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Mass Spectrometry Data Format
Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins ( proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here. Op ... [...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 ionized, for example by bombarding it with a 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 (fragments) are then separated accordin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Union Of Pure And Applied Chemistry
The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is a member of the International Science Council (ISC). IUPAC is registered in Zürich, Switzerland, and the administrative office, known as the "IUPAC Secretariat", is in Research Triangle Park, North Carolina, United States. This administrative office is headed by IUPAC's executive director, currently Lynn Soby. IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, or other bodies representing chemists. There are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPAC's Inter-divisional Committee on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, it has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. As of June 2022, GitHub reported having over 83 million developers and more than 200 million repositories, including at least 28 million public repositories. It is the largest source code host . History GitHub.com Development of the GitHub.com platform began on October 19, 2007. The site was launched in April 2008 by Tom Preston-Werner, Chris Wanstrath, P. J. Hyett and Scott Chacon after it had been made available for a few months prior as a beta release. GitHub has an annual keynote called GitHub Universe. Organizational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Insilicos
Insilicos is a life science software company founded in 2002 by Erik Nilsson, Brian Pratt and Bryan Prazen. Insilicos develops scientific computing software to provide software for disease diagnoses. Technology Insilicos' key technologies includes pattern recognition techniques to interpret proteomics mass spectrometry data. Insilicos products include InsilicosViewer and Insilicos Proteomics Pipeline (IPP). These products support the mzXML, mzDATA and mzML file formats. In 2007, Insilicos received a grant from the National Human Genome Research Institute to further develop software allowing for studies to be conducted more quickly. The open-source software, developed in connection with the Institute for Systems Biology, has been referred to as the Trans Proteomic Pipeline. IPP is commercial version of the Trans-Proteomic Pipeline The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data-independent Acquisition
In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected '' m/z'' range are fragmented and analyzed in a second stage of tandem mass spectrometry. Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time (called broadband DIA) or by sequentially isolating and fragmenting ranges of '' m/z''. DIA is an alternative to data-dependent acquisition (DDA) where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry. Broadband One of the first DIA approaches was a nozzle-skimmer dissociation method called shotgun collision-induced dissociation (CID). Fragmentation can be in the ion source of the mass spectrometer by increasing the nozzle-skimmer voltage in electrospray ionization. MSE is a broadband DIA technique that uses alternating low-energy CID and high-energy CID. The low-energy CID is used to acquire precursor ion ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Relational Database
A relational database is a (most commonly digital) database based on the relational model of data, as proposed by E. F. Codd in 1970. A system used to maintain relational databases is a relational database management system (RDBMS). Many relational database systems are equipped with the option of using the SQL (Structured Query Language) for querying and maintaining the database. History The term "relational database" was first defined by E. F. Codd at IBM in 1970. Codd introduced the term in his research paper "A Relational Model of Data for Large Shared Data Banks". In this paper and later papers, he defined what he meant by "relational". One well-known definition of what constitutes a relational database system is composed of Codd's 12 rules. However, no commercial implementations of the relational model conform to all of Codd's rules, so the term has gradually come to describe a broader class of database systems, which at a minimum: # Present the data to the user as relati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SQLite
SQLite (, ) is a database engine written in the C programming language. It is not a standalone app; rather, it is a library that software developers embed in their apps. As such, it belongs to the family of embedded databases. It is the most widely deployed database engine, as it is used by several of the top web browsers, operating systems, mobile phones, and other embedded systems. Many programming languages have bindings to the SQLite library. It generally follows PostgreSQL syntax, but does not enforce type checking by default. This means that one can, for example, insert a string into a column defined as an integer. History D. Richard Hipp designed SQLite in the spring of 2000 while working for General Dynamics on contract with the United States Navy. Hipp was designing software used for a damage-control system aboard guided-missile destroyers, which originally used HP-UX with an IBM Informix database back-end. SQLite began as a Tcl extension. In August 2000, versio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Universally Unique Identifier
A universally unique identifier (UUID) is a 128-bit nominal number, label used for information in computer systems. The term globally unique identifier (GUID) is also used. When generated according to the standard methods, UUIDs are, for practical purposes, unique. Their uniqueness does not depend on a central registration authority or coordination between the parties generating them, unlike most other numbering schemes. While the probability that a UUID will be duplicated is not zero, it is generally considered close enough to zero to be negligible. Thus, anyone can create a UUID and use it to identify something with near certainty that the identifier does not duplicate one that has already been, or will be, created to identify something else. Information labeled with UUIDs by independent parties can therefore be later combined into a single database or transmitted on the same channel, with a negligible probability of duplication. Adoption of UUIDs is widespread, with many comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry Imaging
Mass spectrometry imaging (MSI) is a technique used in mass spectrometry to visualize the spatial distribution of molecules, as biomarkers, metabolites, peptides or proteins by their molecular masses. After collecting a mass spectrum at one spot, the sample is moved to reach another region, and so on, until the entire sample is scanned. By choosing a peak in the resulting spectra that corresponds to the compound of interest, the MS data is used to map its distribution across the sample. This results in pictures of the spatially resolved distribution of a compound pixel by pixel. Each data set contains a veritable gallery of pictures because any peak in each spectrum can be spatially mapped. Despite the fact that MSI has been generally considered a qualitative method, the signal generated by this technique is proportional to the relative abundance of the analyte. Therefore, quantification is possible, when its challenges are overcome. Although widely used traditional methodologies ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HDF5
Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. Originally developed at the U.S. National Center for Supercomputing Applications, it is supported by The HDF Group, a non-profit corporation whose mission is to ensure continued development of HDF5 technologies and the continued accessibility of data stored in HDF. In keeping with this goal, the HDF libraries and associated tools are available under a liberal, BSD-like license for general use. HDF is supported by many commercial and non-commercial software platforms and programming languages. The freely available HDF distribution consists of the library, command-line utilities, test suite source, Java interface, and the Java-based HDF Viewer (HDFView). The current version, HDF5, differs significantly in design and API from the major legacy version HDF4. Early history The quest for a portable scientific data format, originally dubbed AEHOO (All Encompassing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Application Program Interface
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build or use such a connection or interface is called an ''API specification''. A computer system that meets this standard is said to ''implement'' or ''expose'' an API. The term API may refer either to the specification or to the implementation. In contrast to a user interface, which connects a computer to a person, an application programming interface connects computers or pieces of software to each other. It is not intended to be used directly by a person (the end user) other than a computer programmer who is incorporating it into the software. An API is often made up of different parts which act as tools or services that are available to the programmer. A program or a programmer that uses one of these parts is said to ''call'' that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database Schema
The database schema is the structure of a database described in a formal language supported by the database management system (DBMS). The term "schema" refers to the organization of data as a blueprint of how the database is constructed (divided into database tables in the case of relational databases). The formal definition of a database schema is a set of formulas (sentences) called integrity constraints imposed on a database. These integrity constraints ensure compatibility between parts of the schema. All constraints are expressible in the same language. A database can be considered a structure in realization of the database language. The states of a created conceptual schema are transformed into an explicit mapping, the database schema. This describes how real-world entities are modeled in the database. "A database schema specifies, based on the database administrator's knowledge of possible applications, the facts that can enter the database, or those of interest to the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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