Methods disclosed herein concern cancer proteogenomics, which integrates genomics, transcriptomics and mass spectrometry (MS)-based proteomics to gain insights into cancer biology and treatment efficacy. To promote clinical utility of embodiments herein, proteogenomics approaches were developed for frozen core needle biopsies using tissue-sparing specimen processing with or without a microscaled proteomics workflow.

Provided is a method by which the disaccharides derived from glycosaminoglycans can be analyzed in a stable and highly reproduceable manner. A method for analyzing a glycosaminoglycan according to the present invention includes: a first process for producing a plurality of kinds of disaccharides derived from a glycosaminoglycan in a biological sample by adding a plurality of kinds of glycosaminoglycan-specific enzymes to the biological sample: and a second process for separating and analyzing the plurality of kinds of disaccharides by a liquid chromatography-mass spectrometry method, where a column used for liquid chromatography in the liquid chromatography-mass spectrometry method is a column packed with a stationary-phase support to which an amide group as a functional group is bound, or a column packed with a stationary-phase support to which an adamantyl group as a functional group is bound.

Provided are methods for quantifying peanut proteins in food products using a matrix-specific calibration curve. Methods provided include exposing a food sample comprising a matrix and one or more peanut proteins to an extractant to extract the one or more peanut proteins from the food sample; heating the food sample to reduce protein interference in the food sample; digesting one or more peanut proteins in the food sample to form one or more peanut peptides; determining a relative response value of the one or more peanut peptides in the food sample by analyzing the food sample using liquid chromatography with tandem mass spectrometry; and determining an amount of the one or more peanut proteins by comparing the determined relative response value of the one or more peanut peptides in the food sample to a matrix-specific calibration curve.

The present invention relates to a method for quantifying an anti-TNF antibody in a sample of a human individual comprising a step of adding to a test sample which may contain therapeutic anti-TNF antibodies a known amount of two or more labeled forms of said anti-TNF antibodies.

Molecule having the structural formula (I): (I) for use as targeting probe of translating ribosomes and ribosome-interacting proteins. ##STR00001##

The present disclosure provides an improved method for accurately measuring the amino acid sequence of a therapeutic protein, in particular, an antibody, to insure the homogeneity of the protein such that it is suitable for administering to a human subject for treating a disease or disorder. The methods employ analytical physical chemistry techniques, in particular, a guided electron-transfer dissociation (ETD) and mass spectrometry (MS) approach for robust sequence coverage of the molecule with high accuracy and speed of use.

The present invention discloses methods for identifying a protein interaction between one or more first proteins and one or more further proteins comprising the steps of: exposing one or more samples comprising the proteins to at least one preselected condition for at least one preselected duration; isolating and separating at least one soluble fraction from an insoluble fraction of said one or more samples; and analyzing the at least one soluble fraction or the insoluble fraction to identify said protein interaction between one or more first proteins and one or more further proteins. Use of the method of the invention are also disclosed.

Provided is a method for simultaneously detecting Vitamin K1 and Vitamin K2 in traces of blood. The method includes: constructing a two-dimensional liquid chromatography-tandem mass spectrometer, establishing an analytical method, and detecting at least three mixed standard solutions using the constructed two-dimensional liquid chromatography-tandem mass spectrometer to obtain a first detection result; fitting standard curve equations respectively corresponding to Vitamin K1 and Vitamin K2; and mixing and centrifuging a blood sample to which an extraction reagent and a certain amount of internal standard substance are added, collecting a supernatant, blowing the supernatant to dry with nitrogen, redissolving the residue, and detecting the dry supernatant using the constructed two-dimensional liquid chromatography-tandem mass spectrometer to obtain a second detection result. In this manner, concentrations of Vitamin K1 and Vitamin K2 in the blood sample are obtained.

Embodiments provide for methods of predicting glycation percentage of an amino acid in a therapeutic biomolecule. In one example, a method of predicting a glycation percentage of an amino acid in a biomolecule includes determining a first set of rates for a de-glycation reaction for a first set of temperatures, inferring a second set of one or more rate(s) for the de-glycation reaction for a second set of temperatures, and using the second set of one or more rate(s) to predict the glycation percentage at any temperature corresponding to the second set of temperatures and over any time duration. Also provided are methods for maintaining a glycation percentage of an amino acid within a predetermined glycation percentage range over a shelf-life of a therapeutic biomolecule, and methods for either reducing or increasing a potency of a therapeutic biomolecule in a subject at a time of administration.

Methods and system for protein characterization using online chromatography and electrospray ionization mass spectrometry are provided.