Immunohistochemical (IHC) techniques that enable the sequential evaluation of at least seven biomarkers in one formalin-fixed paraffin-embedded (FFPE) tissue section are disclosed. The methods involve high-throughput multiplexed, quantitative IHC imaging, sequential IHC with iterative labeling, digital scanning, image coregistration and merging, and subsequent stripping of sections.

The present disclosure provides a method of identifying a substrate for a protease including contacting a protease to one of a first array and a second array, each array having the same plurality of features, each feature including at least one sequence linked to a solid support. The at least one sequence includes a candidate protease substrate linked to a reporter. The method further includes contacting a detectable element to each of the arrays to allow binding of the detectable element to the reporter, and detecting first and second signals resulting from binding of the detectable element to the each of the reporters in the first and second arrays. The method further includes comparing the first signal and the second signal to identify a difference in the first signal and the second signal, and identifying at least one candidate protease substrate as a substrate for the protease.

Methods are disclosed for identifying one or more proteins or polypeptides comprised by a sample. The methods comprise determining binding of each polypeptide with respect to each binding pool of a plurality of binding pools, wherein each binding pool comprises one or more probes which bind a structure comprised by a protein or polypeptide. In some aspects, polypeptides can be denatured and separated into individual polypeptide strands and immobilized on a solid support prior to determining binding of the binding pools. A protein, polypeptide or polypeptide strand can be identified by searching, in at least one database, for a protein or polypeptide sequence comprising binding pool targets either identical to or most similar to the binding pool targets comprised by the protein, polypeptide or polypeptide strand to be identified. Kits for identifying proteins, polypeptides and polypeptide strands are also disclosed.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

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.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., clocking), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

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.

An isotopic ratio outlier analysis (IROA) standard sample of metabolite compounds is disclosed. Each of whose compounds has a molecular weight of 2000 AMU or less, and is present as first and second isotopomers that are equally present at two predetermined isotopomeric balances, and contain 2 to 10% of a first isotope, and 90 to 98% of a second isotope, respectively. An internal standard is also disclosed that contains the same metabolite compounds as the IROA standard sample, but contains only compounds containing the heavier of the two isotopes. Methods of making and using the above and related materials are also disclosed.

The present disclosure relates to library compositions, methods of making and screening libraries of peptidase-cleavable substrate sequences. In particular, the libraries are useful in identifying substrate sequences for a variety of disease- or tissue-specific peptidases. The present disclosure also relates to use of identified peptidase substrates to design therapeutic agents and diagnostic tools.

The present invention relates to compositions and methods for identifying odorant-odorant receptor interactions. In particular, the present invention relates to methods for identifying odorant receptor-odorant interactions based on odorant receptor amino acid sequence and other properties of odorant receptors and odorants. The methods provide, in part, for the broad surveying of OR responses, using an in vivo strategy, against a diverse panel of 10 odorants, followed by using the resulting interaction profiles to uncover relationships between OR responses, odorants, odor molecular properties, and OR sequences.