Apparatus and methods for the detection of proteins in biological fluids such as urine using a label-free assay is described. Specific proteins are detected by their binding to highly specific capture reagents such as SOMAmers that are attached to the surface of a substrate. Changes to these capture reagents and their local environment upon protein binding modify the behavior of color centers (e.g., fluorescence, ionization state, spin state, etc.) embedded in the substrate beneath the bound capture reagents. These changes can be read out, for example, optically or electrically, for an individual color center or as an average response of many color centers.

Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

A method for evaluating a subject for a biological condition associated with metal metabolism includes sampling positions along a biological sample of the subject to obtain several ion samples. Each ion sample corresponds to a position on the biological sample and each position represents an amount of growth of the biological sample. The obtained ions are analyzed with a mass spectrometer thereby obtaining a plurality of traces. Each such trace represents a concentration of a corresponding elemental isotope, in a plurality of elemental isotopes, over time. A set of features is derived from the traces. Each feature is determined by a variation of a single isotope or a combination of isotopes in the plurality of traces. The set of features is inputted into a trained classifier to obtain a probability that the subject has the biological condition associated with metal metabolism.

Provided herein are methods of measuring glycogen and methods of diagnosing a disease. One method of measuring includes separating sugar monomers and sugar phosphates using gas-chromatography, and analyzing the monomers and phosphates using mass spectrometry. Another method of measuring includes adding an isoamylase to a sample, the isoamylase cleaving glucose chains from glycogen; applying a matrix-assisted laser desorption ionization (MALDI) ionization matrix to the sample; and analyzing the samples using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The method of diagnosing a disease includes determining an amount and location of glycogen accumulation in a subject; and diagnosing a disease when over-accumulation of glycogen is determined.

Effectiveness of a neoepitope-based immunotherapeutic composition against a tumor can be increased by predicting the surface presentation of the neoepitope bound to the HLA molecule of the tumor cell. Surface presentation levels of neoepitopes can be predicted by identifying any changes in omics data of the tumor cell that may affect the expression or surface trafficking of the HLA molecule and that may affect binding affinities of neoepitopes to the HLA molecule.

The current disclosure provides methods and compositions for treating food allergies, infections, autoimmune conditions, and other allergic conditions. Accordingly, the current disclosure relates to a method for treating an infectious, autoimmune, or allergic disease in a subject comprising administering a composition comprising bacterium Anaerostipes caccae to the subject. Further aspects relate to a method for treating a food allergy or for reducing an allergic response to an allergen or for treating or preventing an anaphylactic response in a subject comprising administering a composition comprising bacterium Anaerostipes caccae and a prebiotic to the subject.

Disclosed are methods and systems using liquid chromatography/tandem mass spectrometry (LC-MS/MS and 2D-LC-MS/MS) for the proteomic analysis of genotypes. In certain embodiments, samples used in the analysis comprise dried bodily fluids.

Described herein are methods for assessing the risk of cardiovascular disease in a subject in need thereof by detecting the presence of one or more cleavage products of the one or more natriuretic peptides over a period of time, wherein the presence of one or more cleavage products is indicative of an increased risk of the subject developing cardiovascular disease. Provided herein are compositions and kits comprising a non-natural natriuretic peptide comprising one or more D-amino acids. Also provided herein are methods of diagnosing a subject for a disease and treating the subject for the disease, wherein the method comprises the use of a non-natural natriuretic peptide comprising one or more D-amino acids.

Materials and non-invasive methods are provided for determining a subject's present drug metabolic capacity by assessing a biofluid sample taken from the subject following administration of a compound and identifying phenotypic variations in activity of one or more drug absorption, distribution, metabolism and excretion (ADME) enzymes extracted from extracellular vesicles (EVs) in the biofluid sample. Additional materials and methods are provided for determining compound (e.g., drug) efficacy and dose ranging, either in a subject or in a treatment cohort, by quantifying level of expression of such ADME enzymes EVs selectively isolated from biofluid.

Provided herein are methods of obtaining and applying measurements of metabolites to quantifying maternal risk of having a child with autism spectrum disorder (ASD), with high specificity and sensitivity.