View source for Physics:Mass (mass spectrometry)

{{Short description|Physical quantities being measured}}
[[File:Discovery of neon isotopes.JPG|thumb|right|300 px|[[Biography:J. J. Thomson|J. J. Thomson]] discovered the isotopes of neon using mass spectrometry.]]
The '''mass''' recorded by a [[Physics:Mass spectrometer|mass spectrometer]] can refer to different physical quantities depending on the characteristics of the instrument and the manner in which the [[Physics:Mass spectrum|mass spectrum]] is displayed.

==Units==
The [[Dalton (unit)|dalton]] (symbol: Da) is the standard [[Unit of measurement|unit]] that is used for indicating [[Physics:Mass|mass]] on an atomic or molecular scale ([[Physics:Atomic mass|atomic mass]]).<ref name=bipm9th>Bureau International des Poids et Mesures (2019): ''[https://www.bipm.org/utils/common/pdf/si-brochure/SI-Brochure-9-EN.pdf The International System of Units (SI)]'', 9th edition, English version, page 134. Available at the [https://www.bipm.org/en/publications/si-brochure/ BIPM website].</ref>  The [[Physics:Unified atomic mass unit|unified atomic mass unit]] (symbol: u) is equivalent to the dalton. One dalton is approximately the mass of one a single proton or neutron.<ref name="Stryer 2007 35">{{cite book|last=Stryer|first=Jeremy M. Berg; John L. Tymoczko; Lubert|title=Biochemistry|date=2007|publisher=Freeman|location=New York|isbn=978-0-7167-8724-2|edition=3rd print, 6th|page=35|chapter=2}}</ref> The unified atomic mass unit has a value of {{val|1.660538921|(73)|e=-27|ul=kg}}.<ref name="CODATA">[http://physics.nist.gov/constants Fundamental Physical Constants from NIST]</ref> The ''amu'' without the "unified" prefix is an obsolete unit based on oxygen, which was replaced in 1961.
 
==Molecular mass==
[[File:Caffeine mass.gif|right|thumb|300 px|Theoretical isotope distribution for the molecular ion of [[Biology:Caffeine|caffeine]]]]
The [[Physics:Molecular mass|molecular mass]] (abbreviated M<sub>r</sub>) of a [[Chemistry:Chemical compound|substance]], formerly also called molecular weight and abbreviated as MW, is the [[Physics:Mass|mass]] of one [[Physics:Molecule|molecule]] of that substance, relative to the [[Physics:Unified atomic mass unit|unified atomic mass unit]] u (equal to 1/12 the mass of one [[Physics:Atom|atom]] of [[Physics:Carbon-12|<sup>12</sup>C]]). Due to this relativity, the molecular mass of a substance is commonly referred to as the relative molecular mass, and abbreviated to M<sub>r</sub>.

==Average mass==
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 [[Chemistry:Water|water]] with formula H<sub>2</sub>O is 1.00794 + 1.00794 + 15.9994 = 18.01528 Da.

==Mass number==
The [[Chemistry:Mass number|mass number]],  also called the [[Physics:Nucleon|nucleon]] number, is the number of [[Physics:Proton|proton]]s and [[Physics:Neutron|neutron]]s in an [[Physics:Atomic nucleus|atomic nucleus]]. The mass number is unique for each [[Physics:Isotope|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, [[Physics:Carbon-12|carbon-12]] (<sup>12</sup>C) has 6 protons and 6 neutrons.

==Nominal mass==
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.<ref name="Gross2011">{{cite book|author=Jürgen H Gross|title=Mass Spectrometry: A Textbook|url=https://books.google.com/books?id=xHOQiaquq24C&pg=PA71|date=14 February 2011|publisher=Springer Science & Business Media|isbn=978-3-642-10709-2|pages=71–}}</ref><ref name="WatsonSparkman2013">{{cite book|author1=J. Throck Watson|author2=O. David Sparkman|title=Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation|url=https://books.google.com/books?id=mUsSAAAAQBAJ&pg=PT385|date=9 July 2013|publisher=John Wiley & Sons|isbn=978-1-118-68158-9|pages=385–}}</ref> Isotope abundances are tabulated by IUPAC:<ref name="BerglundWieser2011">{{cite journal|last1=Berglund|first1=Michael|last2=Wieser|first2=Michael E.|title=Isotopic compositions of the elements 2009 (IUPAC Technical Report)|journal=Pure and Applied Chemistry|volume=83|issue=2|pages=397–410|year=2011|issn=1365-3075|doi=10.1351/PAC-REP-10-06-02|doi-access=free|hdl=11858/00-001M-0000-0029-C408-7|hdl-access=free}}</ref> for example carbon has two stable isotopes <sup>12</sup>C at 98.9% natural abundance and <sup>13</sup>C 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 [[Physics:Isotopes of iron|iron has isotopes]] <sup>54</sup>Fe, <sup>56</sup>Fe, <sup>57</sup>Fe, and <sup>58</sup>Fe 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 H<sub>2</sub>O is 18 Da.

In mass spectrometry, the difference between the nominal mass and the monoisotopic mass is the mass defect.<ref name="Sleno2012">{{cite journal|last1=Sleno|first1=Lekha|title=The use of mass defect in modern mass spectrometry|journal=Journal of Mass Spectrometry|volume=47|issue=2|year=2012|pages=226–236|issn=1076-5174|doi=10.1002/jms.2953|pmid=22359333|bibcode=2012JMSp...47..226S}}</ref> 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.<ref name="FerrerThurman2009">{{cite book|author1=Imma Ferrer|author2=E. M. Thurman|title=Liquid Chromatography Time-of-Flight Mass Spectrometry|url=https://books.google.com/books?id=nhU0dZ9sklwC&pg=PA19|date=6 May 2009|publisher=John Wiley & Sons|isbn=978-0-470-42995-2|pages=18–22}}</ref>

==Accurate mass==
The '''accurate mass''' (more appropriately, the measured accurate mass<ref name="ODS">{{cite book| author=O. David Sparkman| title=Mass Spec Desk Reference| year=2006|edition= 2nd.| page=60 |isbn=0-9660813-9-0}}</ref>) is an experimentally determined mass that allows the elemental composition to be determined.<ref name="pmid16124033">{{Citation|author=Grange AH |author2=Winnik W |author3=Ferguson PL |author4=Sovocool GW|title=Using a triple-quadrupole mass spectrometer in accurate mass mode and an ion correlation program to identify compounds|journal=Rapid Commun. Mass Spectrom.|volume=19|issue=18|pages=2699–715|date=2005|pmid=16124033|doi=10.1002/rcm.2112|bibcode=2005RCMS...19.2699G |postscript=.|url=https://zenodo.org/record/1229344 |type=Submitted manuscript }}</ref> For molecules with mass below 200 [[Dalton (unit)|Da]], 5 [[Parts per million|ppm]] accuracy is often sufficient to uniquely determine the elemental composition.<ref name=Gross1994>{{Citation|last=Gross|first=M. L.|date=1994|title=Accurate Masses for Structure Confirmation|journal=J. Am. Soc. Mass Spectrom.|volume=5|page=57|doi=10.1016/1044-0305(94)85036-4|pmid=24222515|issue=2|postscript=.|doi-access=free}}</ref>

==Exact mass==
The '''exact mass''' of an isotopic species (more appropriately, the calculated exact mass<ref name="ODS"/>) is obtained by summing the masses of the individual isotopes of the molecule. For example, the exact mass of water containing two hydrogen-1 (<sup>1</sup>H) and one oxygen-16 (<sup>16</sup>O) is 1.0078 + 1.0078 + 15.9949 = 18.0105 Da. The exact mass of [[Chemistry:Heavy water|heavy water]], containing two hydrogen-2 ([[Physics:Deuterium|deuterium]] or <sup>2</sup>H) and one oxygen-16 (<sup>16</sup>O) 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.

==Monoisotopic mass==
{{main|Chemistry:Monoisotopic mass}}
The monoisotopic mass is the sum of the [[Physics:Mass|mass]]es of the [[Physics:Atom|atom]]s in a [[Physics:Molecule|molecule]] using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element.<ref>{{Cite book|chapter=Monoisotopic mass spectrum|journal=IUPAC Compendium of Chemical Terminology|date=2009|doi=10.1351/goldbook.M04014|isbn=978-0-9678550-9-7}}</ref><ref name="WatsonSparkman2013" /> 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 [[Chemistry:Iron|iron]] and [[Chemistry:Argon|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.<ref name="SenkoBeu1995">{{cite journal|last1=Senko|first1=Michael W.|last2=Beu|first2=Steven C.|last3=McLaffertycor|first3=Fred W.|title=Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions|journal=Journal of the American Society for Mass Spectrometry|volume=6|issue=4|year=1995|pages=229–233|issn=1044-0305|doi=10.1016/1044-0305(95)00017-8|pmid=24214167|doi-access=free}}</ref>

==Most abundant mass==
[[File:Glucagon mass.gif|right|thumb|300 px|Theoretical isotope distribution for the molecular ion of [[Biology:Glucagon|glucagon]] (C<sub>153</sub>H<sub>224</sub>N<sub>42</sub>O<sub>50</sub>S)]]
This refers to the mass of the molecule with the most highly represented isotope distribution, based on the [[Chemistry:Natural abundance|natural abundance]] of the isotopes.<ref name="pmid15928922">{{Citation|author=Goraczko AJ|title=Molecular mass and location of the most abundant peak of the molecular ion isotopomeric cluster|journal=Journal of Molecular Modeling|volume=11|issue=4–5|pages=271–7|date=2005|pmid=15928922|doi=10.1007/s00894-005-0245-x|s2cid=21949927|postscript=.}}</ref>

==Isotopomer and isotopologue==
[[Physics:Isotopomer|Isotopomer]]s (isotopic isomers) are [[Chemistry:Isomer|isomer]]s having the same number of each [[Physics:Isotope|isotopic]] atom, but differing in the positions of the isotopic atoms.<ref>{{GoldBookRef|title=isotopomer|file=I03352}}</ref> For example, CH<sub>3</sub>CHDCH<sub>3</sub> and CH<sub>3</sub>CH<sub>2</sub>CH<sub>2</sub>D are a pair of [[Chemistry:Structural isomer|structural]] isotopomers.

Isotopomers should not be confused with [[Physics:Isotopologue|isotopologue]]s, which are chemical species that differ in the [[Physics:Isotope|isotopic]] composition of their [[Physics:Molecule|molecule]]s or [[Physics:Ion|ion]]s. For example, three isotopologues of the [[Chemistry:Properties of water|water molecule]] with different isotopic composition of hydrogen are: HOH, HOD and DOD, where D stands for deuterium (<sup>2</sup>H).

==Kendrick mass==
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.<ref name='Kendrick 1963'>{{Citation|doi=10.1021/ac60206a048|title=A mass scale based on CH<sub>2</sub> = 14.0000 for high resolution mass spectrometry of organic compounds|journal=Anal. Chem.|date=1963|first=Edward|last=Kendrick|volume=35|issue=13|pages=2146–2154|postscript=. }}</ref><ref name="pmid14730994">{{Citation |author=Marshall AG |author2=Rodgers RP |title=Petroleomics: the next grand challenge for chemical analysis |journal=Acc. Chem. Res. |volume=37 |issue=1 |pages=53–9 |date=January 2004 |pmid=14730994 |doi=10.1021/ar020177t |postscript=.}}</ref> The method of stating mass was suggested in 1963 by the [[Chemist|chemist]] Edward Kendrick.

According to the procedure outlined by Kendrick, the mass of CH<sub>2</sub> is defined as 14.000 Da, instead of 14.01565 Da.<ref>{{Citation | last1 = Mopper | first1 = Kenneth | last2 = Stubbins | first2 = Aron | last3 = Ritchie | first3 = Jason D. | last4 = Bialk | first4 = Heidi M. | last5 = Hatcher | first5 = Patrick G. | title = Advanced Instrumental Approaches for Characterization of Marine Dissolved Organic Matter: Extraction Techniques, Mass Spectrometry, and Nuclear Magnetic Resonance Spectroscopy | journal = Chemical Reviews | volume = 107 | issue = 2 | pages = 419–42 | date = 2007 | pmid = 17300139 | doi = 10.1021/cr050359b}}</ref><ref>{{Citation | last1 = Meija | first1 = Juris | title = Mathematical tools in analytical mass spectrometry | journal = Analytical and Bioanalytical Chemistry | volume = 385 | issue = 3 | pages = 486–99 | date = 2006 | pmid = 16514517 | doi = 10.1007/s00216-006-0298-4| s2cid = 44611533 }}</ref>

The Kendrick mass for a family of compounds <math>F</math> is given by<ref>{{citation|last1=Kim|first1=Sunghwan|last2=Kramer|first2=Robert W.|last3=Hatcher|first3=Patrick G.|title=Graphical Method for Analysis of Ultrahigh-Resolution Broadband Mass Spectra of Natural Organic Matter, the Van Krevelen Diagram|journal=Analytical Chemistry|volume=75|issue=20|pages=5336–44|date=2003|pmid=14710810|doi=10.1021/ac034415p }}</ref>

:<math>\mbox{Kendrick mass}~(F) = (\mbox{observed mass}) \times \frac{\mbox{nominal mass}~(F)}{\mbox{exact mass}~(F)}.</math>

For hydrocarbon analysis, <math>F</math> = CH<sub>2</sub>.

==Mass defect (mass spectrometry)==
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.<ref name="WatsonSparkman2007">{{cite book|author1=J. Throck Watson|author2=O. David Sparkman|title=Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation|url=https://books.google.com/books?id=ox1bWqYqZT4C&pg=PA274|date=4 December 2007|publisher=John Wiley & Sons|isbn=978-0-470-51634-8|pages=274–}}</ref><ref name="Gross2017">{{cite book|author=Jürgen H Gross|title=Mass Spectrometry: A Textbook|url=https://books.google.com/books?id=PdMnDwAAQBAJ&pg=PA143|date=22 June 2017|publisher=Springer|isbn=978-3-319-54398-7|pages=143–}}</ref>

The Kendrick mass defect is the exact Kendrick mass subtracted from the nearest integer Kendrick mass.<ref name="HugheyHendrickson2001">{{cite journal|last1=Hughey|first1=Christine A.|last2=Hendrickson|first2=Christopher L.|last3=Rodgers|first3=Ryan P.|last4=Marshall|first4=Alan G.|last5=Qian|first5=Kuangnan|title=Kendrick Mass Defect Spectrum: A Compact Visual Analysis for Ultrahigh-Resolution Broadband Mass Spectra|journal=Analytical Chemistry|volume=73|issue=19|year=2001|pages=4676–4681|issn=0003-2700|doi=10.1021/ac010560w|pmid=11605846}}</ref>

Mass defect filtering can be used to selectively detect compounds with a mass spectrometer based on their chemical composition.<ref name="Sleno2012" />

==Packing fraction (mass spectrometry)==
[[File:Francis William Aston.jpg|right|thumb|250 px|[[Biography:Francis William Aston|Francis William Aston]] won the 1922 Nobel Prize in Chemistry 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.<ref>{{cite web | url=http://nobelprize.org/nobel_prizes/chemistry/laureates/1922/  | title=The Nobel Prize in Chemistry 1922  | access-date=2008-04-14  | publisher=Nobel Foundation }}</ref><ref name='a804629h'>{{cite journal | title=Francis Aston and the mass spectrograph | journal=Dalton Transactions | date=1998 | first=Gordon | last=Squires | issue= 23| pages=3893–3900 | doi= 10.1039/a804629h }}</ref>]]
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 [[Physics:Oxygen-16|oxygen-16]] mass scale) divided by the quantity comprising the mass number multiplied by ten thousand:<ref name="Aston1927">{{cite journal|last1=Aston|first1=F. W.|title=Atoms and their Packing Fractions1|journal=Nature|volume=120|issue=3035|year=1927|pages=956–959|issn=0028-0836|doi=10.1038/120956a0|bibcode=1927Natur.120..956A|s2cid=22601204}}</ref>

:<math>f=\frac{M-I}{10^4\ I} </math>.

Aston's early model of [[Physics:Nuclear structure|nuclear structure]] (prior to the [[Physics:Discovery of the neutron|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.<ref name="BudzikiewiczGrigsby2006">{{cite journal|last1=Budzikiewicz|first1=Herbert|last2=Grigsby|first2=Ronald D.|title=Mass spectrometry and isotopes: A century of research and discussion|journal=Mass Spectrometry Reviews|volume=25|issue=1|year=2006|pages=146–157|issn=0277-7037|doi=10.1002/mas.20061|pmid=16134128|bibcode=2006MSRv...25..146B}}</ref> A low packing fraction is indicative of a stable nucleus.<ref name="Dempster1938">{{cite journal|last1=Dempster|first1=A. J.|title=The Energy Content of the Heavy Nuclei|journal=Physical Review|volume=53|issue=11|year=1938|pages=869–874|issn=0031-899X|doi=10.1103/PhysRev.53.869|bibcode=1938PhRv...53..869D}}</ref>

==Nitrogen rule==
The [[Nitrogen rule|nitrogen rule]] states that [[Chemistry:Organic compound|organic compound]]s containing exclusively [[Chemistry:Hydrogen|hydrogen]], [[Chemistry:Carbon|carbon]], [[Chemistry:Nitrogen|nitrogen]], [[Chemistry:Oxygen|oxygen]], [[Chemistry:Silicon|silicon]], [[Chemistry:Phosphorus|phosphorus]], [[Chemistry:Sulfur|sulfur]], and the [[Chemistry:Halogen|halogen]]s either have an odd nominal mass that indicates an [[Odd number|odd number]] of nitrogen atoms are present or an even nominal mass that indicates an [[Even number|even number]] of nitrogen atoms are present in the molecular ion.<ref name="isbn0-935702-25-3">{{cite book |author=Tureček, František |author2=McLafferty, Fred W. |title=Interpretation of mass spectra |publisher=University Science Books |location=Sausalito, Calif |date=1993 |pages= 37–38|isbn=978-0-935702-25-5 }}</ref><ref name="isbn0-9660813-9-0">{{cite book |author=David O. Sparkman |title=Mass Spectrometry Desk Reference |publisher=Global View Pub |location=Pittsburgh |date=  2007|isbn=978-0-9660813-9-8 |page=64}}</ref>

==Prout's hypothesis and the whole number rule==
The [[Physics:Whole number rule|whole number rule]] states that the masses of the isotopes are [[Integer|integer]] multiples of the mass of the [[Chemistry:Hydrogen|hydrogen]] atom.<ref name="pmid16134128">{{cite journal |author=Budzikiewicz H |author2=Grigsby RD |title=Mass spectrometry and isotopes: a century of research and discussion |journal=Mass Spectrometry Reviews |volume=25 |issue=1 |pages=146–57 |date=2006 |pmid=16134128 |doi=10.1002/mas.20061|bibcode=2006MSRv...25..146B }}</ref> The rule is a modified version of [[Chemistry:Prout's hypothesis|Prout's hypothesis]] proposed in 1815, to the effect that [[Physics:Atomic weight|atomic weight]]s are multiples of the weight of the hydrogen atom.<ref>{{cite journal |title=On the relation between the specific gravities of bodies in their gaseous state and the weights of their atoms. |journal=[[Philosophy:Annals of Philosophy|Annals of Philosophy]] |date=1815 |first=William |last=Prout |volume=6 |pages=321–330 |url=http://web.lemoyne.edu/~giunta/PROUT.HTML |access-date=2007-09-08 }}</ref>

== See also ==
*List of elements by atomic mass
*[[Dalton (unit)]]

==References==
{{Reflist}}

==External links==
* [http://research.smilems.com/molecule-tk/ web tools to compute molecule masses & isotopic distribution]

{{Mass spectrometry}}

[[Category:Mass]]
[[Category:Mass spectrometry]]

{{Sourceattribution|Mass (mass spectrometry)}}