Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

Methods for peptide and/or protein quantification by mass spectrometry using labeled peptides, wherein multiple labels lead to distinct fragments for the labeled peptides and their unlabeled variant, thus facilitating data analysis and enhancing the potential for quantification. Methods for selecting the label and label position are further given, as well as sets of labeled peptides resulting from or for use in the above-mentioned methods. The methods and substances are especially useful for data-independent or multiplexed parallel reaction monitoring proteomics applications involving peptide quantification.

A method for the in situ derivatization of at least one biogenic amine, precursor, or metabolite thereof in an isolated aqueous sample includes the steps of: (i) contacting the sample with a propionic anhydride/acetonitrile solution in the presence of a phosphate buffer having a pH in the range of 7.0 to 9.0 and allowing the conversion of amine and/or hydroxyl moieties of the biogenic amine, precursor, or metabolite thereof to form a propionyl derivative of the biogenic amine; followed by (ii) adding to the reaction mixture obtained in step (i) a carbodiimide compound and an electrophilic amine-containing compound, and allowing the carbodiimide-mediated derivatization of carboxylic acid moieties of the biogenic amine, precursor, or metabolite thereof.

A method of analysis using mass spectrometry and/or ion mobility spectrometry is disclosed comprising: (a) using a first device to generate smoke, aerosol or vapour from a target in vitro or ex vivo cell population; (b) mass analysing and/or ion mobility analysing said smoke, aerosol or vapour, or ions derived therefrom, in order to obtain spectrometric data; and (c) analysing said spectrometric data in order to identify and/or characterise said target cell population or one or more cells and/or compounds present in said target cell population.

This disclosure provides methods, systems, and compositions of matter for studying solvent accessibility and three-dimensional structure of biological molecules. A plasma can be used to generate marker radicals, which can interact with a biological molecule and mark the solvent-accessible portions of the biological molecule.

There is provided method of profiling protein tyrosine phosphorylation of a sample, the method comprising: contacting the sample with an SH2 Superbinder in order to bind pTyr-including peptides contained in the sample with the SH2 Superbinder; isolating the bound pTyr-including peptides from the sample; and identifying the isolated pTyr-including peptides.

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, inter alia, are compositions and methods for cross-linking biomolecules. In an aspect is provided a method of detecting a covalently conjugated molecule, the method including i) contacting a first biomolecule and a second biomolecule with a crosslinking agent to form a covalently conjugated biomolecule; ii) identifying a first point of attachment of the crosslinking agent to the first biomolecule using mass spectroscopy; and iii) identifying a second point of attachment of the crosslinking agent to the second biomolecule using mass spectroscopy; thereby detecting a covalently conjugated molecule.

Systems and methods for characterizing cancer cells are disclosed. In certain embodiments, the systems and methods involve coating a first chamber with ECM material and adding a first plurality of cells to the first chamber, adding media to a second chamber, and adding a second plurality of cells and media to a third chamber. The first, second, and third chambers are then clipped together to form a chamber array. The chamber array is mounted to an electric cell impedance sensing reader and impedance readouts of cell invasion are collected from the electric array at time intervals. Cells detected to invade into the second chamber are extracted and characterized.

Disclosed are methods for identifying a pregnant female who is susceptible to spontaneous preterm delivery. In particular, disclosed are methods for identifying a pregnant female who is susceptible to spontaneous preterm delivery based on ratios of steroids in samples obtained from the pregnant female.