAG), diacylglycerols (DAG), free fatty acids (FFA), cholesteryl esters (CE), cholesterol (CH), and combinations thereof. The method includes a) subjecting the sample to an ionization source to produce one or more ions detectable by mass spectrometry from each of the one or more lipid species; b) measuring, by mass spectrometry, the amount of the one or more ions from each of the one or more lipid species; and c) using the measured amount of the one or more ions to determine the presence, absence or amount of each of the one or more lipid species.

Abstract: The present invention provides a method for diagnosing a disease or disorder selected from the group consisting of insulin resistance, a metabolic disorder, diabetes and pre-diabetes in a subject. The method comprises the step of determining the level of a compound represented by structural formula (VI): or a salt thereof. Compositions and method of making thereof are also described.

Abstract: The present invention provides a compound of formula (I) or a salt thereof and their use as a biomarker in assessing or monitoring kidney function in a subject, determining predisposition to developing reduced kidney function, classifying a subject according to level of kidney function, diagnosing or monitoring chronic kidney disease. Compositions and method of making of the compound of formula (I) are also described.

Abstract: The present invention provides a method for diagnosing a disease or disorder selected from the group consisting of insulin resistance, a metabolic disorder, diabetes and pre-diabetes in a subject. The method comprises the step of determining the level of a compound represented by structural formula (VI): or a salt thereof. Compositions and method of making thereof are also described.

Abstract: The present invention is based on the identification of a predominant ligand of CD8+ T cells that are responsible for type 1 diabetes. That ligand is islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP). Several CD8+ T cell-binding peptides from IGRP are identified, including the peptide comprising amino acids 206-214 of the IGRP sequence, which has high avidity to the most prevalent T cell receptor of pathogenic CD8+ T cells in autoimmune diabetes. The invention thus provides oligopeptide and polypeptide compositions comprising YLKTN(A/I/L/V)FL (SEQ ID NO:3), FLWSVFWLI (SEQ ID NO:4), (T/A)YY(G/T)FLNFM (SEQ ID NO:5), LR(L/V)(F/L)(G/N)IDLL (SEQ ID NO:6), KWCANPDWI (SEQ ID NO:7), and SFCKSASIP (SEQ ID NO:8). Also provided are oligopeptide compositions 8-10 amino acids in length and completely homologous with a mammalian IGRP, where the oligopeptide is capable of binding a human MHC class I molecule.

Abstract: Systems, methods, and computer-readable media for determining composition of chemical constituents in a complex mixture are disclosed. According to one aspect, a method for determining composition of chemical constituents in a complex mixture includes generating, using a separation tool and a mass spectrometer, separation and mass spectrometry data of a sample, wherein the separation data includes peak information and wherein the mass spectrometry data includes primary and secondary mass spectrometry data. The analysis results, including the generated separation and mass spectrometry data, are collected and stored. A chemical constituent of the sample is determined by comparing the analysis results to a library of information indicating characteristics of chemical entities, where the comparison is based on the separation and mass spectrometry information.

Abstract: Systems, methods, and computer-readable media for determining composition of chemical constituents in a complex mixture are disclosed. According to one aspect, a method for determining composition of chemical constituents in a complex mixture includes generating, using a separation tool and a mass spectrometer, separation and mass spectrometry data of a sample, wherein the separation data includes peak information and wherein the mass spectrometry data includes primary and secondary mass spectrometry data. The analysis results, including the generated separation and mass spectrometry data, are collected and stored. A chemical constituent of the sample is determined by comparing the analysis results to a library of information indicating characteristics of chemical entities, where the comparison is based on the separation and mass spectrometry information.

Abstract: The present invention is based on the identification of a predominant ligand of CD8+ T cells that are responsible eq for type 1 diabetes. That ligand is islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP). Several CD8+ T cell-binding peptides from IGRP are identified, including the peptide comprising amino acids 206-214 of the IGRP sequence, which has high avidity to the most prevalent T cell receptor of pathogenic CD8+ T cells in autoimmune diabetes. The invention thus provides oligopeptide and polypeptide compositions comprising YLKTN/A/I/L/V)FL, FLWSVFWLI, (T/A)YY/G/T)FLNFM, LR(LV)(F/L)(G/N)IDLL, KWCANPDWI, and SFCKSASIP. Also provided are oligopeptide compositions 8-10 amino acids in length and completely homologous with a mammalian IGRP, where the oligopeptide is capable of binding a human MHC class I molecule. Additionally, various methods of treating a mammal using the above compositions are provided, where the mammal is at risk for or has type 1 diabetes.