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Peptide-mass Fingerprint
In bio-informatics, a peptide-mass fingerprint or peptide-mass map is a mass spectrum of a mixture of peptides that comes from a digested protein being analyzed. The mass spectrum serves as a fingerprint in the sense that it is a pattern that can serve to identify the protein. The method for forming a peptide-mass fingerprint, developed in 1993, consists of isolating a protein, breaking it down into individual peptides, and determining the masses of the peptides through some form of mass spectrometry. Once formed, a peptide-mass fingerprint can be used to search in databases for related protein or even genomic sequences, making it a powerful tool for annotation of protein-coding genes. One major advantage to mass fingerprinting is that it is significantly faster to carry out than peptide sequencing, yet the results are equally useful. Disadvantages include the need for a single protein for analysis and the requirement that the protein sequence is located, at least with significant ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bio-informatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for ''in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (esp. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrospray Ionization
Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized. ESI is different from other ionization processes (e.g. matrix-assisted laser desorption/ionization (MALDI)) since it may produce multiple-charged ions, effectively extending the mass range of the analyser to accommodate the kDa-MDa orders of magnitude observed in proteins and their associated polypeptide fragments. Mass spectrometry using ESI is called electrospray ionization mass spectrometry (ESI-MS) or, less commonly, electrospray mass spectrometry (ES-MS). ESI is a so-called 'soft ionization' technique, since there is very little fragmentation. This can be advantageous in the sense that the molecular ion (or more accurately a pseudo molecular ion) is almost alw ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Mass Spectrometry
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids. The two primary methods used for the ionization of protein in mass spectrometry are electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). These ionization techniques are used in conjunction with mass analyzers such as tandem mass spectrometry. In general, the prote ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mascot (software)
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm. Mascot is freely available to use on the website of Matrix Science. A license is required for in-house use where more features can be incorporated. History means MOWSE was one of the first algorithms developed for protein identification using peptide mass fingerprinting. It was originally developed in 1993 as a collaboration between Darryl Pappin of the Imperial Cancer Research Fund (ICRF) and Alan Bleasby of the Science and Engineering Research Council (SERC). MOWSE stood apart from other protein identification algorithms in that it produced a probability-based score for identification. It was also the first to take into account the non-uniform distribution of peptide sizes, caused ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quadrupole Ion Trap
A quadrupole ion trap or paul trap is a type of ion trap that uses dynamic electric fields to trap charged particles. They are also called radio frequency (RF) traps or Paul traps in honor of Wolfgang Paul, who invented the device and shared the Nobel Prize in Physics in 1989 for this work. It is used as a component of a mass spectrometer or a trapped ion quantum computer. Overview A charged particle, such as an atomic or molecular ion, feels a force from an electric field. It is not possible to create a static configuration of electric fields that traps the charged particle in all three directions (this restriction is known as Earnshaw's theorem). It is possible, however, to create an ''average'' confining force in all three directions by use of electric fields that change in time. To do so, the confining and anti-confining directions are switched at a rate faster than it takes the particle to escape the trap. The traps are also called "radio frequency" traps because the switc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Time Of Flight
Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium. This information can then be used to measure velocity or path length, or as a way to learn about the particle or medium's properties (such as composition or flow rate). The traveling object may be detected directly (direct time of flight, dToF, e.g., via an ion detector in mass spectrometry) or indirectly (indirect time of flight, iToF, e.g., by light scattered from an object in laser doppler velocimetry). Overview In electronics, one of the earliest devices using the principle are ultrasonic distance-measuring devices, which emit an ultrasonic pulse and are able to measure the distance to a solid object based on the time taken for the wave to bounce back to the emitter. The ToF method is also used to estimate the electron mobility. Originally, it was designed for measurement of low-conductive thin films, later adju ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MS/MS
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass spectrometry, mass analyzers are coupled together using an additional reaction step to increase their abilities to Analytical chemistry, 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 Ionization, ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q). Ions of a particular m/z-ratio coming from MS1 are selected and then made to split into smaller Fragmentation (mass spectrometry), fragment ions, e.g. by collision-induced dissociation, Gas-phase ion chemistry, ion-molecule reaction, or photodissociation. These fragments are then introduced into the second mass spectrometer (MS2), which in turn separates the fragments by their m/z-ratio and Mass spectrometry#Detectors, detects them. The fragm ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MALDI-TOF
In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and carbohydrates) and various organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft (low fragmentation) ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions. MALDI methodology is a three-step process. First, the sample is mixed with a suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polyacrylamide Gel Electrophoresis
Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation, and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species. Hydration of acrylonitrile results in formation of acrylamide molecules () by nitrile hydratase. Acrylamide monomer is in a powder state before addition of water. Acrylamide is toxic to the human nervous system, therefore all safety measures must be followed when working with it. Acrylamide is soluble in water and upon addition of free-radical initiators it polymerizes resulting in formation of polyacrylamide. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrum
A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example, some mass spectrometers break the analyte molecules into '' fragments''; others observe the intact molecular masses with little fragmentation. A mass spectrum can represent many different types of information based on the type of mass spectrometer and the specific experiment applied. Common fragmentation processes for organic molecules are the ''McLafferty rearrangement'' and ''alpha cleavage''. Straight chain alkanes and alkyl groups produce a typical series of peaks: 29 (CH3CH2+), 43 (CH3CH2CH2+), 57 (CH3CH2CH2CH2+), 71 (CH3CH2CH2CH2CH2+) etc. X-axis: ''m/z'' (mass-to-charge ratio) The x-axis of a mass spectrum represents a relationship between the mass of a given ion and the number of elementary charges that it carries. This is writte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chymotrypsin
Chymotrypsin (, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum, where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the side chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their side chain that fits into a hydrophobic pocket (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 side chain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly tho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
