A method of performing targeted multiplexed mass spectrometry includes performing, at a mass spectrometer, a targeted MS3 analysis of an isobaric tag-labeled target analyte included in a multiplex sample eluting from a column. The targeted MS3 analysis is performed during an acquisition segment scheduled based on an expected retention time of the isobaric tag-labeled target analyte. The method further includes performing, during the acquisition segment, a plurality of MS2 analyses of product ions derived from components included in the multiplex sample and eluting from the column. The method further includes determining, based on MS3 mass spectra acquired by the targeted MS3 analysis and MS2 mass spectra acquired by the plurality of MS2 analyses, a relative quantity of the isobaric tag-labeled target analyte in the multiplex sample.

Embodiments described herein generally relate to systems and methods for processing mass spectrometry samples. Aspects of the disclosure include systems and methods for processing samples. Additionally, embodiments of the disclosure can also include systems and methods for sample analysis. Various embodiments include data analysis systems and methods for comparing data across samples and sample runs. Data analysis systems can run normalization methods for normalizing raw abundance mass spectrometry data. In some aspects, the normalized data can be used as input for predictive models.

Antibody-free processes are disclosed that provide accurate quantification of a wide variety of low-abundance target analytes in complex samples. The processes can employ high-pressure, high-resolution chromatographic separations for analyte enrichment. Intelligent selection of target fractions may be performed via on-line Selected Reaction Monitoring (SRM) or off-line rapid screening of internal standards. Quantification may be performed on individual or multiplexed fractions. Applications include analyses of, e.g., very low abundance proteins or candidate biomarkers in plasma, cell, or tissue samples without the need for affinity-specific reagents.

A method for the in situ derivatization of at least one biogenic amine, precursor, or metabolite thereof in an isolated aqueous sample includes the steps of: (i) contacting the sample with a propionic anhydride/acetonitrile solution in the presence of a phosphate buffer having a pH in the range of 7.0 to 9.0 and allowing the conversion of amine and/or hydroxyl moieties of the biogenic amine, precursor, or metabolite thereof to form a propionyl derivative of the biogenic amine; followed by (ii) adding to the reaction mixture obtained in step (i) a carbodiimide compound and an electrophilic amine-containing compound, and allowing the carbodiimide-mediated derivatization of carboxylic acid moieties of the biogenic amine, precursor, or metabolite thereof.

A method for determining in a sample, by mass spectrometry, the amount of one or more analytes selected from the group consisting of N-acetylthreonine, TMAP, phenylacetylglutamine, tryptophan, creatinine, meso-erythritol, arabitol, myo-inositol, N-acetyl serine, N-acetylalanine, 3-methylhistidine, trans-4-hydroxyproline, kynurenine, urea, C-glycosyltryptophan, 3-indoxyl sulfate, pseudouridine, and combinations thereof 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 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 amount of each of the one or more analytes in the sample. Also described is a kit comprising one or more isotopically labeled analogues as internal standards for each of the one or more analytes.

The present invention provides a method in which a porous body having a monoclonal antibody to be measured immobilized in pores thereof is brought into contact with nanoparticles having a protease immobilized thereonto in a liquid to perform selective protease digestion of the monoclonal antibody and a peptide fragment obtained by the digestion is detected by liquid chromatography mass spectrometry (LC-MS), wherein the monoclonal antibody is digested with the protease in the presence of an antibody specifically binding to the monoclonal antibody or a target molecule of the monoclonal antibody.

A method includes applying distinct isobaric tags to each of a plurality of samples; combining the samples; performing a separation of species within the combined samples; isolating and fragmenting labeled parent ions within a m/z range to produce a plurality of reporter ions, each reporter ion corresponding to one of the isobaric tags; determining intensities of the plurality of reporter ions and ions representative of a parent species at a plurality of points along a peak; and fitting the intensity of the ions representative of a parent species and the plurality of reporter ions at the plurality of points to obtain a relative abundance of the parent species in each of the plurality of samples.

The present disclosure provides a microbead and a method for preparing the same. Also provided is a method for detecting and analyzing biomolecules in sample by using element analysis.

Described herein are methods for screening for a disease state. The method may include obtaining multiple data sets, and identifying the disease state based on a combination of the data sets. The data sets may include biomolecule measurements obtained by multiple methods, such as through the use of particles and reference biomolecules.

Disclosed herein are methods for identifying novel drug candidates.