# MOS controlled vocabulary (Terms)
# spectrum generation information [MS:1001458]
# scan [MS:1000441]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000018 | scan direction | "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] |
| 2 | MS:1000465 | scan polarity | "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] |
| 3 | MS:1000503 | scan attribute | "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS] |
| 4 | MS:1000549 | selection window attribute | "Selection window properties that are associated with a value." [PSI:MS] |
| 5 | MS:1000503 | isolation window attribute | "Isolation window parameter." [PSI:MS] |
# scan attribute [MS:1000503]
| No | id | name | value type | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1000011 | mass resolution | string | "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] | |
| 2 | MS:1000015 | scan rate | Th/s | float | "Rate in Th/sec for scanning analyzers." [PSI:MS] |
| 3 | MS:1000016 | scan start time | second | float | "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] |
| 4 | MS:1000512 | filter string | string | "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] | |
| 5 | MS:1000616 | preset scan configuration | string | "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." [PSI:MS] | |
| 6 | MS:1000880 | interchannel delay | second | float | "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] |
| 7 | MS:1000927 | ion injection time | millisecond | float | "The length of time spent filling an ion trapping device." [PSI:MS] |
| 8 | MS:1002527 | instrument specific scan attribute | "Instrument specific scan properties that are associated with a value." [PSI:PI] | ||
| 9 | MS:1003057 | scan number | "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] |
# spectrum [MS:1000442]
def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS]
# peak [MS:1000231]
def: "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." [PSI:MS]
# ion selection attribute [MS:1000455]
def: "Ion selection properties that are associated with a value." [PSI:MS]
# precursor activation [MS:1000456]
def: "Terms to describe the precursor activation." [PSI:MS]
# spectrum attribute [MS:1000499]
def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS]
# binary data array [MS:1000513]
def: "A data array of values." [PSI:MS]
# binary data type [MS:1000518]
def: "Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000519 | 32-bit integer | def: "Signed 32-bit little-endian integer." [PSI:MS] |
| 2 | MS:1000521 | 32-bit float | def: "32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] |
| 3 | MS:1000522 | 64-bit integer | def: "Signed 64-bit little-endian integer." [PSI:MS] |
| 4 | MS:1000523 | 64-bit float | def: "64-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] |
| 5 | MS:1001479 | null-terminated ASCII string | def: "Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte." [PSI:MS] |
# spectrum representation [MS:1000525]
def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000127 | centroid spectrum | def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] |
| 2 | MS:1000128 | profile spectrum | def: "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." [PSI:MS] |
# spectrum type [MS:1000559]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000928 | calibration spectrum | def: "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." [PSI:MS] |
| 2 | MS:1000294 | mass spectrum | def: "A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z)." [PSI:MS] |
# spectra combination [MS:1000570]
def: "Method used to combine the mass spectra." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000571 | sum of spectra | def: "Spectra Sum." [PSI:MS] |
| 2 | MS:1000573 | median of spectra | def: "Spectra is combined by calculating the median of the spectra." [PSI:MS] |
| 3 | MS:1000575 | mean of spectra | def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS] |
| 4 | MS:1000795 | no combination | def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS] |
# binary data compression type [MS:1000572]
def: "Compression Type." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000574 | zlib compression | def: "Zlib." [PSI:MS] |
| 2 | MS:1000576 | no compression | def: "No Compression." [PSI:MS] |
| 3 | MS:1002312 | MS-Numpress linear prediction compression | def: "Compression using MS-Numpress linear prediction compression." ms-numpress (opens new window) |
| 4 | MS:1002313 | MS-Numpress positive integer compression | def: "Compression using MS-Numpress positive integer compression." ms-numpress (opens new window) |
| 5 | MS:1002314 | MS-Numpress short logged float compression | def: "Compression using MS-Numpress short logged float compression." ms-numpress (opens new window) |
| 6 | MS:1002746 | MS-Numpress linear prediction compression followed by zlib compression | def: "Compression using MS-Numpress linear prediction compression and zlib." ms-numpress (opens new window) |
| 7 | MS:1002747 | MS-Numpress positive integer compression followed by zlib compression | def: "Compression using MS-Numpress positive integer compression and zlib." ms-numpress (opens new window) |
| 8 | MS:1002748 | MS-Numpress short logged float compression followed by zlib compression | def: "Compression using MS-Numpress short logged float compression and zlib." ms-numpress (opens new window) |
| 9 | MS:1003088 | truncation and zlib compression | def: "Data array compression using mantissa bit truncation followed by zlib compression." pwiz (opens new window) |
| 10 | MS:1003089 | truncation, delta prediction and zlib compression | def: "Data array compression using mantissa bit truncation, delta prediction and zlib compression." pwiz (opens new window) |
| 11 | MS:1003090 | truncation, linear prediction and zlib compression | def: "Data array compression using mantissa bit truncation, linear prediction and zlib compression." pwiz (opens new window) |
# spectrum property [MS:1003058]
| No | id | name | synonym | value type | units | def |
|---|---|---|---|---|---|---|
| 1 | MS:1000285 | total ion current | "TIC" EXACT [] | float | "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." [PSI:MS] | |
| 2 | MS:1000504 | base peak m/z | float | m/z [MS:1000040] | "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] | |
| 3 | MS:1000285 | base peak intensity | float | number of detector counts [MS:1000131] percent of base peak [MS:1000132] counts per second [MS:1000814] percent of base peak times 100 [MS:1000905] | "The intensity of the greatest peak in the mass spectrum." [PSI:MS] | |
| 4 | MS:1000527 | highest observed m/z | float | m/z [MS:1000040] | "Highest m/z value observed in the m/z array." [PSI:MS] | |
| 5 | MS:1000528 | lowest observed m/z | float | m/z [MS:1000040] | "Lowest m/z value observed in the m/z array." [PSI:MS] | |
| 6 | MS:1000797 | peak list scans | string | "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." [PSI:MS] | ||
| 7 | MS:1000798 | peak list raw scans | string | "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." [PSI:MS] | ||
| 8 | MS:1003059 | number of peaks | int | "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] | ||
| 9 | MS:1003060 | number of data points | int | "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] |
# binary data compression parameter [MS:1003091]
def: "Settable parameter for a binary data compression event." [PSI:MS]
| No | id | name | type vale | def |
|---|---|---|---|---|
| 1 | MS:1003092 | number of mantissa bits truncated | positiveInteger | def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] |
# data transformation (data processing) [MS:1000452]
# file format conversion [MS:1000530]
def: "Conversion of one file format to another." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000544 | Conversion to mzML | def: "Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS] |
| 2 | MS:1000545 | Conversion to mzXML | def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS] |
| 3 | MS:1000546 | Conversion to mzData | def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] |
| 4 | MS:1000741 | Conversion to dta | def: "Conversion to dta format." [PSI:MS] |
# processingMethod
# data processing action [MS:1000543]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000033 | 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." [PSI:MS] |
| 2 | MS:1000034 | charge deconvolution | "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS] |
| 3 | MS:1000035 | peak picking | "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS] |
| 4 | MS:1000592 | 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." [PSI:MS] |
| 5 | MS:1000593 | 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." [PSI:MS] |
| 6 | MS:1000745 | retention time alignment | "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS] |
| 7 | MS:1000778 | charge state calculation | "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS] |
| 8 | MS:1000780 | precursor recalculation | "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS] |
| 9 | MS:1001484 | intensity normalization | "Normalization of data point intensities." [PSI:MS] |
| 10 | MS:1001485 | m/z calibration | "Calibration of data point m/z positions." [PSI:MS] |
| 11 | MS:1001486 | data filtering | "Filtering out part of the data." [PSI:MS] |
| 12 | MS:1003220 | adduct deconvolution | "Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule." [PSI:MS] |
| 13 | MS:1003222 | ion mobility deconvolution | "Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte." [PSI:MS] |
# sample [MS:1000457]
def: "Terms to describe the sample." [PSI:MS]
# sample attribute [MS:1000548]
def: "Sample properties that are associated with a value." [PSI:MS]
| No | id | name | type vale | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1000001 | sample number | string | def: "A reference number relevant to the sample under study." [PSI:MS] | |
| 2 | MS:1000002 | sample name | string | def: "A reference string relevant to the sample under study." [PSI:MS] | |
| 3 | MS:1000003 | sample state | def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] | ||
| 4 | MS:1000004 | sample mass | float | gram | def: "Total mass of sample used." [PSI:MS] |
| 5 | MS:1000005 | sample volume | float | milliliter | def: "Total volume of solution used." [PSI:MS] |
| 6 | MS:1000006 | sample concentration | float | gram per liter | def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] |
| 7 | MS:1000053 | sample batch | string | def: "Sample batch lot identifier." [PSI:MS] |
# sample preparation [MS:1000831]
def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1002985 | in-gel digestion | def: "Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI] |
| 2 | MS:1002986 | in-solution digestion | def: "Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI] |
# MALDI matrix application [MS:1000832]
def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS]
# instrument (instrument configuration) [MS:1000463]
def: "Description of the instrument or the mass spectrometer." [PSI:MS]
# instrument model [MS:1000031]
def: "Instrument model name not including the vendor's name." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000121 | SCIEX instrument model | def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems |
| 2 | MS:1000126 | Waters instrument model | def: "Waters Corporation instrument model." [PSI:MS] |
| 3 | MS:1000490 | Agilent instrument model | def: "Agilent instrument model." [PSI:MS] |
# mass analyzer (analyzer) [MS:1000451]
def: "Terms used to describe the Analyzer." [PSI:MS]
# mass analyzer type [MS:1000443]
def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS]
| No | id | name | synonym | def |
|---|---|---|---|---|
| 1 | MS:1000079 | fourier transform ion cyclotron resonance mass spectrometer | "FT_ICR" EXACT [] | def: "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." [PSI:MS] |
| 2 | MS:1000080 | magnetic sector | def: "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." [PSI:MS] | |
| 3 | MS:1000081 | quadrupole | def: "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." [PSI:MS] | |
| 4 | MS:1000084 | time-of-flight | "TOF" EXACT [] | def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] |
| 5 | MS:1000254 | electrostatic energy analyzer | "ESA" EXACT [] | def: "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." [PSI:MS] |
| 6 | MS:1000264 | ion trap | "IT" EXACT [] | def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] |
| 7 | MS:1000284 | stored waveform inverse fourier transform | "SWIFT" EXACT [] | def: "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 MS2 experiments." [PSI:MS] |
| 8 | MS:1000288 | cyclotron | def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS] | |
| 9 | MS:1000484 | orbitrap | def: "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." [PSI:MS] |
# mass analyzer attribute [MS:1000480]
def: "Analyzer properties that are associated with a value." [PSI:MS]
# detector [MS:1000453]
def: "The device that detects ions." [PSI:MS]
# detector type [MS:1000026]
def: "Type of detector used in the mass spectrometer." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000346 | conversion dynode | def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] |
| 2 | MS:1000347 | dynode | def: "One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS] |
# detector acquisition mode [MS:1000027]
def: "Method by which detector signal is acquired by the data system." [PSI:MS]
| No | id | name | synonym | def |
|---|---|---|---|---|
| 1 | MS:1000117 | analog-digital converter | "ADC" EXACT [] | def: "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." [PSI:MS] |
| 2 | MS:1000118 | pulse counting | def: "Definition to do." [PSI:MS] | |
| 3 | MS:1000119 | time-digital converter | "TDC" EXACT [] | def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS] |
| 4 | MS:1000120 | transient recorder | def: "A detector acquisition mode used for detecting transient signals." [PSI:MS] |
# detector attribute [MS:1000481]
def: "Detector attribute recognized as a value." [PSI:MS]
| No | id | name | value type | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1000028 | detector resolution | float | def: "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." [PSI:MS] | |
| 2 | MS:1000029 | sampling frequency | float | hertz | def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] |
| 3 | MS:1002273 | detector potential | float | volt | def: "Detector potential difference in volts." [PSI:MS] |
# source [MS:1000458]
def: "Terms to describe the source." [PSI:MS]
# inlet type [MS:1000007]
def: "The nature of the sample inlet." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1000057 | electrospray inlet | def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS] |
# ionization type [MS:1000008]
def: "The method by which gas phase ions are generated from the sample." [PSI:MS]
| No | id | name | synonym | def |
|---|---|---|---|---|
| 1 | MS:1000071 | chemical ionization | "CI" EXACT [] | def: "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." [PSI:MS] |
| 2 | MS:1000389 | electron ionization | "EI" EXACT [] | def: "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." [PSI:MS] |
| 3 | MS:1000073 | electrospray ionization | "ESI" EXACT [] | def: "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." [PSI:MS] |
# electrospray ionization [MS:1000073]
def: "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." [PSI:MS]
| No | id | name | synonym | def |
|---|---|---|---|---|
| 1 | MS:1000397 | microelectrospray | def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray." [PSI:MS] | |
| 2 | MS:1000398 | nanoelectrospray | "nanospray" EXACT [] | def: "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." [PSI:MS] |
# source attribute [MS:1000482]
def: "Property of a source device that need a value." [PSI:MS]
| No | id | name | value type | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1000392 | ionization efficiency | float | def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] | |
| 2 | MS:1000486 | source potential | float | volt | def: "Potential difference at the MS source in volts." [PSI:MS] |
| 3 | MS:1002040 | inlet temperature | float | degree Celsius | def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] |
| 4 | MS:1002041 | source temperature | float | degree Celsius | def: "The temperature of the source of a mass spectrometer." [PSI:MS] |
# source interface [MS:1001931]
def: "The source interface." [PSI:MS]
# source interface model [MS:1001932]
def: "The source interface model." [PSI:MS]
# source interface manufacturer [MS:1001953]
def: "The source interface manufacturer." [PSI:MS]
# source sprayer [MS:1001933]
def: "The source sprayer." [PSI:MS]
# source sprayer type [MS:1001934]
def: "The source sprayer type." [PSI:MS]
# source sprayer manufacturer [MS:1001935]
def: "The source sprayer manufacturer." [PSI:MS]
# source sprayer model [MS:1001936]
def: "The source sprayer model." [PSI:MS]
# sample plate [MS:1001937]
def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS]
# sample plate type [MS:1001938]
def: "The sample plate type." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1001939 | stainless steel plate | def: "Stainless steel plate." [PSI:MS] |
| 2 | MS:1001940 | coated glass plate | def: "Coated glass plate." [PSI:MS] |
| 3 | MS:1000839 | precoated MALDI sample plate | def: "Precoated MALDI sample plate." [PSI:MS] |
# electrospray supply type [MS:1001941]
def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS]
| No | id | name | def |
|---|---|---|---|
| 1 | MS:1001942 | static supply electrospray | def: "The sprayer is loaded with sample once." [PSI:MS] |
| 2 | MS:1001943 | fed supply electrospray | def: "The sprayer is continuously fed with sample." [PSI:MS] |
# inlet attribute [MS:1002039]
def: "Inlet properties that are associated with a value." [PSI:MS]
| No | id | name | type vale | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1002040 | inlet temperature | float | degree Celsius | def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] |
# instrument attribute [MS:1000496]
def: "Instrument properties that are associated with a value." [PSI:MS]
| No | id | name | type vale | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1000032 | customization | string | def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] | |
| 2 | MS:1000236 | transmission | float | def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] | |
| 3 | MS:1000529 | instrument serial number | string | def: "Serial Number of the instrument." [PSI:MS] |
# object attribute [MS:1000547]
# source data file (source file) [MS:1000577]
def: "Data file from which an entity is sourced." [PSI:MS]
# data file content [MS:1000524]
def: "Describes the data content on the file." [PSI:MS]
# data file checksum type [MS:1000561]
def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS]
# native spectrum identifier format [MS:1000767]
def: "Describes how the native spectrum identifiers are formated." [PSI:MS]
# native spectrum identifier format, combined spectra [MS:1002646]
def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
# measurement method [MS:1000596]
def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS]
# resolution measurement method [MS:1000012]
def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS]
# data processing parameter[MS:1000630]
def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS]
| No | id | name | type vale | unit | def |
|---|---|---|---|---|---|
| 1 | MS:1002435 | data processing start time | datetime | def: "The time that a data processing action was started." [PSI:MS] | |
| 2 | MS:1000747 | completion time | datetime | def: "The time that a data processing action was finished." [PSI:MS] | |
| 1 | MS:1000629 | low intensity threshold | float | cps | def: "Threshold below which some action is taken." [PSI:MS] |
| 1 | MS:1000631 | high intensity threshold | float | cps | def: "Threshold above which some action is taken." [PSI:MS] |
| 3 | MS:1000787 | inclusive low intensity threshold | float | cps | def: "Threshold at or below which some action is taken." [PSI:MS] |
| 4 | MS:1000788 | inclusive high intensity threshold | float | cps | def: "Threshold at or above which some action is taken." [PSI:MS] |
# transition (reaction) [MS:1000908]
def: "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." [PSI:MS]
# transition validation method [MS:1000909]
def: "The strategy used to validate that a transition is effective." [PSI:MS]
# transition validation attribute [MS:1001882]
def: "Attributes of the quality of a transition that affect its selection as appropriate." [PSI:MS]
# target list [MS:1000918]
def: "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." [PSI:MS]
# target inclusion exclusion priority [MS:1000919]
def: "A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS]
# acquisition parameter [MS:1001954]
def: "Parameters used in the mass spectrometry acquisition." [PSI:MS]
# mass spectrometry acquisition method [MS:1003213]
def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS]
# ms spectrum match scoring algorithm [new add]
def: "Algorithm used to score the match between a spectrum and a ion."
like: SEQUEST Comet Byonic OpenXQuest OpenPepXL ProteinProphet
| No | id | name | def |
|---|---|---|---|
| 1 | expectation value | def: "The QUEST result 'Expectation value'." | |
| 2 | intsum | sum of matched peak intensity subscore | |
| 3 | wTIC | weighted percent of total ion current subscore | |
| 4 | new | newadd |