108 articles
18O labeling
18O labeling is a stable isotope labeling method in quantitative proteomics in which a protease exchanges the C-terminal oxygen atoms of peptides for heavy oxygen, letting a mass spectrometer read protein abundance.
6-Carboxyfluorescein
6-Carboxyfluorescein (6-FAM, CAS 3301-79-9) is a fluorescein derivative carrying an additional carboxylic acid group, used chiefly as a green fluorescent label for oligonucleotides and other biomolecules.
Activity-based proteomics
Activity-based proteomics, usually called activity-based protein profiling (ABPP), is a chemical proteomics method that uses activity-based probes to label active enzymes in complex biological samples and identify them by mass spectrometry.
Affinity capture
Affinity capture is a biochemical method that enriches a target protein or complex from cell extract using an antibody or affinity tag on a solid medium.
Affinity labeling
Affinity labeling covalently tags a biomolecule's binding site using a reactive analog of its ligand, identifying binding partners, drug targets, and active-site residues; in its photoaffinity form, light activates the probe.
Agarose
Agarose, a neutral polysaccharide from red algae, forms thermoreversible gels used as the standard electrophoresis matrix for DNA fragments above roughly 1 kb, and as microspheres and hydrogels for chromatography, drug delivery, and tissue engineering.
Alcian blue
Alcian blue is a copper phthalocyanine dye used as a biological stain for acidic carbohydrates such as mucins and glycosaminoglycans, at pH 2.5 or pH 1.0.
Alizarin red S
Alizarin red S is a synthetic anthraquinone dye, used as its sodium salt, that binds calcium salts and produces red staining; the gold standard for calcium deposits since 1871.
Benedict's reagent
Benedict's reagent (Benedict's solution): alkaline copper sulfate, sodium citrate, and sodium carbonate reagent devised by Stanley Benedict in 1908 to detect reducing sugars, chiefly urine glucose, by forming yellow-to-red Cu2O precipitate.
Bicinchoninic acid assay
The bicinchoninic acid (BCA) assay is a colorimetric biochemical assay measuring total protein concentration, tolerant of detergents and sensitive over a broad range.
Bimolecular fluorescence complementation
Bimolecular fluorescence complementation (BiFC) is a microscopy technique that detects protein-protein interactions in living cells, introduced by Chang-Deng Hu and Tom K. Kerppola in 2002.
Bioanalysis
Bioanalysis: quantitative measurement of drugs, metabolites, and analytes in biological samples using LC-MS and ligand binding assays; term coined in the 1970s; also a Taylor & Francis peer-reviewed journal (ISSN 1757-6180) founded 2009.
Bioautography
Bioautography is a chromatography-based detection method that combines chemical separation and biological detection: compounds separated on a paper or thin-layer plate show as inhibition zones against a test organism.
Biuret test
Biuret test, also called Piotrowski's test, detects peptide bonds: CuSO4 in alkaline solution with tartrate gives a violet complex absorbing at 540–560 nm, and is the standard clinical serum total protein assay.
Bottom-up proteomics
Bottom-up proteomics is a mass spectrometry method that digests proteins into peptides, usually with trypsin, and infers which proteins were present, and in what amounts, from the peptides identified.
Bovine serum albumin
Bovine serum albumin (BSA), also called Fraction V albumin, is the ~66.5 kDa liver-synthesized protein making up about 50% of cow serum protein; a carrier protein widely used as a lab standard, blocking agent, and stabilizer.
Bradford protein assay
Bradford protein assay: 1976 colorimetric dye-binding method using Coomassie Brilliant Blue G-250 (465 to 595 nm shift) to quantify microgram protein; arginine-driven response, detergent-sensitive, 96-well compatible.
Bromothymol blue
Bromothymol blue (BTB), bromothymol sulfone phthalein, is a sulfonephthalein pH indicator: yellow below pH 6.0, green to 7.6, blue above; pKa 7.5; used as a CO2 indicator and in diagnostics and sensors.
Chemiluminescence assay
A chemiluminescence assay is a biochemical method that detects biomolecules like proteins and nucleic acids by measuring light from a chemical reaction, used in Western blots and clinical immunoassays.
Chemiluminescence imaging
Chemiluminescence imaging is a bench-biology detection technique that visualizes proteins and nucleic acids on blots by capturing light from an enzyme-catalyzed reaction, with enhanced chemiluminescence (ECL) largely replacing radioactive detection.
Covalent inhibitor discovery via chemoproteomics
Covalent inhibitor discovery via chemoproteomics is the use of mass spectrometry methods that profile interactions between electrophilic small molecules and proteins, identifying targets, discovering hits, and characterizing the selectivity of covalent drugs such as ibrutinib.
Covalent labeling
Covalent labeling is a structural biology method that irreversibly modifies solvent-accessible amino acid side chains in proteins, read out by mass spectrometry to map structure, conformational change, and interaction surfaces.
Covalent ligand screening
Covalent ligand screening is a drug-discovery and chemical-biology method testing electrophilic small-molecule libraries against proteins or proteomes to find compounds that bond specific amino acid residues.
Crosslinking mass spectrometry
Cross-linking mass spectrometry (XL-MS) is a structural biology method that covalently links amino acid residues close together in proteins, then uses tandem mass spectrometry to identify the pairs as distance restraints for modeling.
Crystal violet
Crystal violet (gentian violet, C.I. Basic Violet 3, C25H30ClN3) is a triphenylmethane dye patented in 1883, the primary stain of the Gram stain, a biofilm biomass assay dye, and an IARC Group 2B possible human carcinogen.
Cysteine chemoproteomics
Cysteine chemoproteomics encompasses chemical proteomic methods, including isoTOP-ABPP, for quantifying cysteine reactivity in native systems and discovering covalent small-molecule ligands in lysates and intact cells.
DAPI
DAPI (4′,6-diamidino-2-phenylindole) is a blue-fluorescent AT-minor-groove DNA stain, excitation/emission 358/461 nm, used for fixed-cell nuclear counterstaining, flow cytometry viability, and DNA content analysis; less cell-permeable than Hoechst 33342.
Data-dependent acquisition
Data-dependent acquisition (DDA) is a mass spectrometry acquisition mode that automatically selects and fragments the most abundant ions from each survey scan, the most common mode in shotgun proteomics.
Data-independent acquisition
Data-independent acquisition (DIA) is a mass spectrometry method for quantitative proteomics in which the instrument fragments all peptide ions in predefined isolation windows, without selecting precursors in real time.
De novo peptide sequencing
De novo peptide sequencing is a computational mass spectrometry method that infers a peptide's amino acid sequence directly from its MS/MS spectrum, without searching a protein database.