Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.

The invention features a computer-implemented biological data classification method executed by one or more processors and including receiving, by the one or more processors, a first biological data set comprising a first plurality of biological sample data collected from a set of patients; processing, by the one or more processors, the first biological data set using a first variational autoencoder (VAE) to generate a first trained VAE comprising a first latent space vector of the first biological data set comprising a plurality of values corresponding to each latent space dimension of the latent space vector, the latent space vector having lower dimensionality than the biological sample data set; receiving, by the one or more processors, a second biological data set comprising a second plurality of biological sample data collected from a patient, different from the set of patients; and generating, by the one or more processors, a latent space representation of the second biological data set based on a first latent space vector.

Provided herein are methods for determining the serotype of a virus particle and/or or determining the heterogeneity of a virus particle (e.g., an AAV particle). In other embodiments, the invention provides methods to determine the heterogeneity of AAV particles. In some aspects, the invention provides viral particles (e.g., rAAV particles) with improved stability and/or improved transduction efficiency by increasing the acetylation and/or deamidation of capsid proteins.

A method of processing of a biological sample containing multiple metabolites is described The method comprising the steps of pre-treating the biological sample with a metabolite extraction solvent to provide a pre-treated sample, separating a first aliquot of the pretreated sample by reverse phase liquid chromatography (RPLC) to provide a first eluent containing resolved hydrophobic metabolites, and separating a second aliquot of the pre-treated sample by hydrophilic interaction liquid interaction chromatography (HILIC) to provide a second eluent containing resolved hydrophilic metabolites. The first and second eluents are assayed using targeted tandem mass spectroscopy operated in multiple reaction monitoring mode. Each liquid chromatography step (LC) is directly hyphenated with the tandem mass spectrometry (MS/MS) into a single LC-MS/MS analysis. The extraction solvent typically comprises methanol, isopropanol and an acetate buffer.

Disclosed are techniques for mass spectrometry. In one example, an isotopologue of a target analyte is added to a sample. The sample and isotopologue are analyzed as it elutes from a chromatography system to form precursor ions. The precursor ions are mass analysed using a data independent acquisition (DIA) methodology comprising performing mass analysis scans in the MS1 domain and performing mass analysis scans in the MS2 domain. Upon identifying that the isotopologue is eluting from the chromatography system, a plurality of target scans are performed, each having a target isolation window including a mass to charge ratio representative of the target analyte over the duration of a chromatographic peak of the isotopologue for at least one of identification and quantitation of the target analyte. The target scans are configured to provide additional quantitation data for the target analyte.

This disclosure relates to the field of mass spectrometry analysis. In some embodiments, the disclosure relates to compositions and methods for detecting and quantifying proteins in the AKT-mTOR pathway by immunoprecipitation enrichment followed by mass spectrometry analysis.

To provide a method for discriminating a microorganism by selecting and using a marker protein capable of reproducibly and quickly discriminating a bacterial species of the genus Listeria. The method for discriminating a microorganism according to the present invention includes: a step of subjecting a sample containing a microorganism to mass spectrometry to obtain a mass spectrum; a reading step of reading a mass-to-charge ratio m/z of a peak derived from a marker protein from the mass spectrum; and a discrimination step of discriminating which bacterial species of Listeria bacteria the microorganism contained in the sample contains based on the mass-to-charge ratio m/z, in which at least one of 17 ribosomal proteins L3, L4, L23, L2, L24, L6, L18, S5, L15, S13, S11, L10, L21, L13, S9, L31, S16 is used as the marker protein and particularly at least one of 8 ribosomal proteins L24, L6, L18, L15, S9, L31, S16 among the 17 ribosomal proteins is used.

Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

The present disclosure provides a system comprising a communication interface and computer for assigning a label to the biomolecule fingerprint, wherein the label corresponds to a biological state. The present disclosure also provides a sensor arrays for detecting biomolecules and methods of use. In some embodiments, the sensor arrays are capable of determining a disease state in a subject.

Systems and methods are provided for microbial identification using cleavable tags. Control information is sent to a mass spectrometer to fragment one or more nucleic acid primers labeled with a first tag and monitor for an intensity of the first tag in a mass spectrometry (MS) method. An ion source provides a beam of ions from a polymerase chain reaction amplified sample that includes one or more nucleic acid primers labeled with the first tag. The first tag binds to one or more nucleic acid primers of a known microbe and is cleaved from the nucleic acid primers during the MS method. The mass spectrometer receives the beam of ions and is adapted to perform the MS method on the beam of ions. If the intensity of the first tag received from the mass spectrometer exceeds a threshold value, the known microbe is identified in the sample.