Provided herein are methods for identifying a compound that alters fluorescence resonance energy transfer (FRET) of a protein. In one embodiment, the method includes providing a target protein, where the target protein includes two heterologous domains, each domain having chromophores that together act as a FRET pair. In another embodiment, the method includes providing a target protein and a second protein, wherein the target protein includes a first heterologous domain including a chromophore, and the second protein includes a second heterologous domain including a chromophore, where the chromophores together act as a FRET pair. The method further includes contacting a sample including the target protein and optional second protein with a test compound to form a mixture, and measuring a fluorescence emission spectrum of the mixture during exposure to a light source. The fluorescence emission spectrum is decomposed into at least two component spectra, where in one embodiment the component spectra include a donor chromophore emission and an acceptor chromophore emission. A ratio (R) is then calculated, and in one embodiment, R is determined according to

[00001]$R=\frac{\mathrm{Acceptor}\mathrm{emission}}{\mathrm{Donor}\mathrm{emission}}=\frac{{\mathrm{bF}}_A}{{\mathrm{aF}}_D}.$

The invention relates to methods of identifying compounds that modulate mTORC1 activity in a cell by modulating the activity of CASTOR1, as well as to the use of such identified compounds in the modulation of mTORC1 and the treatment of diseases and conditions characterized by aberrant mTORC1 activity.

The present invention relates to methods for high multiplex protein or cellular constituent analysis in single cells or single isolated aggregations of cellular constituents. The methods provide for embedding cells or isolated aggregations of cellular constituents in a hydrogel mesh and labeling of cellular constituents with labeling ligands linked to a nucleic acid tag. Cellular constituents can be determined using sequencing methods.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

High-throughput methods for screening large populations of variant proteins are provided. The methods utilize large-scale arrays of microcapillaries, where each microcapillary comprises a solution containing a variant protein, an immobilized target molecule, and a reporter element. Immobilized target molecules may include any molecule of interest, including proteins, nucleic acids, carbohydrates, and other biomolecules. The association of a variant protein with a molecular target is assessed by measuring a signal from the reporter element. The contents of microcapillaries identified in the assays as containing variant proteins of interest can be isolated, and cells expressing the variant proteins of interest can be characterized. Also provided are systems for performing the disclosed screening methods.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Disclosed herein are methods and systems for determining microsatellite instability. In some embodiments, the disclosed methods and systems are used for determining whether a cancer patient has high microsatellite instability (MSI-H). MSI-H patients have remarkably good responses to immunotherapy, such as checkpoint inhibitors immunotherapy. Therefore, the disclosed methods and systems can be used for identifying MSI-H and thus, patients as candidates for immunotherapy. In turn, the disclosed methods and systems can be used to predict responsiveness to immunotherapy. In some embodiments, the methods further include providing an immunotherapy to the MSI-H patient. Also disclosed are vaccines and compositions.

Methods of detecting an interaction between a macromolecule and an interaction partner are described. Kits are also described.

Synthesis of a sulfoxide-containing homobifunctional cysteine-reactive mass spectrometry-cleavable cross-linker for mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex is provided. Methods for mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex and cross-linking mass spectrometry for identifying one or more cross-linked peptides using the cross-linker are provided.

Methods and systems for performing assays in compartmentalized nano-volumes to screen for functional bispecific or multispecific biologics, including: providing a plurality of at least two distinct types of cells, wherein two or more first-type cells are engineered to express substantially a single genetic-variant per cell for a bispecific or multispecific biologic in a secreted form, wherein two or more second-type cells are selected or engineered to produce a positive reporter molecule signal that is triggered by a functional variant of the said biologic expressed by a first-type cell; providing a plurality of compartmentalized nano-volumes, wherein two or more nano-volumes are each provided with substantially one first-type cell, and one or more second-type cell(s); incubating the said nano-volumes over a period of time to allow the expression and secretion of the said biologics inside the said nano-volumes; collecting data representing the positive reporter molecule signal triggered by secreted biologics inside the said nano-volumes, and recovering cells from the nano-volumes with the positive reporter molecule signal and extracting the genetic information representing respective functional variants of the biologics.