In some embodiments, a mass spectrometry tag may comprise a linker region, a mass balance region, and a reporter region. The mass spectrometry tag may be configured to fragment in a mass spectrometer via an energy dependent process to produce multiple reporter molecules. For example, the reporter region of the tag may be configured to produce at least two reporter molecules via fragmentation. In some embodiments, one or more regions of the tag may comprise at least one heavy isotope. In some such embodiments, the ability to fragment into multiple reporter molecules as well as the placement and/or number of heavy isotope(s) allows the mass spectrometry tag to be distinguished from other similar mass spectrometry tags. In some such embodiments, the ability to distinguish between tags having the same or substantially similar total mass to charge ratio and reporter region mass may allow the system to have a greater multiplexing capacity than conventional systems.

The embodiments herein provide methods to analyze the in vitro stability of recalcitrant or membrane-bound proteins in simulated gastric fluid (SGF) comprising the proteolytic enzyme, pepsin, and in combination with a novel pepsin-trypsin assay employing state-of-the-art mass spectrometric approaches, such as LC-MS/MS, to monitor the precise degradation products. The extent of protein digestion can be evaluated by the appearance of peptic products and the disappearance of tryptic peptide products (as a proxy for intact protein). The embodiments herein also provide methods for protein quantitation using high-sensitivity LC-MRM-MS quantification. The methods embodied herein are particularly useful in charactering proteins produced in transgenic plants, such as canola genetically engineered to produce long chain omega-3 polyunsaturated fatty acids.

A method is disclosed comprising obtaining or acquiring chemical or other non-mass spectrometric data from one or more regions of a target (2) using a chemical sensor (20). The chemical or other non-mass spectrometric data may be used to determine one or more regions of interest of the target (2). An ambient ionisation ion source 1 may then be used to generate aerosol, smoke or vapour (5) from one or more regions of the target (2).

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

Molecule having the structural formula (I): (I) for use as targeting probe of translating ribosomes and ribosome-interacting proteins.

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The present invention relates to a biomarker and target for diagnosis, prognosis and treatment of ankylosing spondylitis (AS). The present invention also relates to a method for producing an animal model for AS, an animal model produced therefrom, and a method for screening for an agent pharmaceutically active in the treatment of A S using such animal model.

An apparatus for ligand binding assays includes an incubator that incubates a plurality of beads with a sample of interest wherein each of the plurality of beads comprises a tag of predetermined mass and a bait molecule. A washer washes the incubated beads so that weakly bound molecules are removed while strongly bound molecules are retained. A sample plate loader loads the washed beads into the sample plate such that respective ones of the plurality of beads are loaded into respective ones of the plurality of well. A sprayer deposits matrix assisted laser desorption ionization (MALDI) matrix material on the surface of the sample plate so that each of the plurality of beads is exposed to MALDI matrix material. A MALDI-TOF mass spectrometer receives the sample plate and performs mass spectrometry on samples in the plurality of wells. A computer executes an algorithm that analyzes the mass spectra.

A method of assessing whether a candidate subject is suitable for probiotic treatment is disclosed. The method comprises determining a signature of the gut microbiome of the candidate subject, wherein when the signature of the microbiome of the candidate subject is statistically significantly similar to a signature of a gut microbiome of a control subject known to be responsive to probiotic treatment, it is indicative that the subject is suitable for probiotic treatment.

A method for determining an amino acid sequence of a polypeptide, including comprising: contacting a first sample containing the polypeptide with a first protease (e.g., Trypsin) to produce a first set of digested peptide fragments; fragmenting the first set of digested peptide fragments to produce a first set of fragmented peptide ions; determining masses of the first set of fragmented peptide ions; contacting a second sample containing the polypeptide with a second protease (e.g., Tryp-N); fragmenting the second set of digested peptide fragments to produce a second set of fragmented peptide ions; selecting pairs of peptide ions from the first and the second set of fragmented peptide ions that differ in mass by a mass of an arginine amino acid residue or a lysine amino acid residue; assigning an ion type (either N-terminal peptide ion or C-terminal peptide ion) to the selected pairs of the peptide ions from two sets of fragmented peptide ions; selecting a mass ladder of the same-type peptide ions in either set of fragmented peptide ions with incremental mass by the mass of amino acid residue(s), and assembling the identified amino acid residues from the mass ladder to determine the amino acid sequence of the polypeptide of interest.

The present invention provides a method for pretreatment of a biological sample in order to measure a protein contained in the biological sample by liquid chromatography/mass spectrometry. The method includes the step of adding an acetic acid aqueous solution to the biological sample, so as to prepare a pretreatment sample containing an acetic acid at a concentration ranging from 20 to 50 weight percent, both inclusive. In the present invention, a target protein contained in a biological sample is less prone to be adsorbed to a sample container, thereby resulting in an increased sensitivity of measuring the protein in the biological sample by mass spectrometry. Further, reproducibility of results of the mass spectrometry is improved, and reliability is increased.