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Peptide Mass Fingerprinting
Peptide mass fingerprinting (PMF), also known as protein fingerprinting, is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. The method was developed in 1993 by several groups independently. The peptide masses are compared to either a database containing known protein sequences or even the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides, and calculate the absolute masses of the peptides from each protein. They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match. The advantage of this method is that only the masses of the peptides have to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptide Mass Fig
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. Peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies. Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond.. All peptides except cyclic peptides have an N-terminal (amine group) and C-terminal (carboxyl group) residu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pipette
A pipette (sometimes spelled as pipet) is a type of laboratory tool commonly used in chemistry and biology to transport a measured volume of liquid, often as a media dispenser. Pipettes come in several designs for various purposes with differing levels of accuracy and precision, from single piece glass pipettes to more complex adjustable or electronic pipettes. Many pipette types work by creating a Vacuum, partial vacuum above the liquid-holding chamber and selectively releasing this vacuum to draw up and dispense liquid. Measurement accuracy varies greatly depending on the instrument. History The first simple pipettes were made of glass, such as Pasteur pipettes. Large pipettes continue to be made of glass; others are made of squeezable plastic for situations where an exact volume is not required. During or prior to 1877, Joseph Lister (1827 – 1912) invented the first adjustable micropipette, consisting of a "pipette with a syringe" (photograph shown at right). The micr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Methods
Protein methods are the techniques used to study proteins. There are experimental methods for studying proteins (e.g., for detecting proteins, for isolating and purifying proteins, and for characterizing the structure and function of proteins, often requiring that the protein first be purified). Computational methods typically use computer programs to analyze proteins. However, many experimental methods (e.g., mass spectrometry) require computational analysis of the raw data. Genetic methods Experimental analysis of proteins typically requires expression and purification of proteins. Expression is achieved by manipulating DNA that encodes the protein(s) of interest. Hence, protein analysis usually requires DNA methods, especially cloning. Some examples of genetic methods include conceptual translation, Site-directed mutagenesis, using a fusion protein, and matching allele with disease states. Some proteins have never been directly sequenced, however by translating codons from known ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bottom-up Proteomics
Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry. BUP techniques can be an alternative to Maldi-Tof MS approaches, as they allow the identification of bacterial strains and the characterization of potential resistance and virulence factors in a single run. The major alternative workflow used in proteomics is called top-down proteomics where intact proteins are purified prior to digestion and/or fragmentation either within the mass spectrometer or by 2D electrophoresis. Essentially, bottom-up proteomics is a relatively simple and reliable means of determining the protein make-up of a given sample of cells, tissues, etc. In bottom-up proteomics, the crude protein extract is enzymatically digested, followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass spectrometry ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Top-down Proteomics
Top-down proteomics is a method of protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ... identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance ( Penning trap), quadrupole ion trap (Paul trap) or Orbitrap mass spectrometer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shotgun Proteomics
Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides. Targeted proteomics using SRM and data-independent acquisition methods are often considered alternatives to shotgun proteomics in the field of bottom-up proteomics. While shotgun proteomics uses data-dependent selection of precursor ions to generate fragment ion scans, the aforementioned methods use a deterministic method for acquisition of fragment ion scans. History Shotgun proteomics arose from the d ... [...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] |
Swissprot
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, USA. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Georgetown Uni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Capillary Electrophoresis
Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other electrophoresis, electrophoretic techniques including capillary gel electrophoresis (CGE), capillary isoelectric focusing (CIEF), capillary isotachophoresis and micellar electrokinetic chromatography (MEKC) belong also to this class of methods. In CE methods, analytes migrate through electrolyte solutions under the influence of an electric field. Analytes can be separated according to ionic mobility and/or partitioning into an alternate phase via non-covalent interactions. Additionally, analytes may be concentrated or "focused" by means of gradients in Electrical resistivity and conductivity, conductivity and pH. Instrumentation The instrumentation needed to perform capillary electrophoresis is relatively simple. A basic schematic of a capil ... [...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). Time of flight technology has found valuable applications in the monitoring and characterization of material and biomaterials, hydrogels included. 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. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Desorption
Desorption is the physical process where Adsorption, adsorbed atoms or molecules are released from a surface into the surrounding vacuum or fluid. This occurs when a molecule gains enough energy to overcome the activation barrier and the binding energy that keep it attached to the surface. Desorption is the reverse of the process of adsorption, which differs from absorption in that adsorption refers to substances bound to the surface, rather than being absorption (chemistry), absorbed into the bulk. Desorption can occur from any of several processes, or a combination of them: it may result from heat (thermal energy); incident light such as infrared, visible, or ultraviolet photons; or an incident beam of energetic particles such as electrons. It may also occur following chemical reactions such as oxidation or reduction in an electrochemical cell or after a chemical reaction of a adsorbed compounds in which the surface may act as a catalyst. Mechanisms Depending on the nature ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
