A human who initiates or implementes a task. The person or company that manufactures an instrument, reagent or other product. 0 This defines a broad class that includes any collection of data. It can hold other data collections, it can hold parameters, which are defined as atomic objects in ProPreO (i.e., parameters cannot be further subdivided.) [Will & Satya 02/15/06] A parameter associated with an electrospray ionization source. A chemical compound composed of at least one cation (positive ion) and at least one anion (negative ion). A collection of parameters controlling the operation of the analyzer of a mass spectrometer [James & Satya: 02/24/05] A typical mass spectral data pair consisting of a mass-to-charge (m/z) ratio and the abundance associated with that ratio A parameter used in the annotation of data A data collection that is used or generated by a database search with ms, ms-ms data The family of application software developed by Agilent for processing HPLC data. [James & Satya: 03/27/05] A part of a scientific instrument. Many instruments are modular, assembled by combining several interacting components. The simulation of data from input data. For example, simulation of a theoretical spectrum from a chemical composition. [Dr. York & Satya: 11/21/05] A parameter that specifies the unique identifier that refers to a particular gene or other nucleotide sequence in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/key.html [Dr. York & Satya: 06/23/05] The task of transforming one encoding type into another. For example, binary to ascii. [Dr. York & Satya: 11/21/05] TODO: Find out the various formats, softwares used... A data collection generated by a processing raw gel electrophoresis data. This data will include, for example 1. Spot location 2. Spot Intensity 3. Spot Identity [Dr. York & Satya: 06/28/05] A collection of computational parameters required to process ms or ms-ms data [James & Satya: 03/27/05] A parameter that defines the units used to describe the intensity of a laser pulse A data collection that is generated by a Spectrum Mill database search with ms, ms-ms data [James & Satya: 03/29/05] This describes the task of transforming a given glycan structure from one representation format into another. For example from LINUCS to GLYDE. [Dr. York & Satya: 11/21/05] A parameter that is measured during an HPLC experiment - E.G. the detector signal intensity at a particular time. A parameter that specifies the unique identifier for a particular protein in the PDB database. URL: http://www.rcsb.org/pdb/ [Dr. York & Satya: 06/14/05] The process of separating components by size-exclusion chromatography. The raw data output from this intrument. [James & Satya: 03/22/05] Electrospray source for flow rates < 3 microlitres/min. [James & Satya: 02/24/05] A High Performance Liquid Chromatograph manufactured by Agilent Technologies. [James & Satya: 01/31/05] The raw data output from this intrument. [James & Satya: 03/22/05] A mass spectrometer that can perform both MS and MS/MS analysis. [James & Satya: 03/27/05] The collection of processing parameters used by Proteinlynx when converting a ms/ms survey '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05] A single time-point generated by an HPLC experiment - This corresponds to a pair of parameters, the internal HPLC time and the detector signal at that time. A parameter that describes the detection wavelength of the HPLC detector, which may be either an absorbance detector or a fluorescence detector. [James & Satya: 01/31/05] This describes the tranformation of a given peptide sequence from one format into another. [Dr. York & Satya: 11/21/05] A data collection used or generated by a high performance liquid chromatography experiment The raw data output from this intrument. [James & Satya: 03/22/05] A type of MS analyzer 0 The second component of a semantic Universal Resource Identifier (semURI) module. This identifies a specific instance (within the context of a provenance chain) of a SemURI concept. It is important to note that the same SemURI_instance_ID can be used for two distinct instances of the same concept, as long as the two instances are not present at the same location of a single provenance chain. This allows the SemURI_instance_ID to be short and still insures that the SemURI as a whole is unique. Uniqueness stems from the entire SemURI, which consists of several SemURI modules. That is, two SemURIs can be unique even if they share a common SemURI module, just as two words can be unique even if they share a common letter of series of letters. [will & satya 03/03/06] A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A parameter that identifies a molecule or molecular aggergate. An instrument that measures the transmittance of ultraviolet light through a sample (usually a liquid). A type of HPLC pump. [James & Satya: 01/31/05] A diverse group of prokaryotic organisms, distinct from the Archaea. A parameter that specifies the unique identifier for a particular protein in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/ [Dr. York & Satya: 06/14/05] An enzyme is a protein or protein complex that catalyzes a specific set of chemical reactions. An ion, generated in a mass spectrometer, that is subsequently dissociated into fragment ions in an MS/MS experiment A parameter that describes some aspect of part of an organism that was used as the source of a biological_sample or biomolecule. A biological source parameter refers to, for example, a species, organ, cell type, life-cycle stage, develomental stage, etc. Within the context of ProPreO, biological source parameters are meant to describe laboratory samples that are analyzed by or used in proteomics or glycoproteomics methods. A parameter that specifies the unique glycan identifier in SWEETDB. URL: http://www.glycosciences.de/sweetdb/index.php [Dr. York & Satya: 06/13/05] The raw data output from this intrument. [James & Satya: 03/22/05] A chemical agent is a chemical or molecule (such as an enzyme) that implements or initiates a molecular process. The complex task of quantifying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and signal integration (i.e., quantify_data). 0 A parameter that defines the type of TOF analyzer. It may either be: a) Reflectron or b) Linear [James & Satya: 02/24/05] The raw data output from this intrument. [James & Satya: 03/22/05] A parameter that is used to control the execution of a task, such as a physical parameter required for recording a mass spectrum or a computational parameter for processing a data set. The task of transforming the format of data, usually creating a new data file with either new file format or data encoding. [Dr. York & Satya: 11/21/05] A parameter that identifies the elution buffer used in HPLC. A mixture of buffers is often prepared in a mixing device to form a time-dependent elution gradient. The HPLC_buffer parameter is a substance identifier, which points to an instance of "solution". A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [James & Satya: 01/31/05] 0 A parameter that defines the voltage applied to the ESI capillary. [James & Satya: 02/24/05] A parameter describing the identities of chemical elements and the number of atoms of each element that constitute a molecule. [Dr. York & Satya: 11/21/05] 0 A parameter describing the index (within the parent protein) of the C- terminus of a fragment peptide. [will & satya 04/25/06] A parameter that defines the operating state of the mass spectrometer analyzer during data collection [Will & Satya 02/15/06] A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are in XML. [James & Satya: 03/29/05] A parameter describing the amount of a substance in absolute terms (total mass, total volume, total number of moles, as appropriate). [will & satya 04/13/06] A data collection that is classified according to the process that uses/creates/generates it. A data collection produced by performing PEAKKS denovo sequecing. [James & Satya: 03/29/05] A type of HPLC column Application software developed by Bruker Daltonics for processing mass spectrometer data. [James & Satya: 03/27/05] A fluorescence spectrometer measures the intensity of light that is re-emitted by a fluorescent molecule. An HPLC component that is used for manual injection of the sample onto the column. [James & Satya: 01/31/05] A type of HPLC column A task involved in the processing of data by a computational application. [Dr. York & Satya: 11/21/05] A parameter that defines the number of laser shots in a MALDI experiment. This is a pure integer (no units). [James & Satya: 02/24/05] 0 A data collection that is generated by a Sequest database search with ms, ms-ms data [James & Satya: 03/29/05] A parameter that specifies the unique identifier for a glycan instance in glycan domain ontology: GlycO. URL: http://lsdis.cs.uga.edu/projects/glycomics/glyco/ [Dr. York & Satya: 06/13/05] A parameter describing the measured charge of a particular ion. A parameter that describes the excitation wavelength of a fluorescence HPLC detector. [James & Satya: 01/31/05] A collection of parameters that describe the solvent gradient for an HPLC run [Dr. York & Satya: 05/17/05] A type of tandem_mass_spectrometer. [James & Satya: 03/27/05] A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] A data collection generated by a gel electrophoresis experiment Describes the pH at which a zwitter ionic molecule has no charge also called pI. [Dr. York & Satya: 06/28/05] The complex task of identifhying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and peak matching (i.e., classify_data). Tthe physical task of running a mass spectrometer on a specific sample and recording the resulting spectra. [Dr. York & Satya: 11/21/05] A parameter defining the physical units of potential, such as electrical potential, gravitational potential, etc. Potentials generally have units "energy per amount", for example volts are Joules per Coulomb Defines type of tandem mass spectrometer. Tandem time-of-flight spectrometer can perform ms and ms/ms type of analysis. [James & Satya: 01/31/05] A parameter that defines the center of the mass range or the center of the calibration curve for the given mass range. [James & Satya: 02/24/05] A biological species, such as Homo sapiens or Arabidopsis thaliana. The taxonomic classification of a biological species are modeled in other ontologies. http://obo.sourceforge.net/cgi-bin/detail.cgi?ncbi_taxonomy http://obo.sourceforge.net/cgi-bin/detail.cgi?newt Instances of specific organisms may be specified iwithin ProPreO, but their complete systematic taxonomy should be found in these other ontologies. [Dr. York & Satya: 06/28/05] A parameter describing the measured chemical mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05] A parameter that is used by an application that processes mass spectral data A solvent molecule that does not contain carbon, e.g., water. A biomolecule composed of amino acids connected by amide bonds. In ProPreO, a protein is distinguished from an oligopeptide mainly by its size (proteins are larger, and so are polypeptides rather than oligopeptides) . [Dr. York & Satya: 06/10/05] polypeptide A parameter describing the theoretical (calculated) monoisotopic mass of a particular molecule or ion. [Dr. York & Satya: 06/13/05] A parameter that defines the operating state of the chromatograph during data collection A parameter that defines the operating state of the mass spectrometer during data collection c A parameter that defines the length of time for an MS or MS-MS scan. [James & Satya: 02/24/05] A parameter describing the units of electrical potential A collection of parameters required to perform or analyze an HPLC run. [Dr. York & Satya: 05/17/05] This is for self-manufactured or modified that are not found under the mass spectrometer instruments. [James & Satya: 02/24/05] A type of HPLC autosampler. An individual molecule, categorized according to a few broadly defined classes. [Dr. York & Satya: 06/10/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A parameter that specifies the unique identifier for a glycan structure in the CARBANK database. URL: http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm#ccsd [Dr. York & Satya: 06/14/05] A mixture in the form of a homogeneous liquid contaning a solvent and at least one solute. A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (dissolved molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [Satya & Will 03/02/06] A type of tandem mass spectrometer. [James & Satya: 03/27/05] This is a Mascot specific result file, produced from a database search - it is in text format. The sections of the file are delimited by a unique ID string and a Content-Type specification. [James & Satya: 03/29/05] A parameter describing the sequence of residues in a biopolymer. [Dr. York & Satya: 06/28/05] A parameter describing the theoretical abundance of a particular ion. 2 This describes the two-component, basic building block of the Semantic URI provenance scheme. The two components are: 1- SemURI_concept_ID 2- SemURI_instance_ID [will & satya 03/03/06] A parameter describing the properties of an ion. An electrically charged chemical species, which may be a single atom (e.g., Na+), or many atoms (e.g., NH4+). The raw data output from this intrument. [James & Satya: 03/22/05] A parameter describing the amount of a substance in a mixture. This is expressed as some sort of fractional amount, such as weight percent, molarity, etc. A task that combines both physical and computational tasks. [Dr. York & Satya: 11/21/05] For for > microlitre/min flow rates. [James & Satya: 02/24/05] An object manufactured to perform a specfic task. Examples are bolts (which hold other objects together), computers (which execute software), and mass spectrometers (which separate and count ions based on their mass to charge ratios). A type of tandem mass spectrometer. [James & Satya: 03/27/05] A type of tandem_mass_spectrometer. [James & Satya: 03/27/05] A type of HPLC detector. [James & Satya: 01/31/05] The raw data output from this intrument. [James & Satya: 03/22/05] A parameter defining the physical units of time A type of HPLC column Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05] An organism whose cells contain a nucleus and internal membranes. [Dr. York & Satya: 06/28/05] A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] The raw data output from this intrument. [James & Satya: 03/22/05] A data collection that is generated by a database search with ms, ms-ms data [James & Satya: 03/27/05] A parameter defining the physical units of time A type of tandem mass spectrometer. [James & Satya: 03/27/05] A parameter that is classified according to the process that uses/creates/generates it. [will & satya 02/17/06] A parameter that specifies the identifier for a glycan record in the CARBANK database. URL: ftp://ncbi.nlm.nih.gov/repository/carbbank/ [Dr. York & Satya: 06/14/05] 1 Describes the molecular mass of a molecule or ion . [Dr. York & Satya: 06/13/05] A parameter describing the amount of a particular substance in a solution. The mass-volume percent of the substance is usually expressed as the number of grams of the substance divided by the number of milliliters of the solution, all divided by 100. Sometimes the mass-volume percent is abbreviated %w/v. Defines the type of source. [James & Satya: 02/24/05] A parameter describing the sequence of amino acid residues of a peptide or protein. Amino acids are listed starting at the N-terminus and continuing to the C-terminus using standard one-letter amino acid nomenclature. The name of the amino acid sequence is same as the sequence string. [Dr. York & Satya: 06/10/05] A computational task involving the reordering of data elements according to a specific set of criteria. A type of HPLC pump. [James & Satya: 01/31/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A matrix-containing tube that is used for high-performance liquid chromatography. The sample is separated into its components by injecting it into the column and elutimng with a solvent or buffer. A parameter that defines the operating state of the mass spectrometer ion source during data collection [Will & Satya 02/15/06] A data collection produced by performing Proteinlynx denovo sequecing. [James & Satya: 03/29/05] A parameter that defines the analyzer mode associated with a MS experiment. This parameter can have values of positive or negative. It describes the charge of the ions that are detected. [James & Satya: 02/24/05] A data collection generated by a gel electrophoresis experiment - this corresponds to an image of the gel, stored in a file format. [James & Satya: 03/29/05] The raw data output from this intrument. [James & Satya: 03/22/05] The first component of a semantic Universal Resource Identifier (semURI) module. Each instance of this parameter maps the module to a specific concept in ProPreO. [will & satya 03/03/06] 0 A parameter defining the physical units of power A computational task involving the identification of specific data elements and their replacement by another data element. A collection of parameters required to perform a database search with ms, ms-ms data. [James & Satya: 03/27/05] A parameter that specifies the organ from which the biological sample is taken. A data collection used or generated by a mass spectrometry experiment A type of HPLC column 2 A pair of parameters that describes the amount of a particular component of a mixture. For example "0.5 M NaCl" describes the amount of sodium chloride in a solution - there are two parts to this description - 0.5 M specifies the amount (half molar) - NaCl identifies the component that is present at that concentration. The computational simulation of the structure, physical properties or behavior of a molecule, such as conformational trajectory or reaction kinetics. [Dr. York & Satya: 11/21/05] A data collection generated by a mass spectrometer or mass spectral data processing application A parameter that is measured during an MS experiment - E.G. the abundance of an ion having a particular m/z value. A parameter defining the physical units of concentration A parameter that describes the injuection loop volume for an HPLC experiment. Following a Mascot db search, the data is saved in a HTML format. The results may further be converted into other representation formats. [James & Satya: 03/29/05] A data collection that is generated by a Matrix Science Mascot database search with ms, ms-ms data A type of HPLC column A parameter describing the sequence of nucleotides in an RNA molecule. Nucleotides are listed from the 5' end to the 3' end. A parameter describing the theoretical (calculated) mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05] A string parameter that contains the URL of a data file. A type of HPLC pump. [James & Satya: 01/31/05] A parameter describing the theoretical charge of a particular ion. A string parameter that specifies the location of a resource (such as a data file) on the internet - I.e., a Universal Resource Locator The task of processing data using computational applications. [Dr. York & Satya: 11/21/05] The raw data output from this intrument. [James & Satya: 03/22/05] A type of HPLC autosampler. [James & Satya: 01/31/05] A Matrix-Assisted-Laser-Desorption-Time-of-Flight mass spectrometer. Such a spectrometer contains a MALDI source and a TOF analyzer. [James & Satya: 03/27/05] A parameter that describes the detector signal measured at a particular time of an HPLC experiment. A type of HPLC pump. [James & Satya: 01/31/05] A parameter describing the (measured or theoretical) charge of a particular ion. A type of MS analyzer Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05] 1 Describes the molecule, its properties, origin etc. [Dr. York & Satya: 06/13/05] A collection of parameters required to perform a task that generates or processes mass spectral data A collection of parameters required to perform a gel electrophoresis experiment. [James & Satya: 03/27/05] The collection of processing parameters used by Proteinlynx when converting a electrospray '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05] The task of recording raw data using an analytical instrument. [Dr. York & Satya: 11/21/05] A parameter that describes the time (measured from the start of the experiment) within a HPLC experiment that an event occurs. This time parameter can be associated, for example, with a signal intensity or a buffer gradient condition. An HPLC fraction collector that directs the eluant from an microscale HPLC experiment. [James & Satya: 01/31/05] A type of HPLC detector. [James & Satya: 01/31/05] This task converts a raw mass spec data file into the mzXML format. Organisms, including the Crenarchaeota, Euryarchaeota and Korarchaeota, with a cell structure that is similar to other prokaryotes, but with some biochemical features that are similar to eukaryotes, some similar to bacteria, and some unique to archaea. A collection of mass spectral data that has NOT been computationally processed in any way. That is, the raw output from the mass spectrometer. These may be of multiple formats [James & Satya: 03/22/05] A solvent molecule that contains carbon, e.g., methanol. Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05] A parameter defining the physical units of mass A task that is performed by a human or physical instrument working on a physical sample. The solvent of a solution, consisting of many copies of the solvent molecule. A parameter that is used by a data processing application A type of HPLC pump. [James & Satya: 01/31/05] A component of a hgh-performance liquid chromatograph A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. PSD peak lists exported from Grams as .PKS files contain data from a single PSD spectrum. Since the .PKS format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05] The raw data output from this instrument. [James & Satya: 03/22/05] The computational processing in which data elements are matched to a spcific group to which they belong. This includes: a) identifying molecules associated with experimental data features such as ion masses (e.g., MASCOT analysis) b) categorize features in data using a set of parameters. For example, distinguish peptides from glycopeptides [Dr. York & Satya: 11/21/05] This describes collections of experimental (measured) data, either raw or processed. Such data can serve as the input to a data processing task or the output of an experimental measurement or computational task. Class of related proteolytic enzymes that cleave after basic amino acids K & R except when followed by P. [Dr. York & Satya: 06/28/05] A molecular aggregate composed of more than one type of molecule. A mixture is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the component itself. Separate components of a mixture by filtration. The filter allows some components to pass through while retaining other components. A parameter describing the amount of a particular substance in a mixture. The mass percent of the substance is its percent contribution to the total mass of the mixture. Sometimes mass percent is called weight/weight percent, and abbreviated %w/w. A type of tandem_mass_spectrometer. [James & Satya: 03/27/05] An analytical instrument is a piece of hardware designed to measure a parameter or analyze a sample. The raw data output from this intrument. [James & Satya: 03/22/05] The raw data output from this intrument. [James & Satya: 03/22/05] A data collection (chromatogram) generated by an HPLC experiment -This typically consists of a collection of time/signal intensity pairs [James & Satya: 03/29/05] Application software used in processing/manipulating data. [James & Satya: 03/27/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A collection of instrumental parameters required to record mass spectral data [James & Satya: 03/27/05] The raw data output from this instrument. [James & Satya: 03/22/05] An aggregate of molecules, which may or may not be homogeneous. E.G.: a liter of water (homogeneous) a pound of wheat flour (heterogeneous) a milligram of extracted protein (heterogeneous) [will & satya 03/02/06] A parameter that describes a physical substance such as a buffer, gas etc. An experimentally measured parameter, either raw or processed. (E.G., signal intensity) A collection of such parameters can serve as the input to a data processing task or the output of an experimental measurement or computational task. A type of tandem mass spectrometer. [James & Satya: 03/27/05] Separate components of a mixture by dialysis. The dialysis membrane allows some components to pass through while retaining other components. A type of tandem_mass_spectrometer. [James & Satya: 03/27/05] A molecular aggragate that is used in a MALDI source. The MALDI matrix absorbs energy from the laser, and this energy promotes transfer to the gas phase and ionizaton of the analyte. A parameter that corresponds to the CHEBI ID from the ChEBI Ontology http://www.ebi.ac.uk/chebi/ An organism whose cells do not have a nucleus or internal membranes. [Dr. York & Satya: 06/28/05] The raw data output from this intrument. [James & Satya: 03/27/05] The process of separating components by high-performance liquid chromatography. A collection of mass spectral data that has NOT been computationally processed, except that it has been converted to mzXML format A parameter describing the index (within the parent protein) of the N- terminus of a fragment peptide. [will & satya 04/25/06] A parameter that defines the maximum mass range associated with a MS experiment. Mass range is determined by the user and the instrument. It typically has a value from 0 to 500,000. [James & Satya: 02/24/05] A collection of parameters that defines a HPLC run time and the associated buffer mixture that comprises the eluent at that time. It can have multiple values of component portion for that time value. [Dr. York & Satya: 06/28/05] The collection of processing parameters used by Proteinlynx when converting a MALDI '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05] A parameter describing the amount of a particular substance in a mixture. The volume percent of the substance is its percent contribution to the total volume of the mixture. Sometimes volume percent is called volume/volume percent, and abbreviated %v/v. A parameter describing the identity or a physical property of a molecule. [James & Satya: 04/01/05] A parameter that is used/created/generated during the acquisition or processing of HPLC data a data collection that is used to annotate other data A parameter that describes the eluant flow rate for an HPLC experiment. [James & Satya: 01/31/05] A collection of mass spectral data that has NOT been computationally processed, except that its digital format has been modified A biomolecule composed of glycosyl residues. A glycan is a type of carbohydrate molecule. [Dr. York & Satya: 06/10/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] a data collection that describes the physical substances such as buffers, gases etc. An HPLC instrument component that directs the eluant from the HPLC column to a series of separate vessels (tubes of wells). The collector may direct the eluant to different vessels based on elution time, detector response, or some other criterion. A type of HPLC detector. [James & Satya: 01/31/05] A collection of mass spectral data that has been computationally processed - E.G. a peak list [James & Satya: 03/22/05] A component of a mass spectrometer A protein that catalyzes the cleavage of peptide bonds in proteins to generate peptides. [Dr. York & Satya: 06/28/05] A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] A type of HPLC detector. [James & Satya: 01/31/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05] A type of HPLC column A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Peak lists exported from PE Sciex API III contain data from a single MS/MS spectrum. Since the file format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05] The type of tandem_mass_spectrometer. [James & Satya: 03/27/05] A parameter that specifies the unique identifier in a database that refers to a particular molecule or gene. The name of each accession number instance should contain the accession number itself. [Dr. York & Satya: 06/13/05] A type of tandem_mass_spectrometer. [James & Satya: 03/27/05] Application software used in processing/manipulating HPLC data. [James & Satya: 03/27/05] Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05] A parameter that corresponds to the Chemical Abstrracts Accession number of a molecule. 0 A parameter that specifies the organism from which the biological sample is taken. A collection of parameters controlling the operation of a matrix-assisted laser-desorption ionization source of a mass spectrometer [Will & Satya 02/15/06] 0 A parameter defining the physical units of a parameter (measurement of setting) [will &satya 04/14/06] The process of separating components by lectin-affinity chromatography. A data collection used or generated by a denovo sequencing process with ms-ms data. Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05] The computational processing in which a quantity (e.g. amount) is associated with various data elements. A molecular aggregate composed of many copies of same molecule. [will & satya 03/02/06] Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05] A specific biological organ, such as heart or leaf. Several OBO ontologies model anatomical features of organsims, including their organs, tissues, cells, etc. and additional semantic information can be specified by cross reference to these other ontologies. The raw data output from this intrument. [James & Satya: 03/27/05] A parameter that specifies the unique glycan identifier in the KEGG database. URL: http://www.genome.jp/kegg/ [Dr. York & Satya: 06/14/05] The process of separating components by chromatography. [Dr. York & Satya: 11/21/05] A parameter that describes the time within a process that an event occured. E.G., a "retention time" in HPLC or a "scan acquisition time" in mass spectrometry. A mass spectrometer separates and counts ions based on their mass to charge ratios. [James & Satya: 03/27/05] A parameter that defines the voltage applied to the inlet cone. [James & Satya: 02/24/05] A parameter that specifies the unique identifierfor a glycan. [Dr. York & Satya: 06/13/05] A process that is initiated or implemented by an agent. A type of HPLC detector. [James & Satya: 01/31/05] The raw data output from this instrument. [James & Satya: 03/27/05] A parameter that defines the matrix used in the MALDI analysis. It may be of multiple types like: a) DHB b) Alpha-Cyano [James & Satya: 02/24/05] A data collection used or generated by gel electrophoresis experiments A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. The DTA format is very simple. The first line contains the singly protonated peptide mass (MH+) and the peptide charge state as a pair of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05] A parameter that specifies the unique identifier for a particular protein in the UNIPROT (formerly SWISSPROT) database. URL: www.uniprot.org/ [Dr. York & Satya: 06/14/05] A parameter describing the theoretical mass-to-charge ratio (m/z) of a particular ion. [will & satya 03/02/06] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are generally tab, space or comma separated. [James & Satya: 03/29/05] A parameter describing the measured monoisotopic mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A collection of parameters required to perform a denovo sequencing with ms-ms data. [James & Satya: 03/27/05] The body of the report contains a tabular summary of the best matching proteins. [Dr. York & Satya: 07/19/05] In ProPreO, a parameter is a single, indivisible datum (i.e., parameters cannot be further subdivided.) Collections of parameters are called data_collections in ProPreO. Note that in ProPreO, a parameter (such as a substance_identifier or biological_source_parameter) may refer to a specific object (such as an organism or a molecule), but the parameter and the object that it refers to are separate. In these cases, the parameter is piece of information that may be found, for example, in a data file and the object it points to is a real world object of class of objects. These two entities are related by the property "refers_to_material_continuant". [satya 02/15/06] 0 A parameter that defines the minimum mass range associated with a MS experiment. An organism in the form it adopts at a specific stage in its life-cycle. For example, an epimastigote is a life-cycle form of a Trypanosome. Ontologies that more fully model life-cycle stages are in development, for example, http://obo.sourceforge.net/cgi-bin/detail.cgi?plasmodium_life_cycle Application software used in processing/manipulating ms or ms-ms data. [James & Satya: 03/27/05] A parameter that specifies the cell type from which the biological sample is taken. A type of tandem mass spectrometer. [James & Satya: 03/27/05] The raw data output from this intrument. [James & Satya: 03/22/05] A parameter defining the physical units of length A type of tandem mass spectrometer. [James & Satya: 03/27/05] A parameter associated with a matrix assisted laser induced ionization source. [James & Satya: 02/24/05] A collection of mass spectral data that has NOT been computationally processed other than to change its digital format A type of HPLC column A type of HPLC column The body of the Peptide Summary report contains a tabular listing of the proteins, sorted by descending protein score. [Dr. York & Satya: 07/19/05] A parameter that describes the time within a mass spectrometry that an event occurs. E.G., the time (measured from the start of the experiment) that a particular mass spectrum was recorded. A parameter that is used/created/generated during the acquisition or processing of MS data [Will & Satya: 01/19/06] A parameter describing the total mass of a particular substance (e.g., 5 grams of NaCl) in a molecular aggregate The raw data output from this intrument. [James & Satya: 03/22/05] The raw data output from this intrument. [James & Satya: 03/22/05] A parameter describing the amount of a substance in a solution. The molarity is the number of moles of the substance that is dissolved in one Liter of the solution. A parameter describing the measured abundance of a particular ion. A data collection that is used to control the execution of a task, such as the physical parameters required for recording a mass spectrum or the computational parameters for processing a data set. A string parameter that contains the URL of a meta-data file. A parameter that specifies the unique identifier for a particular protein in a database. [Dr. York & Satya: 06/13/05] A molecule that is very generally classified by its small size. This class is intended to allow the classification of molecules that are encountered in proteomics analysis (such as a solvent molecule or a MALDI matrix component), but are not classified as a major type of biomolecule. A parameter describing the sequence of deoxynucleotides in a DNA molecule. Nucleotides are listed from the 5' end to the 3' end. A parameter describing the measured mass to charge ratio (m/z) of a particular ion. An HPLC component that pumps the eluant through the HPLC column, usually at high pressure and at a tightly controlled flow rate. An agent is a real world object that causes something to happen, i.e., it initiates or implements a process. Examples are human operators, analytical instruments, enzymes, and software applications A parameter describing the amount of a substance. A material continuant is a real-world object. The transformation of the representational format of data. For example, FASTA format to GCG format. [Dr. York & Satya: 11/21/05] An HPLC instrument component that detects molecules that are eluted from the HPLC column. [James & Satya: 01/31/05] The semantic Universal Resource Identifier (semURI) for a specific instance defined in ProPreO or other aligned ontology. By semantic URI we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history. The raw data output from this intrument. [James & Satya: 03/22/05] A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Often, the abundance of the ion is included in the peak list. The ms/ms peak list can be used to perform database searching or denovo sequencing. [James & Satya: 03/27/05] An HPLC component that is programmed to automatically inject samples into the HPLC column. [James & Satya: 01/31/05] A type of MS analyzer A type of HPLC column The simulation of the output of an analytical instrument like NMR, ms or chromatography. It is computed based on a set of input parametres. [Dr. York & Satya: 11/21/05] A parameter that defines the time period between MS and MS-MS scans. [James & Satya: 02/24/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] A parameter describing the measured mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05] Measured from an experiment. [Dr. York & Satya: 06/28/05] The raw data output from this intrument. [James & Satya: 03/22/05] Data constitute the basic units of information. Data can include collections of information or individual units of information. Data can be experimental (measured) or theoretical (calculated). [satya 02/15/06] A parameter describing the (measured or theoretical) abundance of a particular ion. A mass spectromete component that separates ions according to their mass to charge ratio. Ions are produced in the ion source. The raw data output from this intrument. [James & Satya: 03/22/05] A type of HPLC column An HPLC instrument component that uses a vacuum to remove dissolved gas from a sample or eluant before it is pumped through the HPLC column. A type of MS analyzer An instrument that performs a type of flow cytometry (cell counting), sorting cells in a suspension according to their fluorescence properties. A type of MS analyzer A type of HPLC autosampler. [James & Satya: 01/31/05] A cell, such as a neutrophil or a stem cell. These are more fully modeled in the cell ontology http://obo.sourceforge.net/cgi-bin/detail.cgi?cell The raw data output from this intrument. [James & Satya: 03/22/05] A parameter that specifies the unique identifier in a database that refers to a particular gene or other nucleotide sequence. [Dr. York & Satya: 06/24/05] An instrument that separates molecules by passing a solution of the molecules through a column containing a solid matrix that differentially interacts with the molecules. A molecular aggregate that has been prepared in the laboratory from a biological continuant. A small molecule that contains the element carbon. A material continuant that is described chiefly with respect to its chemical composition. A peptide that is generated by treatment of a protein with the proteolytic enzyme trypsin . [Dr. York & Satya: 06/28/05] A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Files in this format are created by the LIST command on the ICIS data system. The header block for each MS/MS dataset begins with a "LIST:" field. The text in this field is used by Mascot to identify the query, equivalent to an embedded TITLE parameter. The ASC file header does not specify a charge state for the precursor peptide. This can be specified (globally) on the search form, or by an embedded CHARGE parameter at the head of the data file. The precursor peptide m/z value is parsed from the "Mode:" field. Mascot uses the prevailing CHARGE value to calculate Mr from the observed m/z. A blank line to delimit MS/MS datasets is optional. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05] A parameter describing the theoretical (calculated) chemical mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] This class includes organisms at various stages of development or life-cycle (e.g., spore, seed, blastula, embryo, adult, epimastigote) and parts of these organisms (e.g., organs, tissues and cells). It also includes cultured cells and tissues (e.g., cultured embryonic stem cells). The ProPreO is not meant to explicitly describe all of these objects. Rather, it is meant to provide access to ontological descriptions of these objects by defining broad classes that are more fully modeled in other ontologies. A parameter describing the (measured or theoretical) mass-to-charge ratio (m/z) of a particular ion. A type of tandem mass spectrometer. [James & Satya: 03/27/05] One of a diverse collection of computational processing tasks including: a) Changing the format b) Search and Replace (e.g., modification of DataBase) c) Sort [Dr. York & Satya: 11/21/05] A molecule that exists as a liquid in the laboratory, and that can dissolve other molecules. E.G. water, methanol. An HPLC fraction collector that directs the eluant from an micro scale HPLC experiment onto specific locatons on a MALDI target for subsequent MALDI MS analysis. A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05] A mixture that is in the solid state, for example, dry baking powder, composed of solid NaHCO3 and tartaric acid. [Satya & Will 03/02/06] Tthe simulation of mass spectra. For example, calculation of an isotopic distribution based on elemental composition and subsequent simulation of a mass spectum based on the calculated isotopic distribution. [Dr. York & Satya: 11/21/05] Calculated from the molecular structure. [Dr. York & Satya: 06/28/05] The task of physcially spearating the components of a mixture. A collection of parameters controlling the operation of the ion source of a mass spectrometer [James & Satya: 02/24/05] A parameter that defines the intensity of the laser used in the MS experiment. [James & Satya: 02/24/05] A parameter describing the total volume of a particular substance (e.g., 5 Liters of water) in a molecular aggregate The raw data output from this intrument. [James & Satya: 03/22/05] By semantic URI (SemURI) we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history. A data collection generated by a denovo sequencing process with ms-ms data. [James & Satya: 03/27/05] An HPLC fraction collector that directs the eluant from an analytical scale HPLC experiment. [James & Satya: 01/31/05] peptide A biomolecule composed of amino acids connected by amide bonds. A peptide can be generated by fragmentation of a protein by a protease (e.g. trypsin). In ProPreO, peptides are distinguished from proteins mainly by size (oligopeptides are smaller, and thereby distinct from polypeptides). [Dr. York & Satya: 06/10/05] A type of HPLC autosampler. [James & Satya: 01/31/05] A type of tandem mass spectrometer. [James & Satya: 03/27/05] Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05] A data collection (in XML format) consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. A collection of parameters controlling the operation of an electrospray ionization source of a mass spectrometer [Will & Satya 02/15/06] A parameter describing the amount of a substance in a solution. The mole fraction is the number of moles of a particular solute divided by the total number of moles of in the solution. A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. QTof users can export peak list data in either DTA or PKL format using the Micromass ProteinLynx package. The PKL format is similar to the DTA file format, but supports multiple MS/MS datasets in a single file. The first line of a PKL dataset contains the observed m/z, intensity, and charge state of the precursor peptide as a triplet of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. Multiple MS/MS datasets are delimited by at least one blank line. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05] A boolean parameter that describes whether a N-glycosylation consensus sequence is present in a peptide or protein. [will & satya 04/25/06] Defines the protein from which the peptide was cleaved. The peptide is a specific entity and not a generic sequence. [Dr. York & Satya: 06/10/05] This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46. This object property describes the canonical composition of all data collection - they are made up of either parameters or data collection itself. [Satya - 02/23/06] All mass spectrometers can produce peak lists containing masses and intensities. Different types of mass spectrometers can produce different formats of ms peak lists. [James & Satya: 03/27/05] This is an 'abstract' property that subsumes properties that denote causality in the passive voice. [Will & Satya: 01/19/06] This property enables mapping of each concept in ProPreO to a concept in the SemURI framework. [will & satya 03/03/06] This property describes the chemical entity in terms of either a collection of parameters (substance_associated_data_collection) or an individual parameter (substance_parameter). [Dr. York & Satya: 04/11/06] This object property is subsumed by "has_agent" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46. This is an 'abstract' property that subsumes properties that denote causality in the active voice. [Will & Satya: 01/19/06] Associates a biomolecule with its biological source. [Dr. York & Satya: 06/28/05] This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06] An abstract object property subsuming object properties that map to an objectified and classified parameter. The objectified parameter wraps a datum value associated with it. For example, has_mass maps to objects of the class "mass", which have the data property "has_value". Then, "has_value" is restricted to float values (amu) for the class "mass" This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06] This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46. associates the peptide with the enzyme that released it. [Dr. York & Satya: 06/28/05] Peak list produced from tandem ms experiments. [James & Satya: 03/27/05] This specialization of the 'part-of' relation is to relate material continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06] One of the top level relations, as defined in the 'Relations in biomedical ontologies', Barry Smith et. al. Genome Biology 2005, 6:R46. Thsi relation has been defined for all the top level classes in ProPreO (through subsumption from owl:Thing) i.e. all classes in ProPreO have a or are a 'part-of' another ProPreO class. [Satya & Will 03/01/2006] A parameter may describe a chemical entity such as a HPLC solvent or a MALDI matrix. This property relates such a parameterto a specific chemical entity which is not a parameter but a continuant. [will & satya 04/10/06] Defines the general concept of the value of a class of data. The explicit restrictions of this value (i.e., its primitive data type, cardinality, etc) are separately defined for each class in the domain. [Dr. York & Satya: 06/13/05] Homo sapiens Man Man [Dr. York & Satya: 06/28/05] The elementary electrical charge is the charge of a single electron e e q The CAS number of alpha-cyano-4-hydroxycinnamic acid 28166-41-8 An aromatic molecule (alpha-cyano-4-hydroxycinnamic acid) used as a MALDI matrix negative mode amu 1 amu ≈ 1.66053886 × 10E-27 kg amu kilograms kg the physical units of mass in kilograms hours the physical units of time in hours An aromatic molecule (2-5-dihydroxybenzoic_acid) used as a MALDI matrix 490-79-9 The CAS number of 2,5-dihydroxybenzoic acid Homo sapiens Homo sapiens Man true alpha-cyano-4-hydroxycinnamic acid A MALDI matrix composed of alpha-cyano-4-hydroxycinnamic acid alpha-cyano-4-hydroxycinnamic acid Defines a matrix composed of alpha-Cyano-4-hydxoxycinnamic_acid, used for MALDI MS ng nanograms the physical units of mass in nanograms The units of electrical potential defined as millivolts, or thousandths of a volt. millivolts false reflectron TOF analyzer the physical units of flowrate in milliliters per minute milliliters per minute Defines a matrix composed of 2,5-dihydroxybenzoic acid, used for MALDI MS liters the physical units of volume in liters minutes the physical units of time in minutes the physical units of mass in grams g grams mg the physical units of mass in milligrams milligrams the physical units of volume in milliliters milliliters moles per liter the physical units of concentration in moles per liter C coulombs The units of electrical charge defined as coulombs, which can also be expresses as Amperes seconds. One coulomb is equivalent to the charge of 6.24151E18 electrons. millimeters the physical units of length in millimeters, or 0.001 meters The CAS number of water 7732-18-5 CHEBI:15377 The ChEBI ID for water A molecule of water, the most common solvent for HPLC water A collection of water molecules, acting as a solvent the physical units of time in seconds seconds The units of electrical potential defined as volts, which can also be expressed as Joules per coulomb volts the physical units of time in milliseconds milliseconds micrograms the physical units of mass in micrograms linear TOF analyzer the physical units of length in nanometers, or 0.000000001 meters nanometers nanoliters per minute the physical units of flowrate in nanoliters per minute A MALDI matrix composed of dihydroxybenzoic acid DHB DHB the physical units of flowrate in microliters per minute microliters per minute microliters the physical units of volume in microliters micrometers the physical units of length in micrometers, or 0.000001 meters The ChEBI ID of alpha-cyano-4-hydroxycinnamic acid