53// remark: coverage: Mass spectrometer output files and spectra interpretation
54// remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
55// remark: creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>
56// remark: creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
57// remark: creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
58// remark: creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se>
59// remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
60// remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group
61// remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html.
124 /// mass resolution: Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
130 /// resolution type: Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z.
142 /// Scan Function: Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum.
148 /// scan law: Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used.
166 /// magnetic field strength: A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity.
169 /// B (magnetic field strength): A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity.
178 /// detector resolution: The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height.
193 /// deisotoping: The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution.
214 /// m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
217 /// mass-to-charge ratio (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
220 /// Th (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
223 /// thomson (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
235 /// intensity unit: Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.
271 /// continuous flow fast atom bombardment: Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
274 /// CF-FAB (continuous flow fast atom bombardment): Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
295 /// membrane separator: A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane.
319 /// atmospheric pressure chemical ionization: Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
322 /// APCI (atmospheric pressure chemical ionization): Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
325 /// chemical ionization: The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization.
328 /// CI (chemical ionization): The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization.
331 /// Electronic Ionization: The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
334 /// EI (Electronic Ionization): The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
337 /// electrospray ionization: A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended.
340 /// ESI (electrospray ionization): A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended.
343 /// fast atom bombardment ionization: The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization.
346 /// FAB (fast atom bombardment ionization): The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization.
349 /// matrix-assisted laser desorption ionization: The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
352 /// MALDI (matrix-assisted laser desorption ionization): The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
364 /// fourier transform ion cyclotron resonance mass spectrometer: A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
367 /// FT_ICR (fourier transform ion cyclotron resonance mass spectrometer): A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
370 /// magnetic sector: A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z.
373 /// quadrupole: A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
376 /// quadrupole ion trap: Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
379 /// Paul Ion trap (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
382 /// QIT (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
385 /// Quistor (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
436 /// constant neutral mass loss: A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
439 /// multiple ion monitoring: Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring.
469 /// channeltron: A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse.
472 /// Channeltron Detector (channeltron): A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse.
475 /// conversion dynode electron multiplier: A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected.
478 /// conversion dynode photomultiplier: A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier.
481 /// daly detector: Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector.
484 /// Daly (daly detector): Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector.
487 /// electron multiplier tube: A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons.
490 /// EMT (electron multiplier tube): A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons.
499 /// microchannel plate detector: A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate.
502 /// multichannel plate (microchannel plate detector): A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate.
514 /// analog-digital converter: Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers.
517 /// ADC (analog-digital converter): Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers.
532 /// AB SCIEX instrument model: The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\".
550 /// centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
553 /// Discrete Mass Spectrum (centroid spectrum): Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
556 /// profile spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
559 /// continuous mass spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
562 /// Continuum Mass Spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
574 /// percent of base peak: The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity.
577 /// collision-induced dissociation: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
580 /// CID (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
583 /// CAD (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
586 /// collision activated dissociation (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
589 /// plasma desorption: The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
592 /// PD (plasma desorption): The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
595 /// post-source decay: A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra.
598 /// PSD (post-source decay): A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra.
607 /// electron volt: A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J.
610 /// eV (electron volt): A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J.
814 /// selected ion monitoring: The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
817 /// Multiple Ion Monitoring (selected ion monitoring): The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
820 /// SIM (selected ion monitoring): The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
823 /// selected reaction monitoring: Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space.
826 /// SRM (selected reaction monitoring): Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space.
829 /// accurate mass: An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition.
835 /// appearance energy: The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended.
838 /// AE (appearance energy): The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended.
841 /// base peak: The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
844 /// BP (base peak): The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
847 /// OBSOLETE charge number: OBSOLETE. The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state.
850 /// z (OBSOLETE charge number): OBSOLETE. The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state.
859 /// electron affinity: The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy.
862 /// EA (electron affinity): The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy.
865 /// electron energy obsolete: The potential difference through which electrons are accelerated before they are used to bring about electron ionization.
877 /// ionization cross section: A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule.
889 /// isotope dilution mass spectrometry: A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
892 /// IDMS (isotope dilution mass spectrometry): A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
895 /// magnetic deflection: The deflection of charged particles in a magnetic field due to a force equal to qv B where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer.
910 /// molecular beam mass spectrometry: A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
913 /// MBMS (molecular beam mass spectrometry): A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
922 /// nitrogen rule: An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms.
925 /// nominal mass: The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value.
928 /// odd-electron rule: Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions.
931 /// peak: A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably.
937 /// proton affinity: The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states.
940 /// PA (proton affinity): The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states.
943 /// mass resolving power: In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported.
946 /// total ion current chromatogram: Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time.
949 /// TIC chromatogram (total ion current chromatogram): Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time.
955 /// unified atomic mass unit: A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg.
958 /// u (unified atomic mass unit): A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg.
961 /// accelerator mass spectrometry: A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy.
964 /// AMS (accelerator mass spectrometry): A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy.
967 /// atmospheric pressure matrix-assisted laser desorption ionization: Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer.
970 /// AP MALDI (atmospheric pressure matrix-assisted laser desorption ionization): Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer.
982 /// APPI (Atmostpheric Pressure Photoionization): Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
985 /// blackbody infrared radiative dissociation: A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation.
988 /// BIRD (blackbody infrared radiative dissociation): A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation.
994 /// CRF (charge-remote fragmentation): A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
997 /// consecutive reaction monitoring: MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
1000 /// CRM (consecutive reaction monitoring): MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
1006 /// CS (charge stripping): The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
1009 /// delayed extraction: The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer.
1012 /// DE (delayed extraction): The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer.
1024 /// DIP (direct insertion probe): A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
1033 /// electron capture dissociation: A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments.
1036 /// ECD (electron capture dissociation): A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments.
1045 /// electron-induced excitation in organics: The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion.
1048 /// EIEIO (electron-induced excitation in organics): The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion.
1051 /// electron multiplier: A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons.
1054 /// EM (electron multiplier): A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons.
1057 /// electrostatic energy analyzer: A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time.
1060 /// ESA (electrostatic energy analyzer): A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time.
1063 /// flowing afterglow: An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa.
1066 /// FA (flowing afterglow): An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa.
1069 /// high-field asymmetric waveform ion mobility spectrometry: The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion.
1072 /// FAIMS (high-field asymmetric waveform ion mobility spectrometry): The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion.
1075 /// field desorption: The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization.
1078 /// FD (field desorption): The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization.
1087 /// glow discharge ionization: The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas.
1090 /// GD-MS (glow discharge ionization): The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas.
1093 /// ion kinetic energy spectrometry: A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
1096 /// IKES (ion kinetic energy spectrometry): A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
1102 /// IMS (ion mobility spectrometry): The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
1105 /// infrared multiphoton dissociation: Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
1108 /// IRMPD (infrared multiphoton dissociation): Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
1111 /// isotope ratio mass spectrometry: The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
1114 /// IRMS (isotope ratio mass spectrometry): The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
1123 /// kinetic energy release distribution: Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
1126 /// KERD (kinetic energy release distribution): Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
1132 /// Laser Ionization MERGE (Laser Desorption): The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
1138 /// mass analyzed ion kinetic energy spectrometry: Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process.
1141 /// MIKES (mass analyzed ion kinetic energy spectrometry): Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process.
1147 /// MS (mass spectrometry): The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
1150 /// mass spectrometry/mass spectrometry: The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
1153 /// MS/MS (mass spectrometry/mass spectrometry): The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
1156 /// multiple stage mass spectrometry: Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
1159 /// MSn (multiple stage mass spectrometry): Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
1168 /// neutralization reionization mass spectrometry: With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species.
1171 /// NRMS (neutralization reionization mass spectrometry): With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species.
1180 /// pyrolysis mass spectrometry: A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source.
1183 /// PyMS (pyrolysis mass spectrometry): A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source.
1186 /// collision quadrupole: A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation.
1189 /// q (collision quadrupole): A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation.
1192 /// resonance enhanced multiphoton ionization: Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species.
1195 /// REMPI (resonance enhanced multiphoton ionization): Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species.
1204 /// surface enhanced laser desorption ionization: The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization.
1207 /// SELDI (surface enhanced laser desorption ionization): The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization.
1213 /// SEND (surface enhanced neat desorption): Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
1216 /// suface ionization: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
1219 /// SI (suface ionization): The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
1228 /// sustained off-resonance irradiation: A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time.
1231 /// SORI (sustained off-resonance irradiation): A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time.
1240 /// stored waveform inverse fourier transform: A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS/MS experiments.
1243 /// SWIFT (stored waveform inverse fourier transform): A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS/MS experiments.
1246 /// total ion current: The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum.
1249 /// TIC (total ion current): The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum.
1252 /// time lag focusing: Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse.
1255 /// TLF (time lag focusing): Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse.
1258 /// time-of-flight mass spectrometer: An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
1261 /// TOF-MS (time-of-flight mass spectrometer): An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
1267 /// double-focusing mass spectrometer: A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam.
1273 /// linear ion trap: A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap.
1276 /// mass spectrograph obsolete: An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate.
1285 /// mattauch-herzog geometry: An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians.
1288 /// nier-johnson geometry: An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians.
1291 /// paul ion trap: A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected.
1294 /// prolate traochoidal mass spectrometer: A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path.
1297 /// quistor: An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term.
1300 /// reflectron: A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time.
1303 /// sector mass spectrometer: A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection.
1309 /// transmission quadrupole mass spectrometer: A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
1321 /// einzel lens: Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle.
1327 /// first stability region: The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole.
1333 /// kinetic energy analyzer: A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field.
1348 /// mathieu stability diagram: A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer.
1351 /// orthogonal extraction: The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage.
1354 /// resonance ion ejection: A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it.
1357 /// space charge effect: The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time.
1363 /// 2E Mass Spectrum: A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained.
1366 /// charge inversion mass spectrum: The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z.
1378 /// constant neutral gain spectrum: A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell.
1381 /// constant neutral mass gain spectrum (constant neutral gain spectrum): A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell.
1384 /// constant neutral loss spectrum: A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
1387 /// constant neutral mass loss spectrum (constant neutral loss spectrum): A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
1390 /// consecutive reaction monitoring: A type of MS/MS experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
1393 /// e/2 mass spectrum: A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions.
1396 /// linked scan: A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum.
1399 /// linked scan at constant b/e: A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors.
1402 /// Linked Scan at Constant E2/V: A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors.
1405 /// Linked Scan at Constant B2/E: A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended.
1408 /// Linked Scan at Constant B[1-(E/E0)]^1/2 / E: A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan.
1411 /// MS/MS in Time: A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.
1414 /// MS/MS in Space: A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition.
1420 /// nth generation product ion: Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated.
1423 /// nth generation product ion scan: The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.
1426 /// nth generation product ion spectrum: The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions.
1429 /// precursor ion: An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is not recommended.
1435 /// product ion: An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated.
1438 /// product ion spectrum: A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions.
1441 /// progeny ion: A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+.
1444 /// Progeny Fragment Ion (progeny ion): A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+.
1450 /// conversion dynode: A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected.
1453 /// dynode: One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode.
1459 /// ion-to-photon detector: A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier.
1465 /// postacceleration detector: A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector.
1468 /// secondary electron: Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go?
1471 /// adduct ion: Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules.
1474 /// aromatic ion: A planar cyclic ion that obeys the Hckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure.
1483 /// cationized molecule: An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used.
1486 /// cluster ion: An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-.
1489 /// Conventional ion: A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion.
1492 /// diagnostic ion: A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives.
1498 /// distonic ion: A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion.
1501 /// enium ion: A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions.
1510 /// Isotopologue ion: An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue.
1513 /// Isotopomeric ion: Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer.
1516 /// metastable ion: An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection.
1519 /// molecular ion: An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion.
1525 /// non-classical ion: Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions.
1528 /// onium ion: A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+.
1531 /// principal ion: Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions.
1537 /// protonated molecule: An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended.
1540 /// radical ion: An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation.
1543 /// reference ion: A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion.
1561 /// autodetachment: The formation of a neutral when a negative ion in a disrtete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source.
1564 /// autoionization: The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source.
1567 /// charge exchange ionization: The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization.
1570 /// chemi-ionization: The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization.
1579 /// electron ionization: The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
1594 /// liquid secondary ionization: The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization.
1600 /// microelectrospray: Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanaoelectrospray.
1603 /// nanoelectrospray: Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray.
1606 /// nanospray (nanoelectrospray): Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray.
1609 /// penning ionization: Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited.
1612 /// plasma desorption ionization: The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
1618 /// secondary ionization: The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions.
1627 /// surface-assisted laser desorption ionization: The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization.
1630 /// surface ionization: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
1636 /// vertical ionization: A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state.
1642 /// alpha-cleavage: A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds.
1645 /// beta-cleavage: A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds.
1651 /// charge-induced fragmentation: Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation.
1654 /// charge inversion reaction: Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion.
1657 /// charge permutation reaction: The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion.
1660 /// charge stripping reaction: Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion.
1663 /// charge transfer reaction: The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species.
1666 /// collisional excitation: The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion.
1672 /// heterolytic cleavage: Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis.
1675 /// high energy collision: Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV.
1678 /// high-energy collision-induced dissociation: A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.
1681 /// HCD (high-energy collision-induced dissociation): A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.
1684 /// homolytic cleavage: Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis.
1687 /// hydrogen/deuterium exchange: Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer.
1690 /// ion energy loss spectrum: A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species.
1696 /// ion/molecule reaction: The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule.
1699 /// ion/neutral complex: A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions.
1702 /// ion/neutral species reaction: A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants.
1705 /// ion/neutral species exchange reaction: In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product.
1708 /// kinetic method: An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account.
1714 /// low-energy collision-induced dissociation: A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative.
1717 /// McLafferty Rearrangement: A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied.
1723 /// multiphoton dissociation (photodissociation): A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
1729 /// partial charge transfer reaction: Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral.
1735 /// superelastic collision: Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners.
1738 /// surface-induced reaction: A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion.
1741 /// unimolecular dissociation: Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion.
1759 /// fast ion bombardment: The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample.
1762 /// FIB (fast ion bombardment): The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample.
1837 /// 1200 series LC/MSD SL: The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS/MS and 11 stages of manual MS/MS.
1840 /// 6110 Quadrupole LC/MS: The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications.
1843 /// 6120 Quadrupole LC/MS: The 6120 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition.
1846 /// 6130 Quadrupole LC/MS: The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
1849 /// 6140 Quadrupole LC/MS: The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
1852 /// 6210 Time-of-Flight LC/MS: The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
1855 /// 6310 Ion Trap LC/MS: The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges.
1858 /// 6320 Ion Trap LC/MS: The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
1861 /// 6330 Ion Trap LC/MS: The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
1864 /// 6340 Ion Trap LC/MS: The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
1867 /// 6410 Triple Quadrupole LC/MS: The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration.
1870 /// 6410 Triple Quad LC/MS (6410 Triple Quadrupole LC/MS): The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration.
1873 /// 1200 series LC/MSD VL: The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor.
1888 /// Thermo Fisher Scientific instrument model: Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific.
1891 /// orbitrap: An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer.
1933 /// zoom scan: Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
1936 /// enhanced resolution scan (zoom scan): Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
2020 /// spectrum representation: Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks.
2059 /// massWolf: A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology.
2062 /// wolf (massWolf): A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology.
2071 /// ReAdW: A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced \"readraw\".
2074 /// MzStar: A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program.
2107 /// Trapper: A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.
2128 /// mass spectrometer file format: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
2155 /// SHA-1: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
2200 /// Single-Stage Mass Spectrometry (MS1 spectrum): Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
2203 /// MSn spectrum: MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
2206 /// multiple-stage mass spectrometry spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
2209 /// nth generation product ion spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
2212 /// product ion spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
2215 /// CRM spectrum: Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
2218 /// SIM spectrum: Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
2221 /// MIM spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
2224 /// multiple ion monitoring spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
2227 /// selected ion monitoring spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
2230 /// SRM spectrum: Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
2233 /// MRM spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
2236 /// multiple reaction monitoring spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
2239 /// selected reaction monitoring spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
2263 /// MzWiff: A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program.
2266 /// smoothing: A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process.
2269 /// baseline reduction: A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values.
2275 /// thresholding (low intensity data point removal): The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
2287 /// electron transfer dissociation: A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them.
2290 /// ETD (electron transfer dissociation): A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them.
2293 /// pulsed q dissociation: A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected.
2296 /// PQD (pulsed q dissociation): A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected.
2350 /// preset scan configuration: A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time.
2389 /// selected ion current chromatogram: Chromatogram created by creating an array of the measurements of a specific single ion current at each time point.
2392 /// SIC chromatogram (selected ion current chromatogram): Chromatogram created by creating an array of the measurements of a specific single ion current at each time point.
2410 /// possible charge state: A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty.
2533 /// 6220 Time-of-Flight LC/MS: The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
2536 /// 6510 Quadrupole Time-of-Flight LC/MS: The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
2539 /// 6520 Quadrupole Time-of-Flight LC/MS: The 6520 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
2848 /// below precursor intensity dominance charge state calculation: Infers charge state as single or amibiguously multiple by determining the fraction of intensity below the precursor m/z.
2851 /// precursor recalculation: A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions.
2854 /// msPrefix precursor recalculation: Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans.
2857 /// Savitzky-Golay smoothing: Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques.
2860 /// LOWESS smoothing: Reduces intensity spikes by applying a modeling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible.
2872 /// moving average smoothing: Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
2875 /// box smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
2878 /// boxcar smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
2881 /// sliding average smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
2884 /// non-standard data array: A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added.
2896 /// time-delayed fragmentation spectrum: MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation.
2917 /// peak list scans: A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
2920 /// peak list raw scans: A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
2923 /// custom unreleased software tool: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added.
2926 /// mass resolving power: The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported.
2929 /// area peak picking: Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported.
2932 /// sum peak picking (area peak picking): Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported.
2935 /// height peak picking: Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported.
2938 /// max peak picking (height peak picking): Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported.
2941 /// analyzer scan offset: Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value.
2947 /// EMR spectrum (electromagnetic radiation spectrum): A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
2971 /// EMR radiation chromatogram (electromagnetic radiation chromatogram): The measurement of electromagnetic properties as a function of the retention time.
3010 /// no nativeID format: No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format.
3022 /// isolation window lower offset: The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
3025 /// isolation window upper offset: The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
3055 /// laser: Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation.
3088 /// solid-state laser: Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states.
3094 /// free electron laser: Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term.
3109 /// fraction identifier: Identier string that describes the sample fraction. This identifer should contain the fraction number(s) or similar information.
3112 /// molecule: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
3127 /// predicted isoelectric point: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
3130 /// predicted pI (predicted isoelectric point): The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
3139 /// molecular formula: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
3142 /// structural formula: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
3145 /// SMILES string: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
3157 /// MaRiMba: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
3187 /// protein: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
3205 /// unmodified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
3208 /// modified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid modifications that are present.
3217 /// unlabeled peptide: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3220 /// light labeled peptide (unlabeled peptide): A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3223 /// peptide group label: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
3226 /// retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit the chromatographic column.
3229 /// local retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit an unspecified local chromatographic column and instrumental setup.
3232 /// normalized retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit a standardized reference chromatographic column and instrumental setup.
3235 /// predicted retention time: A time interval relative to the beginning of a mass spectrometric run when a peptide will exit a chromatographic column as predicted by a referenced software application.
3241 /// de facto standard: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
3247 /// retention time normalization standard: A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column.
3250 /// H-PINS retention time normalization standard: The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column.
3259 /// percent of base peak times 100: The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries.
3265 /// peak targeting suitability rank: Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant.
3268 /// transition: A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely.
3271 /// reaction (transition): A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely.
3277 /// transition optimized on specified instrument: The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined.
3280 /// transition validated with an MS/MS spectrum on specified instrument: The transition has been validated by obtaining an MS/MS spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term.
3283 /// transition purported from an MS/MS spectrum on a different, specified instrument: The transition has been purported by obtaining an MS/MS spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad).
3295 /// retention time window lower offset: The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymetric about the target time.
3298 /// retention time window upper offset: The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymetric about the target time.
3301 /// target list: A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically.
3307 /// includes supersede excludes: A priority setting specifying that included targets have priority over the excluded targets if there is a conflict.
3310 /// excludes supersede includes: A priority setting specifying that excluded targets have priority over the included targets if there is a conflict.
3313 /// Skyline: Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default.
3316 /// TIQAM: Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.
3319 /// MaRiMba: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
3322 /// ATAQS: Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology.
3325 /// product interpretation rank: The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1.
3331 /// calibration spectrum: A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample.
3379 /// database local file path: OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view.
3406 /// DB PI filter: Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value.
3409 /// translation frame: OSBOLETE: use attribute in mzIdentML instead. The translated open reading frames from a nucleotide database considered in the search (range: 1-6).
3514 /// ions series considered in search: The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine.
3568 /// taxonomy nomenclature: OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT).
3592 /// confident distinct peptide sequences: This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere.
3595 /// confident peptide qualification: The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than.
3598 /// confident peptide sequence number: This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere.
3634 /// n-terminal flanking residue: The residue preceeding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.
3637 /// c-terminal flanking residue: The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.
3646 /// single protein result details: Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group).
3661 /// number of matched peaks: The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count.
3664 /// ions series considered: The ion series that were used during the calculation of the count (e.g. b, y, a, b, c, y, z, b, b-NH3, b-H20, b+, z, z-, z+, y-H3PO4, immonium).
3667 /// number of peaks used: The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't.
3829 /// number of molecular hypothesis considered: Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search.
4480 /// spectrum title: OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE.
4594 /// quality estimation with implicite decoy sequences: Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy).
4633 /// taxonomy: common name: This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
4636 /// taxonomy: scientific name: This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
4639 /// taxonomy: Swiss-Prot ID: This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
4645 /// selected ion monitoring chromatogram: Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point.
4648 /// SIM chromatogram (selected ion monitoring chromatogram): Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point.
4651 /// selected reaction monitoring chromatogram: Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point.
4654 /// SRM chromatogram (selected reaction monitoring chromatogram): Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point.
4657 /// consecutive reaction monitoring chromatogram: Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point.
4660 /// CRM chromatogram (consecutive reaction monitoring chromatogram): Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point.
4765 /// Agilent MassHunter file: A data file found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer.
4774 /// Sequence database filters: Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search.
4975 /// FAIMS compensation voltage: The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
4978 /// FAIMS CV (FAIMS compensation voltage): The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
4984 /// MaxQuant: MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.
4987 /// combined pmf + ms-ms search: Search that includes data from Peptide Mass Fingerprint (PMF) and MS/MS (aka Peptide Fragment Fingerprint - PFF).
5002 /// MyriMatch:MVH: Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
5005 /// Pepitome:MVH (MyriMatch:MVH): Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
5008 /// TagRecon:MVH (MyriMatch:MVH): Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
5011 /// MyriMatch:mzFidelity: The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
5014 /// Pepitome:mzFidelity (MyriMatch:mzFidelity): The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
5017 /// TagRecon:mzFidelity (MyriMatch:mzFidelity): The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
5029 /// sequence same-set protein: A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences.
5032 /// spectrum same-set protein: A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra.
5035 /// sequence sub-set protein: A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches.
5038 /// spectrum sub-set protein: A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches.
5047 /// Protein Inference Confidence Category: Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable).
5074 /// ProteomeDiscoverer:Minimum Peak Count: Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow.
5083 /// ProteomeDiscoverer:Spectrum Selector:Precursor Selection: Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3).
5092 /// ProteomeDiscoverer:Total Intensity Threshold: Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value.
5095 /// ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements: Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header.
5098 /// ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements: Specifies the charge state of the precursor ions, if it is not defined in the scan header.
5101 /// ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements: Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header.
5104 /// ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements: Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header.
5107 /// ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements: Specifies the polarity of the ions monitored if it is not included in the scan header.
5113 /// ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset: Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors.
5119 /// ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor: Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed.
5125 /// ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses: Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra.
5128 /// ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones: Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum.
5131 /// ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak: Determines whether precursor artifact peaks from the MS/MS input spectra are removed.
5134 /// ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch: Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type.
5137 /// ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch: Determines whether spectra from different MS order scans can be grouped together.
5140 /// ProteomeDiscoverer:Spectrum Grouper:Max RT Difference: Chromatographic window where precursors to be grouped must reside to be considered the same species.
5143 /// ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion: Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis.
5149 /// ProteomeDiscoverer:Xtract:Highest MZ: Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
5155 /// ProteomeDiscoverer:Xtract:Lowest MZ: Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
5158 /// ProteomeDiscoverer:Xtract:Monoisotopic Mass Only: Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum.
5161 /// ProteomeDiscoverer:Xtract:Overlapping Remainder: Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted).
5176 /// ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores: Determines whether spectra with scores above the threshold score are retained rather than filtered out.
5227 /// ProteomeDiscoverer:Mascot:Protein CutOff Score: Minimum protein score in the IonScore column that each protein must exceed in order to be reported.
5233 /// ProteomeDiscoverer:Mascot:Protein Relevance Factor: Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report.
5251 /// ProteomeDiscoverer:Absolute XCorr Threshold: Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported.
5260 /// ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage: Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained.
5266 /// ProteomeDiscoverer:Max Modifications Per Peptide: Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance.
5275 /// ProteomeDiscoverer:Maximum Protein References Per Peptide: Maximum number of proteins that a single identified peptide can be associated with during protein assembly.
5290 /// ProteomeDiscoverer:Protein Relevance Threshold: Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report.
5341 /// ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method: Specifies which peak to select if more than one peak is found inside the integration window.
5344 /// ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance: Specifies the mass-to-charge window that enables one to look for the reporter peaks.
5524 /// Mascot:ProteinGrouping: Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering').
5527 /// Percolator:features: List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'.
5626 /// Mascot:PreferredTaxonomy: NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences.
5635 /// travelling wave ion mobility mass spectrometer: An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide.
5638 /// TWIMS (travelling wave ion mobility mass spectrometer): An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide.
5671 /// technical replicate: The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'.
5692 /// time series, time point X: The experimental design followed a time series design. The time point of this run is given in the value of this term.
5695 /// dilution series, concentration X: The experimental design followed a dilution series design. The concentration of this run is given in the value of this term.
5725 /// mass trace reporting: rectangles: The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given.
5728 /// mass trace reporting: polygons: The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1,MZ_1,RT_2,MZ_2,...,RT_i,MZ_i,...,RT_n,MZ_n), where the line (RT_n,MZ_n)->(RT_1,MZ_1) is implicite.
5758 /// iTRAQ quantitation analysis: Quantification analysis using the AB SCIEX iTRAQ isobaric labeling workflow, wherein 2-8 reporter ions are measured in MS/MS spectra near 114 m/z.
5764 /// metabolic labeling 14N / 15N quantitation analysis: Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens).
5833 /// normalization to mean of sum of all proteins: Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting).
5887 /// in-source collision-induced dissociation: The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum.
5899 /// signal-to-noise ratio: Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal.
6178 /// delta m/z: The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value.
6181 /// m/z difference (delta m/z): The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value.
6184 /// delta M: The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value.
6187 /// mass difference (delta M): The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value.
6244 /// convex hull baseline reduction: Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures.
6262 /// LIFT: A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID.
6277 /// iRT retention time normalization standard: A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys.
6292 /// decoy SRM transition: A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows.
6295 /// decoy MRM transition (decoy SRM transition): A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows.
6304 /// desorption electrospray ionization: Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
6307 /// DESI (desorption electrospray ionization): Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
6310 /// Mascot:PTM site assignment confidence: Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score).
6376 /// first author: The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution.
6379 /// senior author: The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution.
6391 /// light labeled sample (unlabeled sample): A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\".
6403 /// modulation time: The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column.
9319 /// luminous intensity unit: A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction.
9322 /// meter: A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
9328 /// second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
9331 /// ampere: An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length.
9334 /// kelvin: A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water.
9337 /// mole: A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12.
9340 /// candela: A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian.
9379 /// degree celsius: A temperature unit which is equal to one Kelvin degree. However, they have their zeros at different points. The Centigrade scale has its zero at 273.15 K.
9403 /// month: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
9478 /// speed/velocity unit: A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity.
9523 /// normal: A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule.
9529 /// meter per second per second: An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second.
9532 /// radian per second per second: An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second.
9553 /// candela per square meter: A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter.
9556 /// kilogram per square meter: An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared.
9565 /// cubic meter per mole: A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas.
9568 /// cubic centimeter per mole: A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas.
9631 /// energy unit: A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc).
9658 /// katal: A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second.
9667 /// radian: A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds.
9673 /// steradian: A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared.
9676 /// radiation unit: A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source.
9688 /// exposure unit: A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured.
9691 /// becquerel: An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps).
9694 /// curie: An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps).
9703 /// roentgen: An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs.
9736 /// disintegrations per minute: An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute.
9739 /// counts per minute: An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute.
9748 /// half life: A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration.
9751 /// foot candle: An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux.
9760 /// einstein per square meter per second: An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number.
9766 /// watt per steradian per square meter: A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction.
9772 /// microeinstein per square meter per second: An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2].
9775 /// radiance unit: A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves.
9781 /// mass percentage: A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
9784 /// mass volume percentage: A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
9790 /// parts per notation unit: A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance.
9793 /// parts per hundred: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same.
9796 /// parts per thousand: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same.
9799 /// parts per million: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6].
9802 /// parts per billion: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9].
9805 /// parts per trillion: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12].
9808 /// parts per quadrillion: A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15].
9823 /// unit per volume unit: A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution.
9835 /// enzyme unit: A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute.
9856 /// pi: A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry.
9877 /// degree fahrenheit: A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
9898 /// catalytic (activity) concentration unit: A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume.
9901 /// katal per cubic meter: A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter.
9904 /// katal per liter: A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter.
9907 /// volume per unit volume: A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution.
9910 /// milliliter per cubic meter: A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution.
9940 /// disintegrations per second: An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second.
9943 /// electric potential difference unit: A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field.
9946 /// volt: An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy.
9949 /// electric charge: A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons.
9955 /// dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state.
9967 /// magnetic flux unit: A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field.
9970 /// weber: A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt.
9988 /// bit: An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1).
10009 /// spatial resolution unit: An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels.
10012 /// dots per inch: A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space.
10018 /// pixels per inch: A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions.
10021 /// pixels per millimeter: A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image.
10051 /// surface tension unit: A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces.
10072 /// effective dose unit: A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human.
10078 /// electrical conduction unit: A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor).
10081 /// heat conduction unit: A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature.
10090 /// electronvolt: A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J.
10093 /// electric field strength unit: The electric field strength is a unit which is a measure of the potential difference between two points some distance apart.
10096 /// volt per meter: The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart.
10099 /// absorbance unit: A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light.
10108 /// millimetres of mercury: A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
10123 /// ug/disk: A unit which is equal to one microgram per disk, where a disk is some physical surface/container upon which the substance is deposited.
10126 /// nmole/disk: A unit which is equal to one nanomole per disk, where a disk is some physical surface/container upon which the substance is deposited.
10129 /// milliunits per milliliter: A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter.
10158 /// the short label to be used as a reference tag with which to refer to this particular Controlled Vocabulary source description (e.g., from the cvLabel attribute, in CVParamType elements).
