Tandem mass spectrometryTandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q).
Mass spectrometryMass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio.
Isotopic labelingIsotopic labeling (or isotopic labelling) is a technique used to track the passage of an isotope (an atom with a detectable variation in neutron count) through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the cell's metabolic pathway.
Ion-mobility spectrometry–mass spectrometryIon mobility spectrometry–mass spectrometry (IMS-MS) is an analytical chemistry method that separates gas phase ions based on their interaction with a collision gas and their masses. In the first step, the ions are separated according to their mobility through a buffer gas on a millisecond timescale using an ion mobility spectrometer. The separated ions are then introduced into a mass analyzer in a second step where their mass-to-charge ratios can be determined on a microsecond timescale.
Quantifier (logic)In logic, a quantifier is an operator that specifies how many individuals in the domain of discourse satisfy an open formula. For instance, the universal quantifier in the first order formula expresses that everything in the domain satisfies the property denoted by . On the other hand, the existential quantifier in the formula expresses that there exists something in the domain which satisfies that property. A formula where a quantifier takes widest scope is called a quantified formula.
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
Universal quantificationIn mathematical logic, a universal quantification is a type of quantifier, a logical constant which is interpreted as "given any", "for all", or "for any". It expresses that a predicate can be satisfied by every member of a domain of discourse. In other words, it is the predication of a property or relation to every member of the domain. It asserts that a predicate within the scope of a universal quantifier is true of every value of a predicate variable.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Existential quantificationIn predicate logic, an existential quantification is a type of quantifier, a logical constant which is interpreted as "there exists", "there is at least one", or "for some". It is usually denoted by the logical operator symbol ∃, which, when used together with a predicate variable, is called an existential quantifier ("∃x" or "∃(x)" or "(∃x)"). Existential quantification is distinct from universal quantification ("for all"), which asserts that the property or relation holds for all members of the domain.
Stable isotope labeling by amino acids in cell cultureStable Isotope Labeling by/with Amino acids in Cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics. Two populations of cells are cultivated in cell culture. One of the cell populations is fed with growth medium containing normal amino acids. In contrast, the second population is fed with growth medium containing amino acids labeled with stable (non-radioactive) heavy isotopes.
Branching quantifierIn logic a branching quantifier, also called a Henkin quantifier, finite partially ordered quantifier or even nonlinear quantifier, is a partial ordering of quantifiers for Q ∈ {∀,∃}. It is a special case of generalized quantifier. In classical logic, quantifier prefixes are linearly ordered such that the value of a variable ym bound by a quantifier Qm depends on the value of the variables y1, ..., ym−1 bound by quantifiers Qy1, ..., Qym−1 preceding Qm. In a logic with (finite) partially ordered quantification this is not in general the case.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
Uniqueness quantificationIn mathematics and logic, the term "uniqueness" refers to the property of being the one and only object satisfying a certain condition. This sort of quantification is known as uniqueness quantification or unique existential quantification, and is often denoted with the symbols "∃!" or "∃=1". For example, the formal statement may be read as "there is exactly one natural number such that ". The most common technique to prove the unique existence of a certain object is to first prove the existence of the entity with the desired condition, and then to prove that any two such entities (say, and ) must be equal to each other (i.
ProteomicsProteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system.
DatabaseIn computing, a database is an organized collection of data (also known as a data store) stored and accessed electronically through the use of a database management system. Small databases can be stored on a , while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
Liquid chromatography–mass spectrometryLiquid chromatography–mass spectrometry (LC–MS) is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography (or HPLC) with the mass analysis capabilities of mass spectrometry (MS). Coupled chromatography - MS systems are popular in chemical analysis because the individual capabilities of each technique are enhanced synergistically. While liquid chromatography separates mixtures with multiple components, mass spectrometry provides spectral information that may help to identify (or confirm the suspected identity of) each separated component.
Graph databaseA graph database (GDB) is a database that uses graph structures for semantic queries with nodes, edges, and properties to represent and store data. A key concept of the system is the graph (or edge or relationship). The graph relates the data items in the store to a collection of nodes and edges, the edges representing the relationships between the nodes. The relationships allow data in the store to be linked together directly and, in many cases, retrieved with one operation.
IsotopologueIn chemistry, isotopologues are molecules that differ only in their isotopic composition. They have the same chemical formula and bonding arrangement of atoms, but at least one atom has a different number of neutrons than the parent. An example is water, whose hydrogen-related isotopologues are: "light water" (HOH or ), "semi-heavy water" with the deuterium isotope in equal proportion to protium (HDO or ), "heavy water" with two deuterium isotopes of hydrogen per molecule ( or ), and "super-heavy water" or tritiated water ( or , as well as and , where some or all of the hydrogen atoms are replaced with the radioactive tritium isotope).
Simple random sampleIn statistics, a simple random sample (or SRS) is a subset of individuals (a sample) chosen from a larger set (a population) in which a subset of individuals are chosen randomly, all with the same probability. It is a process of selecting a sample in a random way. In SRS, each subset of k individuals has the same probability of being chosen for the sample as any other subset of k individuals. A simple random sample is an unbiased sampling technique. Simple random sampling is a basic type of sampling and can be a component of other more complex sampling methods.
