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PEAKS
PEAKS is a proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification. Description PEAKS is commonly used for peptide identification (Protein ID) through de novo peptide sequencing assisted search engine A search engine is a software system that provides hyperlinks to web pages, and other relevant information on World Wide Web, the Web in response to a user's web query, query. The user enters a query in a web browser or a mobile app, and the sea ... database searching. PEAKS has also integrated PTM and mutation characterization through automatic peptide sequence tag based searching (SPIDER)Ma B, Johnson. De Novo sequencing and homology searching Molecular & Cellular Proteomics. 10.1074/mcp.O111.014902 (2011). and PTM Identification. PEAKS provides a complete sequence for each peptide, confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, amongst other i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry Software
Mass spectrometry software is used for data acquisition, analysis, or representation in mass spectrometry. Proteomics software In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and ''de novo'' search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample. In contrast, the latter infers Protein primary structure, peptide sequences without knowledge of genomic data. Database search algorithms De novo sequencing algorithms De novo peptide sequencing algorithms are, in general, based on the approach proposed in Bartels ''et al.'' (1990). Homology searching algorithms MS/MS peptide quantification Other software See also * Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters. * List of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass 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. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionization, ionized, for example by bombarding it with a Electron ionization, beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragmen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
De Novo Peptide Sequencing
In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest is essential for studying the biological function of the protein. In the old days, this was accomplished by the Edman degradation procedure. Today, analysis by a tandem mass spectrometer is a more common method to solve the sequencing of peptides. Generally, there are two approaches: database search and de novo sequencing. Database search is a simple version as the mass spectra data of the unknown peptide is submitted and run to find a match with a known peptide sequence, the peptide with the highest matching score will be selected. This approach fails to recognize novel peptides since it can only match to existing sequences in the database. De novo sequencing is an assignment of fragment ions from a mass spectrum. Different algorithms are used for interpretation and most i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Label-free Quantification
Label-free quantification is a method in mass spectrometry that aims to determine the relative amount of proteins in two or more biological samples. Unlike other methods for protein quantification, label-free quantification does not use a stable isotope containing compound to chemically bind to and thus label the protein. Implementation Label-free quantification may be based on precursor signal intensity or on spectral counting. The first method is useful when applied to high precision mass spectra, such as those obtained using the new generation of time-of-flight (ToF), fourier transform ion cyclotron resonance (FTICR), or Orbitrap mass analyzers. The high-resolution power facilitates the extraction of peptide signals on the MS1 level and thus uncouples the quantification from the identification process. In contrast, spectral counting simply counts the number of spectra identified for a given peptide in different biological samples and then integrates the results for all measu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptide Sequence Tag
A peptide sequence tag is a piece of information about a peptide obtained by tandem mass spectrometry that can be used to identify this peptide in a protein database. Mass spectrometry In general, peptides can be identified by fragmenting them in a mass spectrometer. For example, during collision-induced dissociation peptides collide with a gas within the mass spectrometer and break into pieces at their peptide bonds. The resulting fragment ions (called b-ions and y-ions) have mass differences corresponding to the residue masses of the respective amino acids. Thus, a tandem mass spectrum contains partial information about the amino acid sequence of the peptide. The peptide sequence tag approach, developed by Matthias Wilm and Matthias Mann at the EMBL, uses this information to identify the peptide in a database. Briefly, a couple of masses are extracted from the spectrum in order to obtain the peptide sequence tag. This peptide sequence tag is a unique identifier of a specific ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proprietary Software
Proprietary software is computer software, software that grants its creator, publisher, or other rightsholder or rightsholder partner a legal monopoly by modern copyright and intellectual property law to exclude the recipient from freely sharing the software or modifying it, and—in some cases, as is the case with some patent-encumbered and EULA-bound software—from making use of the software on their own, thereby restricting their freedoms. Proprietary software is a subset of non-free software, a term defined in contrast to free and open-source software; non-commercial licenses such as CC BY-NC are not deemed proprietary, but are non-free. Proprietary software may either be closed-source software or source-available software. Types Origin Until the late 1960s, computers—especially large and expensive mainframe computers, machines in specially air-conditioned computer rooms—were usually leased to customers rather than Sales, sold. Service and all software available ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Commercial Software
Commercial software, or, seldom, payware, is a computer software that is produced for sale or that serves commercial purposes. Commercial software can be proprietary software or free and open-source software. Background and challenge While software creation by programming is a time and labor-intensive process, comparable to the creation of physical goods, the reproduction, duplication and sharing of software as digital goods is in comparison disproportionately easy. No special machines or expensive additional resources are required, unlike almost all physical goods and products. Once the software is created it can be copied in infinite numbers, for almost zero cost, by anyone. This made commercialization of software for the mass market in the beginning of the computing era impossible. Unlike hardware, it was not seen as trade-able and commercialize-able good. Software was plainly shared for free (hacker culture) or distributed bundled with sold hardware, as part of the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptide
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 g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Search Engine
A search engine is a software system that provides hyperlinks to web pages, and other relevant information on World Wide Web, the Web in response to a user's web query, query. The user enters a query in a web browser or a mobile app, and the search engine results page, search results are typically presented as a list of hyperlinks accompanied by textual summaries and images. Users also have the option of limiting a search to specific types of results, such as images, videos, or news. For a search provider, its software engine, engine is part of a distributed computing system that can encompass many data centers throughout the world. The speed and accuracy of an engine's response to a query are based on a complex system of Search engine indexing, indexing that is continuously updated by automated web crawlers. This can include data mining the Computer file, files and databases stored on web servers, although some content is deep web, not accessible to crawlers. There have been ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isotope-coded Affinity Tag
An isotope-coded affinity tag (ICAT) is an ''in-vitro'' isotopic labeling method used for quantitative proteomics by mass spectrometry that uses chemical labeling reagents. These chemical probes consist of three elements: a reactive group for labeling an amino acid side chain (e.g., iodoacetamide to modify cysteine residues), an isotopically coded linker, and a tag (e.g., biotin) for the affinity isolation of labeled proteins/peptides. The samples are combined and then separated through chromatography, then sent through a mass spectrometer to determine the mass-to-charge ratio between the proteins. Only cysteine containing peptides can be analysed. Since only cysteine containing peptides are analysed, often the post translational modification is lost. Development The original tags were developed using deuterium, but later the same group redesigned the tags using 13C instead to circumvent issues of peak separation during liquid chromatography due to the deuterium interacting with t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isobaric Tag For Relative And Absolute Quantitation
Isobaric tags for relative and absolute quantitation (iTRAQ) is an isobaric labeling method used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different sources in a single experiment. It uses stable isotope labeled molecules that can be covalent bonded to the N-terminus and side chain amines of proteins. Procedure The ITRAQ method is based on the covalent labeling of the N-terminus and side chain amines of peptides from protein digestions with tags of varying mass. There are currently two mainly used reagents: 4-plex and 8-plex, which can be used to label all peptides from different samples/treatments. These samples are then pooled and usually fractionated by liquid chromatography and analyzed by tandem mass spectrometry Mass 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
