The present disclosure relates to methods of identifying RNA-edited peptides. In an aspect, the identified peptides are capable of eliciting immune responses in individuals or patients. The present disclosure further relates to RNA-edited peptide sequences identified by methods described herein. In a further aspect, the disclosure provides for methods of treating cancer in individuals or patients by utilizing the methodology described herein.

The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated.

Provided herein are methods of single-polypeptide sequencing and reconstruction. Also provided herein are compositions, kits and devices useful for the same.

Aspects of the application provide methods of preparing a multiplexed sample for polypeptide sequencing, and compositions, kits and devices useful for the same.

Aspects of the application provide methods of preparing an enriched sample for polypeptide sequencing, and compositions, kits and devices useful for the same.

Methods and devices for enriching and analyzing target molecules from a sample are provided herein. In some embodiments, methods and devices involve enrichment of target molecules (e.g., using SCODA) and subsequent detection and analysis using sequencing.

Hyperstable constrained peptides and methods and apparatus for designing such peptides are provided. A computing device can determine a peptide backbone using a computing device. The computing device can place zero or more disulfide bonds in the peptide backbone. The computing device can design one or more peptide sequences based on the peptide backbone. The computing device can validate at least one validated peptide sequence of the one or more peptide sequences. An output can be generated based on the at least one validated peptide sequence.

Methods and devices for isolating or enriching target molecules from a sample are provided herein. In some embodiments, methods and devices further involve detection, analysis and/or sequencing of a target molecule.

The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Provided herein are methods of single-cell polypeptide and/or polynucleic acid sequencing, which facilitate the direct sequencing of a single cell without amplification. Also provided herein are compositions, kits and devices useful for the same.