Systems and methods for determining amino acid sequences of peptides that bind to MHC-I or HLA-I complex or MHC-II or HLA-II complex are provided. One embodiment includes isolating peptides from MHC or HLA class I or class II-peptide complexes and adding one or more known labeled peptides of interest to form a sample containing labeled peptides and unlabeled isolated peptides. The method also includes analyzing the sample with an LC-MS/MS system to obtain sequence data of the peptides, and increasing the sensitivity of the LC-MS/MS system when the labeled peptide is detected by the LC-MS/MS system. The method then concludes with determining the amino acid sequence of the unlabeled peptides in an m/z range that includes the m/z of the labeled peptide. The system can be triggered to increase the sensitivity in or near the m/z of the labeled peptide using an algorithm or computer program.

Disclosed are devices and methods capable of multiplexed analysis of multiple cellular activities and pathways in single cells including genomic, transcriptomic, and proteomic analysis.

This invention discloses a pretreatment approach for blood and bodily fluids to remove unwanted protein interferences in the measurement of analytes. Enzymes either contained in a cartridge or immobilized on a solid support break down proteins that complex with the analyte to shield it from detection. This pretreatment significantly enhances the detectability of analytes and does not require subsequent clean-up steps that would normally be required to ensure the functionality of the analysis method, thereby, creating a simple yet powerful approach for sample pretreatment in a variety of settings ranging from a complex laboratory infrastructure to a field deployable application.

The invention provides an isolated peptide comprising a crotonylation site, a Kcr-specific affinity reagent that specifically binds to the peptide, and a method for detecting protein crotonylation in a sample using the reagent.

An apparatus for glycan analysis is disclosed. The apparatus includes a plurality of loading wells adapted to receive a plurality of samples; a plurality of capillaries arranged in correspondence with the loading wells, each of the capillaries including a first portion including a stacking gel and a second portion including a resolving gel; and a plurality of eluting wells arranged in correspondence with the capillaries and adapted to receive a portion of the samples having traversed the capillaries.

Engineered promiscuous biotin ligases and methods of using them in proximity labeling are described. In particular, the invention provides novel biotin ligase variants having increased promiscuous biotinylation activity capable of proximity labeling of proteins in live cells in as little as 10 minutes.

Provided is a reagent composition for measuring glycated albumin to diagnose the presence or absence of diabetes and a method of measuring glycated albumin using the same, and more particularly is a reagent composition for measuring glycated albumin, the composition including a dye-encapsulated silica nanoparticle-boronic acid, and to a method of measuring glycated albumin using the same. In the reagent composition for measuring glycated albumin, since a dye is encapsulated in silica nanoparticles, the inherent absorption wavelength of the dye is not affected by pH and the composition has excellent stability even when stored for one month or more.

Provided herein are methods for identifying new biomarkers for various diseases using proteomics, peptidomics, metabolics, proteoglycomics, glvcomics, mass spectrometry and machine learning. The present disclosure also provides glycopeptides as biomarkers for various diseases such as cancer and autoimmune diseases.

The present invention provides biomimetic sensor devices that utilize proteinssuch G-protein coupled receptorsand are useful in high-sensitivity analysis of analyte-containing samples. These sensors may be used to determine the presence or concentration of one or more analytes in a sample. The invention also includes methods of fabricating the devices and methods of using the devices to assay samples.

The present invention relates to a method for covalently binding a cell surface protein and a ligand, the ligand being capable of specifically binding to the cell surface protein, the method consisting essentially of contacting the living cells expressing the cell surface protein with the ligand comprising at least one furan moiety, thereby covalently binding the cell surface protein and the ligand.