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 invention relates to a method for predicting a response to a treatment of an eye disease on the basis of proteome changes. The invention also relates to a kit for use the method.

Methods, compositions and kits for the prevention and treatment of mitochondrial dysfunction, mitochondrial DNA damage and genomic DNA damage are provided. The methods use the administration of palm fruit juice and/or compositions containing phenolic compounds present in palm fruit juice. The methods, compositions, and kits can be used to reduce DNA damage in subjects being treated with nucleoside reverse transcriptase inhibitors, such as patients having HIV or AIDS.

Disclosed herein is a chemo-proteomic probe for labelling and monitoring a live microbe interacting with a host cell and for qualitative and quantitative analyses of those proteins involved during a microbe infects the host cell. This probe comprises a functional group for conjugating to a surface protein of a live microbe under a physiological condition; a photo-reactive group for covalent cross-linking to an interacting cell protein of a host; and a tag for isolating the cross-linked complex of the surface protein of said live microbe and the interacting protein of a host cell for qualitative and quantitative proteomics analyses. The probe may further comprise a visualization tag. This technology takes advantage of the high throughput feature of mass spectrometry analysis and combines it with a uniquely designed chemistry to achieve high efficient isolation and analysis of host cell proteins interacting with a pathogen at different stages of an infection.

Disclosed is a proteomic reactor, comprising a pipette tip, an ion exchange resin filler and a solid-phase extraction membrane. The solid-phase extraction membrane is filled into the lower end of the pipette tip, and the ion exchange resin filler is filled into the lower end of the pipette tip and is located above the solid-phase extraction membrane. The ion exchange resin filler is a strong cation exchange resin filler or a strong anion exchange resin filler. Disclosed is a protein chromatographic separation platform comprising the proteomic reactor and a liquid chromatography-mass spectrometer. Disclosed is the use of the proteomic reactor and protein chromatographic separation platform in the protein identification and protein quantitative analysis of a cell, a tissue or a blood sample.

The invention provides a carrier and a method for obtaining, removing, or detecting extracellular membrane vesicle or virus present in a sample. In particular, the invention provides (a) a carrier (a Tim carrier) on which a protein (a Tim protein), selected from a T-cell immunoglobulin and mucin domain-containing molecule-4 (a Tim-4) protein, a Tim-3 protein, and a Tim-1 protein, is bound; (b) a method for obtaining the extracellular membrane vesicle or the virus in the sample; (c) a method for removing the extracellular membrane vesicle or the virus in the sample; (d) a method for detecting the extracellular membrane vesicle or the virus in the sample; (e) a kit for capturing the extracellular membrane vesicle or the virus, comprising the Tim carrier; and f) a kit for capturing the extracellular membrane vesicle or the virus, comprising a reagent containing the Tim protein and a reagent containing the carrier.

The present invention relates to a newly developed resorcinarene-based amphipathic compound, a method for producing the same, and a method for extracting, solubilizing, stabilizing, crystallizing, or analyzing a membrane protein by using the same. In addition, compared to a conventional compound, the compound can efficiently extract, from a cell membrane, membrane proteins having a greater variety of structures and characteristics, and can stably store such membrane proteins for a long time in an aqueous solution. Therefore, the compound can be used to analyze the functions and structures of such membrane proteins. Analysis of the structures and functions of membrane proteins, being closely related to the development of new drugs, is one of the fields of greatest interest in biology and chemistry today.

Provided herein are methods, assays and devices for the differential diagnosis and detection of disease progression of autoimmune diseases. The methods, assays and devices provided herein produce and analyze binding patterns of peripheral-blood antibodies on mimetic peptide arrays that differentiate autoimmune diseases, and identify patients progressing to internal organ complications such as interstitial lung disease (ILD), and gastric antral vascular ectasia (GAVE), or renal involvement.

Described herein are methods for identification/discovery of protein biomarkers for chronic kidney disease (CKD) and diagnosing and/or prognosing and/or predicting progression of and/or treating chronic kidney disease (CKD).

Disclosed herein are methods, compositions, probes, polypeptides, assays, and kits for identifying a cysteine containing protein as a binding target for a small molecule fragment. Also disclosed herein are methods, compositions, and probes for mapping a biologically active cysteine site on a protein and screening a small molecule fragment for interaction with a cysteine containing protein.