The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

Chemoproteomic methods for detecting and profiling electrophilic post-translational modifications (PTMs) and oxidative PTMs in proteins are described. The methods including contacting a proteomic mixture with a probe having hydrazine and an affinity handle to form a covalent linkage between the hydrazine moiety of the probe and the endogenous electrophilic PTM or the endogenous oxidative PTM. The resulting derivatized proteins are labelled with an tag via a click chemistry reaction. The labelled proteins can then be detected or profiled using techniques such as, for example, fluorescence imaging or mass spectrometry. Also described are protein conjugates having a covalent linkage formed by reaction of a hydrazine or oxyamine moiety of a probe with an electrophilic or oxidative PTM of a protein.

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3′ ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.

A system for nucleic acid sequencing is provided. The system comprises a sequencing device configured to expose a tagged polynucleotide comprising a combinatorial barcode sequence and a sample polynucleotide to sequential nucleotide flows, each flow comprising one species of nucleotide and the sequential flows being in a predetermined order based on the species of nucleotide such that exposing of the tagged polynucleotide to the sequential nucleotide flows causes incorporations of nucleotides from the sequential nucleotide flows into the tagged polynucleotide over the barcode sequence The sequencing device is configured to detect a series of signals over the barcode sequence resulting from the incorporations, wherein the predetermined order of nucleotide flows comprises a repetition of a flow order motif that is based on a sequence motif. The system comprises a computing device configured to resolve the detected series of signals to determine the combinatorial barcode sequence.

A system for nucleic acid sequencing is provided. The system comprises a sequencing device configured to expose a tagged polynucleotide comprising a combinatorial barcode sequence and a sample polynucleotide to sequential nucleotide flows, each flow comprising one species of nucleotide and the sequential flows being in a predetermined order based on the species of nucleotide such that exposing of the tagged polynucleotide to the sequential nucleotide flows causes incorporations of nucleotides from the sequential nucleotide flows into the tagged polynucleotide over the barcode sequence The sequencing device is configured to detect a series of signals over the barcode sequence resulting from the incorporations, wherein the predetermined order of nucleotide flows comprises a repetition of a flow order motif that is based on a sequence motif. The system comprises a computing device configured to resolve the detected series of signals to determine the combinatorial barcode sequence.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.