The mass recorded by a mass spectrometer can refer to different physical quantities depending on the characteristics of the instrument and the manner in which the mass spectrum is displayed.
The dalton (symbol: Da) is the standard unit that is used for indicating mass on an atomic or molecular scale (atomic mass). [1] The unified atomic mass unit (symbol: u) is equivalent to the dalton. One dalton is approximately the mass of one a single proton or neutron. [2] The unified atomic mass unit has a value of 1.660538921(73)×10−27 kg . [3] The amu without the "unified" prefix is an obsolete unit based on oxygen, which was replaced in 1961.
The molecular mass (abbreviated Mr) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of 12C). Due to this relativity, the molecular mass of a substance is commonly referred to as the relative molecular mass, and abbreviated to Mr.
The average mass of a molecule is obtained by summing the average atomic masses of the constituent elements. For example, the average mass of natural water with formula H2O is 1.00794 + 1.00794 + 15.9994 = 18.01528 Da.
The mass number, also called the nucleon number, is the number of protons and neutrons in an atomic nucleus. The mass number is unique for each isotope of an element and is written either after the element name or as a superscript to the left of an element's symbol. For example, carbon-12 (12C) has 6 protons and 6 neutrons.
The nominal mass for an element is the mass number of its most abundant naturally occurring stable isotope, and for an ion or molecule, the nominal mass is the sum of the nominal masses of the constituent atoms. [4] [5] Isotope abundances are tabulated by IUPAC: [6] for example carbon has two stable isotopes 12C at 98.9% natural abundance and 13C at 1.1% natural abundance, thus the nominal mass of carbon is 12. The nominal mass is not always the lowest mass number, for example iron has isotopes 54Fe, 56Fe, 57Fe, and 58Fe with abundances 6%, 92%, 2%, and 0.3%, respectively, and a nominal mass of 56 Da. For a molecule, the nominal mass is obtained by summing the nominal masses of the constituent elements, for example water has two hydrogen atoms with nominal mass 1 Da and one oxygen atom with nominal mass 16 Da, therefore the nominal mass of H2O is 18 Da.
In mass spectrometry, the difference between the nominal mass and the monoisotopic mass is the mass defect. [7] This differs from the definition of mass defect used in physics which is the difference between the mass of a composite particle and the sum of the masses of its constituent parts. [8]
The accurate mass (more appropriately, the measured accurate mass [9] ) is an experimentally determined mass that allows the elemental composition to be determined. [10] For molecules with mass below 200 Da, 5 ppm accuracy is often sufficient to uniquely determine the elemental composition. [11]
The exact mass of an isotopic species (more appropriately, the calculated exact mass [9] ) is obtained by summing the masses of the individual isotopes of the molecule. For example, the exact mass of water containing two hydrogen-1 (1H) and one oxygen-16 (16O) is 1.0078 + 1.0078 + 15.9949 = 18.0105 Da. The exact mass of heavy water, containing two hydrogen-2 (deuterium or 2H) and one oxygen-16 (16O) is 2.0141 + 2.0141 + 15.9949 = 20.0229 Da.
When an exact mass value is given without specifying an isotopic species, it normally refers to the most abundant isotopic species.
The monoisotopic mass is the sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element. [12] [5] The monoisotopic mass of a molecule or ion is the exact mass obtained using the principal isotopes. Monoisotopic mass is typically expressed in daltons.
For typical organic compounds, where the monoisotopic mass is most commonly used, this also results in the lightest isotope being selected. For some heavier atoms such as iron and argon the principal isotope is not the lightest isotope. The mass spectrum peak corresponding to the monoisotopic mass is often not observed for large molecules, but can be determined from the isotopic distribution. [13]
This refers to the mass of the molecule with the most highly represented isotope distribution, based on the natural abundance of the isotopes. [14]
Isotopomers (isotopic isomers) are isomers having the same number of each isotopic atom, but differing in the positions of the isotopic atoms. [15] For example, CH3CHDCH3 and CH3CH2CH2D are a pair of structural isotopomers.
Isotopomers should not be confused with isotopologues, which are chemical species that differ in the isotopic composition of their molecules or ions. For example, three isotopologues of the water molecule with different isotopic composition of hydrogen are: HOH, HOD and DOD, where D stands for deuterium (2H).
The Kendrick mass is a mass obtained by multiplying the measured mass by a numeric factor. The Kendrick mass is used to aid in the identification of molecules of similar chemical structure from peaks in mass spectra. [16] [17] The method of stating mass was suggested in 1963 by the chemist Edward Kendrick.
According to the procedure outlined by Kendrick, the mass of CH2 is defined as 14.000 Da, instead of 14.01565 Da. [18] [19]
The Kendrick mass for a family of compounds is given by [20]
For hydrocarbon analysis, = CH2.
The mass defect used in nuclear physics is different from its use in mass spectrometry. In nuclear physics, the mass defect is the difference in the mass of a composite particle and the sum of the masses of its component parts. In mass spectrometry the mass defect is defined as the difference between the exact mass and the nearest integer mass. [21] [22]
The Kendrick mass defect is the exact Kendrick mass subtracted from the nearest integer Kendrick mass. [23]
Mass defect filtering can be used to selectively detect compounds with a mass spectrometer based on their chemical composition. [7]
The term packing fraction was defined by Aston as the difference of the measured mass M and the nearest integer mass I (based on the oxygen-16 mass scale) divided by the quantity comprising the mass number multiplied by ten thousand: [26]
Aston's early model of nuclear structure (prior to the discovery of the neutron) postulated that the electromagnetic fields of closely packed protons and electrons in the nucleus would interfere and a fraction of the mass would be destroyed. [27] A low packing fraction is indicative of a stable nucleus. [28]
The nitrogen rule states that organic compounds containing exclusively hydrogen, carbon, nitrogen, oxygen, silicon, phosphorus, sulfur, and the halogens either have an odd nominal mass that indicates an odd number of nitrogen atoms are present or an even nominal mass that indicates an even number of nitrogen atoms are present in the molecular ion. [29] [30]
The whole number rule states that the masses of the isotopes are integer multiples of the mass of the hydrogen atom. [31] The rule is a modified version of Prout's hypothesis proposed in 1815, to the effect that atomic weights are multiples of the weight of the hydrogen atom. [32]
The molecular mass is the mass of a given molecule. Units of daltons (Da) are often used. Different molecules of the same compound may have different molecular masses because they contain different isotopes of an element. The derived quantity relative molecular mass is the unitless ratio of the mass of a molecule to the atomic mass constant.
The mole (symbol mol) is a unit of measurement, the base unit in the International System of Units (SI) for amount of substance, a quantity proportional to the number of elementary entities of a substance. One mole contains exactly 6.02214076×1023 elementary entities (approximately 602 sextillion or 602 billion times a trillion), which can be atoms, molecules, ions, ion pairs, or other particles. The number of particles in a mole is the Avogadro number (symbol N0) and the numerical value of the Avogadro constant (symbol NA) expressed in mol-1. The value was chosen on the basis of the historical definition of the mole as the amount of substance that corresponds to the number of atoms in 12 grams of 12C, which made the mass of a mole of a compound expressed in grams, numerically equal to the average molecular mass or formula mass of the compound expressed in daltons. With the 2019 revision of the SI, the numerical equivalence is now only approximate but may be assumed for all practical purposes.
The dalton or unified atomic mass unit is a unit of mass defined as 1/12 of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at rest. It is a non-SI unit accepted for use with SI. The atomic mass constant, denoted mu, is defined identically, giving mu = 1/12m(12C) = 1 Da.
In chemistry, the molar mass of a chemical compound is defined as the ratio between the mass and the amount of substance of any sample of the compound. The molar mass is a bulk, not molecular, property of a substance. The molar mass is an average of many instances of the compound, which often vary in mass due to the presence of isotopes. Most commonly, the molar mass is computed from the standard atomic weights and is thus a terrestrial average and a function of the relative abundance of the isotopes of the constituent atoms on Earth. The molar mass is appropriate for converting between the mass of a substance and the amount of a substance for bulk quantities.
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures.
An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines.
A mass spectrum is a histogram plot of intensity vs. mass-to-charge ratio (m/z) in a chemical sample, usually acquired using an instrument called a mass spectrometer. Not all mass spectra of a given substance are the same; for example, some mass spectrometers break the analyte molecules into fragments; others observe the intact molecular masses with little fragmentation. A mass spectrum can represent many different types of information based on the type of mass spectrometer and the specific experiment applied. Common fragmentation processes for organic molecules are the McLafferty rearrangement and alpha cleavage. Straight chain alkanes and alkyl groups produce a typical series of peaks: 29 (CH3CH2+), 43 (CH3CH2CH2+), 57 (CH3CH2CH2CH2+), 71 (CH3CH2CH2CH2CH2+) etc.
In chemistry, the amount of substance (symbol n) in a given sample of matter is defined as a ratio (n = N/NA) between the number of elementary entities (N) and the Avogadro constant (NA). The entities are usually molecules, atoms, ions, or ion pairs of a specified kind. The particular substance sampled may be specified using a subscript, e.g., the amount of sodium chloride (NaCl) would be denoted as nNaCl. The unit of amount of substance in the International System of Units is the mole (symbol: mol), a base unit. Since 2019, the value of the Avogadro constant NA is defined to be exactly 6.02214076×1023 mol−1. Sometimes, the amount of substance is referred to as the chemical amount or, informally, as the "number of moles" in a given sample of matter.
Isotopic labeling is a technique used to track the passage of an isotope through chemical reaction, metabolic pathway, or a biological cell. The reactant is 'labeled' by replacing one or more specific atoms with their isotopes. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine what sequence the isotopic atom followed in the reaction or the cell's metabolic pathway. The nuclides used in isotopic labeling may be stable nuclides or radionuclides. In the latter case, the labeling is called radiolabeling.
In chemistry, isotopologues are molecules that differ only in their isotopic composition. They have the same chemical formula and bonding arrangement of atoms, but at least one atom has a different number of neutrons than the parent.
Fast atom bombardment (FAB) is an ionization technique used in mass spectrometry in which a beam of high energy atoms strikes a surface to create ions. It was developed by Michael Barber at the University of Manchester in 1980. When a beam of high energy ions is used instead of atoms, the method is known as liquid secondary ion mass spectrometry (LSIMS). In FAB and LSIMS, the material to be analyzed is mixed with a non-volatile chemical protection environment, called a matrix, and is bombarded under vacuum with a high energy atomic beam. The atoms are typically from an inert gas such as argon or xenon. Common matrices include glycerol, thioglycerol, 3-nitrobenzyl alcohol (3-NBA), 18-crown-6 ether, 2-nitrophenyloctyl ether, sulfolane, diethanolamine, and triethanolamine. This technique is similar to secondary ion mass spectrometry and plasma desorption mass spectrometry.
Monoisotopic mass (Mmi) is one of several types of molecular masses used in mass spectrometry. The theoretical monoisotopic mass of a molecule is computed by taking the sum of the accurate masses of the most abundant naturally occurring stable isotope of each atom in the molecule. For small molecules made up of low atomic number elements the monoisotopic mass is observable as an isotopically pure peak in a mass spectrum. This differs from the nominal molecular mass, which is the sum of the mass number of the primary isotope of each atom in the molecule and is an integer. It also is different from the molar mass, which is a type of average mass. For some atoms like carbon, oxygen, hydrogen, nitrogen, and sulfur, the Mmi of these elements is exactly the same as the mass of its natural isotope, which is the lightest one. However, this does not hold true for all atoms. Iron's most common isotope has a mass number of 56, while the stable isotopes of iron vary in mass number from 54 to 58. Monoisotopic mass is typically expressed in daltons (Da), also called unified atomic mass units (u).
The nitrogen rule states that organic compounds containing exclusively hydrogen, carbon, nitrogen, oxygen, silicon, phosphorus, sulfur, and the halogens either have (1) an odd nominal mass that indicates an odd number of nitrogen atoms are present or (2) an even nominal mass that indicates an even number of nitrogen atoms in the molecular formula of the neutral compound. The nitrogen rule is not a rule as much as a general principle which may prove useful when attempting to solve organic mass spectrometry structures.
The history of mass spectrometry has its roots in physical and chemical studies regarding the nature of matter. The study of gas discharges in the mid 19th century led to the discovery of anode and cathode rays, which turned out to be positive ions and electrons. Improved capabilities in the separation of these positive ions enabled the discovery of stable isotopes of the elements. The first such discovery was with the element neon, which was shown by mass spectrometry to have at least two stable isotopes: 20Ne and 22Ne. Mass spectrometers were used in the Manhattan Project for the separation of isotopes of uranium necessary to create the atomic bomb.
In chemistry, the whole number rule states that the masses of the isotopes are whole number multiples of the mass of the hydrogen atom. The rule is a modified version of Prout's hypothesis proposed in 1815, to the effect that atomic weights are multiples of the weight of the hydrogen atom. It is also known as the Aston whole number rule after Francis W. Aston who was awarded the Nobel Prize in Chemistry in 1922 "for his discovery, by means of his mass spectrograph, of isotopes, in a large number of non-radioactive elements, and for his enunciation of the whole-number rule."
Mass spectral interpretation is the method employed to identify the chemical formula, characteristic fragment patterns and possible fragment ions from the mass spectra. Mass spectra is a plot of relative abundance against mass-to-charge ratio. It is commonly used for the identification of organic compounds from electron ionization mass spectrometry. Organic chemists obtain mass spectra of chemical compounds as part of structure elucidation and the analysis is part of many organic chemistry curricula.
The atomic mass (ma or m) is the mass of an atom. Although the SI unit of mass is the kilogram (symbol: kg), atomic mass is often expressed in the non-SI unit dalton (symbol: Da) – equivalently, unified atomic mass unit (u). 1 Da is defined as 1⁄12 of the mass of a free carbon-12 atom at rest in its ground state. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions. Thus, the numeric value of the atomic mass when expressed in daltons has nearly the same value as the mass number. Conversion between mass in kilograms and mass in daltons can be done using the atomic mass constant .
The Kendrick mass is defined by setting the mass of a chosen molecular fragment, typically CH2, to an integer value in u (unified atomic mass unit). It is different from the IUPAC definition, which is based on setting the mass of 12C isotope to exactly 12 u. The Kendrick mass is often used to identify homologous compounds differing only by a number of base units in high resolution mass spectra. This definition of mass was first suggested in 1963 by chemist Edward Kendrick, and it has been adopted by scientists working in the area of high-resolution mass spectrometry, environmental analysis, proteomics, petroleomics, metabolomics, polymer analysis, etc.
NanoSIMS is an analytical instrument manufactured by CAMECA which operates on the principle of secondary ion mass spectrometry. The NanoSIMS is used to acquire nanoscale resolution measurements of the elemental and isotopic composition of a sample. The NanoSIMS is able to create nanoscale maps of elemental or isotopic distribution, parallel acquisition of up to seven masses, isotopic identification, high mass resolution, subparts-per-million sensitivity with spatial resolution down to 50 nm.
Position-specific isotope analysis, also called site-specific isotope analysis, is a branch of isotope analysis aimed at determining the isotopic composition of a particular atom position in a molecule. Isotopes are elemental variants with different numbers of neutrons in their nuclei, thereby having different atomic masses. Isotopes are found in varying natural abundances depending on the element; their abundances in specific compounds can vary from random distributions due to environmental conditions that act on the mass variations differently. These differences in abundances are called "fractionations," which are characterized via stable isotope analysis.
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