The present invention relates to a method for qualitative analysis of a sample protein, which method comprises the steps of providing a water swollen gel column bed comprising bound protease and a sample protein in liquid buffer, digesting the sample protein into polypeptides by contact with the gel bed and subjecting the polypeptides to mass spectrometry (MS). The method is advantageously performed using back and forth flow of the sample protein including two or more repeats, and may be performed at a temperature of less than about 37° C., such as a temperature of less than about 30° C.

The invention also includes an automated method as well as a device and a kit for performing mass-based analysis of proteins with higher speed than the prior art while maintaining conditions that are tolerable to the protease.

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

A method for determining in a sample, by mass spectrometry, the amount of one or more analytes selected from the group consisting of 12,13-DiHOME, 3-hydroxybutyrate (BHBA), 3-hydroxyoctanoate, 3-methylglutarylcarnitine, 3-ureidopropionate, 7-alpha-hydroxy-4-cholesten-3-one (7-Hoca), citrate, fucose, fumarate, gamma-tocopherol, glutamate, glutarate, glycerol, glycochenodeoxycholate, glycocholate, hypoxanthine, maleate, malonate, mannose, orotate, 2,3-pyrdinedicarboxylate, ribose, serine, taurine, taurochenodeoxycholate, taurocholate, palmitoleate, linolenate, xanthine, xylitol, 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 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 to determine the amount of each of the one or more analytes in the sample.

A method for site-specific quantitation or characterization of drug conjugations of antibody-drug conjugates using protease-assisted drug deconjugation, linker labelling and mass spectrometry, wherein the conjugation includes an attachment linked to a specific conjugation site of a partially conjugated peptide or protein in a sample. The method comprises cleaving a portion of the attachment to generate the peptide or protein containing a cleaved linker, adding a modified linker to an unconjugated conjugation site of the partially conjugated peptide or protein, and subsequently subjecting the sample to mass analysis to identify the peptide or protein containing the cleaved linker and/or the modified linker.

Incorporation of deuterium into the lipids, proteins, and/or genetic material in cells, tissues, organs, or organisms, including animals, such as humans, and plants, by administration of heavy water, allows for the spectral determination of levels of lipids, proteins, and/or genetic material using Raman spectroscopy, such as stimulated Raman spectroscopy. Following administration of a drug, changes in the relative amounts of lipid, protein, and/or genetic materials can be determined, and the efficacy, or lack thereof, of the administered drug can be determined.

In the analysis method according to the present invention, a predetermined peptide is separated by immunoprecipitation using an antibody which specifically binds to either an N-terminus or a C-terminus of the predetermined peptide. The separated predetermined peptide is digested with a protease to prepare peptide fragments, and among the peptide fragments, a peptide fragment at a terminus opposite to a terminus binding to the antibody is mass-spectrometrically detected.

The present disclosure provides methods of imaging neurotransmitters and metabolites present in a biological sample comprising: pneumatically spraying or having sprayed the biological sample with a nanoparticle, introducing the sample to a laser desorption ionization mass spectrometer to collect mass spectral data and identifying the neurotransmitters or metabolites in the sample based on the mass spectral data.

A method of detecting the presence, or monitoring the severity of a condition characterised by the presence of fragments of a marker protein in the brain of a patient. The method comprises: (i) providing a sample comprising macrophages obtained from the patient; and (ii) detecting the presence of the marker protein or fragments thereof in the macrophages. The presence of abnormal levels of the marker protein and/or fragments thereof in the macrophages is indicative of the presence of the condition in the patient. The condition and the marker proteins can be: Alzheimer's Disease and the Abeta peptide, Parkinson's Disease and ubiquitin, Multiple Sclerosis and myelin basic protein, FrontoTemporal Dementia and tau, Amyotrophic Lateral Sclerosis and tau, Parkinson's disease, Lewy Body dementia or Alzheimer's Disease and alpha-synuclein.

There is provided a method of evaluating a liver condition of a subject, the method includes computing a fluctuation parameter from a liver breath test based on at least one of a percentage dose recovery (PDR) curve and a delta over baseline (DOB) curve of an isotope labeled methacetin, or a salt or a derivative thereof, and evaluating at least one liver condition of the subject, based at least on the fluctuation parameter. There is provided herein a method of evaluating a liver condition of a subject, the method includes computing a hepatic impairment score based at least on a breath test related parameter and on a demographic parameter.

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.