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Verze z 11. 3. 2021, 12:45

Souprava pro tandemovou hmotnostní spektrometrii složená z kvadrupólového hmotnostního spektrometru a hmotnostního spektrometru doby letu

Tandemová hmotnostní spektrometrie, zkráceně MS/MS nebo MS² je druh instrumentální analýzy, při kterém se propojuje více hmotnostních spektrometrů za účelem přidání dalšího reakčmího kroku a zlepšení parametrů analýzy chemických vzorků.^[1] Často se používá k analýze biomolekul, jako jsou bílkoviny a peptidy.

Molekuly vzorku se ionizují a první spektrometr (MS1) oddělí vzniklé ionty podle jejich poměru hmotnosti a náboje (značeného m/z nebo m/Q). Ionty o určitých hodnotách m/z-ratio jsou odděleny a následně přeměněny na fragmentované ionty, například srážkami indukovanou disociací, reakcemi iontů s molekulami nebo fotodisociací. Tyto fragmenty poté vstupují do druhého hmotnostního spektrometru (MS2), kde se opět rozdělí podle m/z a jsou detekovány. Fragmentační krok umožňuje identifikaci a oddělení iontů s velmi podobnými hodnotami m/z v běžných hmotnostních spektrometrech.

Struktura

K druhům tandemové hmotnostní spektrometrie na základě uspořádání patří například trojitý kvadrupólový hmotnostní spektrometr (qqq), čtyřnásobný spektrometr doby letu (Q-tof) a hybridní hmotnostní spektrometr.

Trojitý kvadrupólový hmotnostní spektrometr

Trojité kvadrupólové hmotnostní spektrometry používají první a třetí kvadrupól jako hmotnostní filtry. Při průchodu analytů druhým kvadrupólem dochází k fragmentaci srážkami jejich molekul s&nnbsp;plynem. Toto uspořádání je nejběžnější ve farmaceutickén průmyslu.

Kvadrupólový spektrometr doby letu

Kvadrupólové spektrometry doby letu (Q-tof) spojují hmotnostní spektrometrii doby letu a kvadrupólové hmotnostní spektrometry, čímž se dosahuje vysoké hmotnostní přesnonsti u vytvořených iontů a využitelnosti fragmentačních experimentů. Poměr (m/z) je zde určován meřením doby letu iontů.

Hybridní hmotnostní spektrometr

Hybridní hmotnostní spektrometr je soustava vzniklá propojením více než dvou hmotnostních spektrometrů.

Přístroje

Tandemová hmotnostní spektrometrie v prostoru

Při tandemové hmotnostní spektrometrii v prostoru jsou separační zařízení fyzicky oddělená, i když jsou jednotlivé prvky stále propojené, aby bylo zachováno vysoké vakuum. Těmito prvky mohou být sektory, kvadrupóly nebo spektrometry doby letu. Je-li použito více kvadrupólových spektrometrů, tak mohou sloužit jako hmotnostní analyzátory i srážkové komory.

Pro hmotnostní analyzátory se obvykle používá toto značení Q – kvadrupólový hmotnostní analyzátor; q – radiofrekvenční kolizní kvadrupól; TOF – hmotnostní analyzátor doby letu; B – magnetický sektor a E – elektrický sektor. Značení je možné při označování kombinovaných zařízení spojovat, například QqQ' – trojitý kvadrupólový hmotnostní spektrometr; QTOF – kvadrupólový hnotnostní spektrometr doby letu (také značený QqTOF) a BEBE – čtyřsektorový hmotnostníá spektrometr (s obrácenou geometrií).

Tandemová hmotnostní spektrometrie v čase

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@@ Řádek 3: / Řádek 3: @@
 [[Soubor:Q-TOF.jpg|300 px|right|thumb|Souprava pro tandemovou hmotnostní spektrometrii složená z&nbsp;[[kvadrupólový hmotnostní spektrometr|kvadrupólového hmotnostního spektrometru]] a [[hmotnostní spektrometrie doby letu|hmotnostního spektrometru doby letu]]]]
-'''Tandemová hmotnostní spektrometrie''', zkráceně '''MS/MS''' nebo '''MS<sup>2</sup>''' je druh [[instrumentální analýza|instrumentální analýzy]], při kterém se propojuje více [[hmotnostní spektrometrie|hmotnostních spektrometrů]] za účelem přidání dalšího reakčmího kroku a zlepšení parametrů [[analytiká chemie|analýzy]] chemických vzorků.<ref>{{GoldBookRef|title=tandem mass spectrometer|file=T06250}}</ref> Čato se používá k&nbsp;analýze [[biomolekula|biomolekul]], jako jsou [[bílkovina|bílkoviny]] a [[peptid]]y.
+'''Tandemová hmotnostní spektrometrie''', zkráceně '''MS/MS''' nebo '''MS<sup>2</sup>''' je druh [[instrumentální analýza|instrumentální analýzy]], při kterém se propojuje více [[hmotnostní spektrometrie|hmotnostních spektrometrů]] za účelem přidání dalšího reakčmího kroku a zlepšení parametrů [[analytiká chemie|analýzy]] chemických vzorků.<ref>{{GoldBookRef|title=tandem mass spectrometer|file=T06250}}</ref> Často se používá k&nbsp;analýze [[biomolekula|biomolekul]], jako jsou [[bílkovina|bílkoviny]] a [[peptid]]y.
 Molekuly vzorku se [[ionizace|ionizují]] a první spektrometr ('''MS1''') oddělí vzniklé [[ion]]ty podle jejich poměru hmotnosti a náboje (značeného '''m/z''' nebo m/Q). Ionty o určitých hodnotách m/z-ratio jsou odděleny a následně přeměněny na fragmentované ionty, například srážkami indukovanou disociací, reakcemi iontů s&nbsp;molekulami nebo [[fotodisociace|fotodisociací]]. Tyto fragmenty poté vstupují do druhého hmotnostního spektrometru ('''MS2'''), kde se opět rozdělí podle m/z a jsou detekovány. Fragmentační krok umožňuje identifikaci a oddělení iontů s&nbsp;velmi podobnými hodnotami m/z v&nbsp;běžných hmotnostních spektrometrech.
@@ Řádek 9: / Řádek 9: @@
 == Struktura ==
 K&nbsp;druhům tandemové hmotnostní spektrometrie na základě uspořádání patří například trojitý kvadrupólový hmotnostní spektrometr (qqq), čtyřnásobný spektrometr doby letu (Q-tof) a hybridní hmotnostní spektrometr.
+=== Trojitý kvadrupólový hmotnostní spektrometr ===
+Trojité kvadrupólové hmotnostní spektrometry používají první a třetí kvadrupól jako hmotnostní filtry. Při průchodu analytů druhým kvadrupólem dochází k&nbsp;fragmentaci srážkami jejich molekul s&nnbsp;plynem. Toto uspořádání je nejběžnější ve farmaceutickén průmyslu.
+=== Kvadrupólový spektrometr doby letu ===
+Kvadrupólové spektrometry doby letu (Q-tof) spojují [[hmotnostní spektrometrie doby letu|hmotnostní spektrometrii doby letu]] a [[kvadrupólový hmotnostní spektrometr|kvadrupólové hmotnostní spektrometry]], čímž se dosahuje vysoké hmotnostní přesnonsti u vytvořených iontů a využitelnosti fragmentačních experimentů. Poměr (m/z) je zde určován meřením doby letu iontů.
+=== Hybridní hmotnostní spektrometr ===
+Hybridní hmotnostní spektrometr je soustava vzniklá propojením více než dvou hmotnostních spektrometrů.
+== Přístroje ==
+[[Soubor:MS MS.png|thumb|right|400px|Nákres tandemové hmotnostní spektrometrie]]
+=== Tandemová hmotnostní spektrometrie v prostoru ===
+[[Soubor:Triple quadripole.png|thumb|right|250px|Nákres trojitého kvadrupólu a příklad tandemové hmotnostní spektrometrie v prostoru]]
+Při tandemové hmotnostní spektrometrii ''v&nbsp;prostoru'' jsou separační zařízení fyzicky oddělená, i&nbsp;když jsou jednotlivé prvky stále propojené, aby bylo zachováno [[Vakuum#Vakuum experimentální a technické|vysoké vakuum]]. Těmito prvky mohou být [[sektorový hmotnostní spektrometr|sektory]], [[kvadrupólový hmotnostní spektrometr|kvadrupóly]] nebo [[hmotnostní spektrometrie doby letu|spektrometry doby letu]]. Je-li použito více kvadrupólových spektrometrů, tak mohou sloužit jako hmotnostní analyzátory i srážkové komory.
+Pro hmotnostní analyzátory se obvykle používá toto značení ''Q'' – kvadrupólový hmotnostní analyzátor; ''q'' – radiofrekvenční kolizní kvadrupól; ''TOF'' – hmotnostní analyzátor doby letu; ''B'' – magnetický sektor a ''E'' – elektrický sektor. Značení je možné při označování kombinovaných zařízení spojovat, například ''QqQ''' – [[trojitý kvadrupólový hmotnostní spektrometr]]; ''QTOF'' – kvadrupólový hnotnostní spektrometr doby letu (také značený ''QqTOF'') a ''BEBE'' – čtyřsektorový hmotnostníá spektrometr (s&nbsp;obrácenou geometrií).
+=== Tandemová hmotnostní spektrometrie v čase ===
+[[Soubor:LTQ Trap And Dynodes 2.jpg|thumb|right|250px|Hmotnostní spektrometr s&nbsp;iontovou pastí, příklad přístroje na tandemovou hmotnostní spektrometrii v&nbsp;čase]]
+<!-- By doing tandem mass spectrometry ''in time'', the separation is accomplished with ions trapped in the same place, with multiple separation steps taking place over time. A [[quadrupole ion trap]] or [[Fourier transform ion cyclotron resonance]] (FTICR) instrument can be used for such an analysis.<ref>{{Cite journal | vauthors = Cody RB, Freiser BS |title=Collision-induced dissociation in a fourier-transform mass spectrometer |journal=International Journal of Mass Spectrometry and Ion Physics|volume=41|issue=3|pages=199–204|doi=10.1016/0020-7381(82)85035-3|bibcode=1982IJMSI..41..199C|year=1982}}</ref> Trapping instruments can perform multiple steps of analysis, which is sometimes referred to as MS<sup>''n''</sup> (MS to the ''n'').<ref>{{Cite journal | vauthors = Cody RB, Burnier RC, Cassady CJ, Freiser BS |date=1982-11-01|title=Consecutive collision-induced dissociations in Fourier transform mass spectrometry |journal=Analytical Chemistry |volume=54 |issue=13 |pages=2225–2228 |doi=10.1021/ac00250a021}}</ref> Often the number of steps, ''n'', is not indicated, but occasionally the value is specified; for example MS<sup>3</sup> indicates three stages of separation.
+Tandem in time MS instruments do not use the modes described next, but typically collect all of the information from a precursor ion scan and a parent ion scan of the entire spectrum. Each instrumental configuration utilizes a unique mode of mass identification.
+===Tandem in space MS/MS modes===
+When tandem MS is performed with an in space design, the instrument must operate in one of a variety of modes. There are a number of different tandem MS/MS experimental setups and each mode has its own applications and provides different information. Tandem MS in space uses the coupling of two instrument components which measure the same mass spectrum range but with a controlled fractionation between them in space, while tandem MS in time involves the use of an [[ion trap]].
+There are four main scan experiments possible using MS/MS: precursor ion scan, product ion scan, neutral loss scan, and selected reaction monitoring.
+For a precursor ion scan, the product ion is selected in the second mass analyzer, and the precursor masses are scanned in the first mass analyzer. Note that precursor ion<ref>{{GoldBookRef|title=precursor ion|file=P04807}}</ref> is synonymous with parent ion<ref>{{GoldBookRef|title=parent ion|file=P04406}}</ref> and product ion<ref>{{GoldBookRef|title=product ion|file= P04864}}</ref> with daughter ion;<ref>{{GoldBookRef|title=daughter ion|file= D01524}}</ref> however the use of these anthropomorphic terms is discouraged.<ref name=Bursey1991>{{Cite journal| last = Bursey | first =  Maurice M. | year = 1991 | title = Comment to readers: Style and the lack of it | journal = Mass Spectrometry Reviews | volume = 10 | issue =  1 | pages = 1–2 | doi = 10.1002/mas.1280100102 | bibcode = 1991MSRv...10....1B}}</ref><ref name=Adams1992>{{Cite journal| last = Adams | first =  J. | year = 1992 | title = To the editor | journal = Journal of the American Society for Mass Spectrometry | volume = 3 | page = 473 | doi = 10.1016/1044-0305(92)87078-D | issue = 4 | doi-access = free }}</ref>
+In a product ion scan, a precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
+In a neutral loss scan, the first mass analyzer scans all the masses. The second mass analyzer also scans, but at a set offset from the first mass analyzer.<ref name=Louris1985>{{Cite journal| last = Louris | first =  John N. | year = 1985 | title = New scan modes accessed with a hybrid mass spectrometer | journal = Analytical Chemistry | volume = 57 | pages = 2918–2924 | doi = 10.1021/ac00291a039 | last2 = Wright | first2 = Larry G. | last3 = Cooks | first3 = R. Graham. | last4 = Schoen | first4 = Alan E. | name-list-style = vanc | issue = 14}}</ref> This offset corresponds to a neutral loss that is commonly observed for the class of compounds. In a constant-neutral-loss scan, all precursors that undergo the loss of a specified common neutral are monitored. To obtain this information, both mass analyzers are scanned simultaneously, but with a mass offset that correlates with the mass of the specified neutral. Similar to the precursor-ion scan, this technique is also useful in the selective identification of closely related class of compounds in a mixture.
+In selected reaction monitoring, both mass analyzers are set to a selected mass. This mode is analogous to selected ion monitoring for MS experiments. A selective analysis mode, which can increase sensitivity.<ref>{{Cite book| last = deHoffman  | first = Edmond | last2 = Stroobant | first2 = Vincent | name-list-style = vanc | title = Mass Spectrometry: Principles and Applications  | publisher = Wiley  | year = 2003  | location = Toronto  | page = 133 | isbn = 978-0-471-48566-7}}</ref>
+==Fragmentation==
+{{Main|Fragmentation (chemistry)}}
+Fragmentation of gas-phase ions is essential to tandem mass spectrometry and occurs between different stages of mass analysis. There are many methods used to fragment the ions and these can result in different types of fragmentation and thus different information about the structure and composition of the molecule.
+===In-source fragmentation===
+Often, the [[ionization]] process is sufficiently violent to leave the resulting ions with sufficient [[internal energy]] to fragment within the mass spectrometer. If the product ions persist in their non-equilibrium state for a moderate amount of time before auto-dissociation this process is called [[metastable]] fragmentation.<ref>{{GoldBookRef|file=T06451|title=transient (chemical) species}}</ref> Nozzle-skimmer fragmentation refers to the purposeful induction of in-source fragmentation by increasing the nozzle-skimmer potential on usually [[electrospray ionization|electrospray]] based instruments. Although in-source fragmentation allows for fragmentation analysis, it is not technically tandem mass spectrometry unless metastable ions are mass analyzed or selected before auto-dissociation and a second stage of analysis is performed on the resulting fragments. In-source fragmentation can be used in lieu of tandem mass spectrometry through the utilization of Enhanced in-Source Fragmentation Annotation (EISA) technology which generates fragmentation that directly matches tandem mass spectrometry data.<ref>{{cite journal |last1=Domingo-Almenara |first1=Xavier |last2=Montenegro-Burke |first2=J. Rafael |last3=Guijas |first3=Carlos |last4=Majumder |first4=Erica L.-W. |last5=Benton |first5=H. Paul |last6=Siuzdak |first6=Gary |title=Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics |journal=Analytical Chemistry |date=5 March 2019 |volume=91 |issue=5 |pages=3246–3253 |doi=10.1021/acs.analchem.8b03126|pmid=30681830 |pmc=6637741}}</ref> Fragments observed by EISA have higher signal intensity than traditional fragments which suffer losses in the collision cells of tandem mass spectrometers.<ref>{{cite journal |last1=Xue |first1=Jingchuan |last2=Domingo-Almenara |first2=Xavier |last3=Guijas |first3=Carlos |last4=Palermo |first4=Amelia |last5=Rinschen |first5=Markus M. |last6=Isbell |first6=John |last7=Benton |first7=H. Paul |last8=Siuzdak |first8=Gary |title=Enhanced in-Source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification |journal=Analytical Chemistry |date=21 April 2020 |volume=92 |issue=8 |pages=6051–6059 |doi=10.1021/acs.analchem.0c00409|pmid=32242660}}</ref> EISA enables fragmentation data acquisition on MS1 mass analyzers such as time-of-flight and single quadrupole instruments. In-source fragmentation is often used in addition to tandem mass spectrometry (with post-source fragmentation) to allow for two steps of fragmentation in a pseudo MS<sup>3</sup>-type of experiment.<ref>{{cite journal | vauthors = Körner R, Wilm M, Morand K, Schubert M, Mann M | title = Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests | journal = Journal of the American Society for Mass Spectrometry | volume = 7 | issue = 2 | pages = 150–6 | date = February 1996 | pmid = 24203235 | doi = 10.1016/1044-0305(95)00626-5 | doi-access = free}}</ref>
+===Collision-induced dissociation===
+Post-source fragmentation is most often what is being used in a tandem mass spectrometry experiment. Energy can also be added to the ions, which are usually already vibrationally excited, through post-source collisions with neutral atoms or molecules, the absorption of radiation, or the transfer or capture of an electron by a multiply charged ion. [[Collision-induced dissociation]] (CID), also called collisionally activated dissociation (CAD), involves the collision of an ion with a neutral atom or molecule in the gas phase and subsequent dissociation of the ion.<ref name="pmid16401509">{{cite book | vauthors = Wells JM, McLuckey SA | title = Collision-induced dissociation (CID) of peptides and proteins | volume = 402 | pages = 148–85 | year = 2005 | pmid = 16401509 | doi = 10.1016/S0076-6879(05)02005-7 | series = Methods in Enzymology | isbn = 9780121828073 | chapter = Collision‐Induced Dissociation (CID) of Peptides and Proteins }}</ref><ref name="pmid15481084">{{cite journal | vauthors = Sleno L, Volmer DA | title = Ion activation methods for tandem mass spectrometry | journal = Journal of Mass Spectrometry | volume = 39 | issue = 10 | pages = 1091–112 | date = October 2004 | pmid = 15481084 | doi = 10.1002/jms.703 | bibcode = 2004JMSp...39.1091S }}</ref> For example, consider
+:<chem>{AB+} + M -> {A} + {B+} + M</chem>
+where the ion AB<sup>+</sup> collides with the neutral species M and subsequently breaks apart. The details of this process are described by [[collision theory]]. Due to different instrumental configuration, two main different types of CID are possible: ''(i)'' beam-type (in which precursor ions are fragmented on-the-flight)<ref>{{cite journal | vauthors = Xia Y, Liang X, McLuckey SA | title = Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions | journal = Analytical Chemistry | volume = 78 | issue = 4 | pages = 1218–27 | date = February 2006 | pmid = 16478115 | doi = 10.1021/ac051622b }}</ref> and ''(ii)'' ion trap-type (in which precursor ions are first trapped, and then fragmented).<ref>{{Cite journal|last=March|first=Raymond E. | name-list-style = vanc |date=1997-04-01|title=An Introduction to Quadrupole Ion Trap Mass Spectrometry |journal=Journal of Mass Spectrometry |volume=32 |issue=4 |pages=351–369 |doi=10.1002/(sici)1096-9888(199704)32:4<351::aid-jms512>3.0.co;2-y |bibcode=1997JMSp...32..351M }}</ref><ref>{{cite journal | vauthors = Bantscheff M, Boesche M, Eberhard D, Matthieson T, Sweetman G, Kuster B | title = Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer | journal = Molecular & Cellular Proteomics | volume = 7 | issue = 9 | pages = 1702–13 | date = September 2008 | pmid = 18511480 | pmc = 2556025 | doi = 10.1074/mcp.M800029-MCP200 }}</ref>
+A third and more recent type of CID fragmentation is [[higher-energy collisional dissociation]] (HCD). HCD is a CID technique specific to [[orbitrap]] mass spectrometers in which fragmentation takes place external to the ion trap,<ref name="pmid17721543">{{cite journal | vauthors = Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M | title = Higher-energy C-trap dissociation for peptide modification analysis | journal = Nature Methods | volume = 4 | issue = 9 | pages = 709–12 | date = September 2007 | pmid = 17721543 | doi = 10.1038/nmeth1060 | s2cid = 2538231 }}</ref><ref>{{cite journal | vauthors = Senko MW, Remes PM, Canterbury JD, Mathur R, Song Q, Eliuk SM, Mullen C, Earley L, Hardman M, Blethrow JD, Bui H, Specht A, Lange O, Denisov E, Makarov A, Horning S, Zabrouskov V | title = Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates | language = EN | journal = Analytical Chemistry | volume = 85 | issue = 24 | pages = 11710–4 | date = December 2013 | pmid = 24251866 | doi = 10.1021/ac403115c }}</ref> it happens in the HCD cell (in some instruments named "ion routing multipole").<ref>{{cite journal | vauthors = Riley NM, Westphall MS, Coon JJ | title = Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation | journal = Journal of Proteome Research | volume = 16 | issue = 7 | pages = 2653–2659 | date = July 2017 | pmid = 28608681 | pmc = 5555583 | doi = 10.1021/acs.jproteome.7b00249}}</ref> HCD is a trap-type fragmentation that has been shown to have beam-type characteristics.<ref>{{cite journal | vauthors = Nagaraj N, D'Souza RC, Cox J, Olsen JV, Mann M | title = Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation | language = EN | journal = Journal of Proteome Research | volume = 9 | issue = 12 | pages = 6786–94 | date = December 2010 | pmid = 20873877 | doi = 10.1021/pr100637q }}</ref><ref>{{cite journal | vauthors = Jora M, Burns AP, Ross RL, Lobue PA, Zhao R, Palumbo CM, Beal PA, Addepalli B, Limbach PA | title = Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS) | journal = Journal of the American Society for Mass Spectrometry | volume = 29 | issue = 8 | pages = 1745–1756 | date = August 2018 | pmid = 29949056 | pmc = 6062210 | doi = 10.1007/s13361-018-1999-6 | bibcode = 2018JASMS..29.1745J }}</ref> Freely available large scale high resolution tandem mass spectrometry databases exist (e.g. METLIN with 850,000 molecular standards each with experimental CID MS/MS data),<ref>{{Cite journal|title=Article Metrics - METLIN MS 2 molecular standards database: a broad chemical and biological resource {{!}} Nature Methods|url=https://www.nature.com/articles/s41592-020-0942-5/metrics|language=en|issn=1548-7105}}</ref> and are typically used to facilitate small molecule identification.
+===Electron capture and transfer methods===
+The energy released when an electron is transferred to or captured by a multiply charged ion can induce fragmentation.
+====Electron capture dissociation====
+If an [[electron]] is added to a multiply charged positive ion, the [[Coulomb's law|Coulomb energy]] is liberated. Adding a free electron is called [[electron capture dissociation]] (ECD),<ref name="pmid15389856">{{cite journal | vauthors = Cooper HJ, Håkansson K, Marshall AG | title = The role of electron capture dissociation in biomolecular analysis | journal = Mass Spectrometry Reviews | volume = 24 | issue = 2 | pages = 201–22 | year = 2005 | pmid = 15389856 | doi = 10.1002/mas.20014 | bibcode = 2005MSRv...24..201C }}</ref> and is represented by
+:<math chem>[\ce M + n\ce H]^{n+} + \ce{e^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* \ce{-> fragments}</math>
+for a multiply protonated molecule M.
+====Electron transfer dissociation====
+Adding an electron through an ion-ion reaction is called [[electron transfer dissociation]] (ETD).<ref name="pmid15210983">{{cite journal | vauthors = Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF | title = Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 26 | pages = 9528–33 | date = June 2004 | pmid = 15210983 | pmc = 470779 | doi = 10.1073/pnas.0402700101 | bibcode = 2004PNAS..101.9528S }}</ref><ref name="pmid17118725">{{cite journal | vauthors = Mikesh LM, Ueberheide B, Chi A, Coon JJ, Syka JE, Shabanowitz J, Hunt DF | title = The utility of ETD mass spectrometry in proteomic analysis | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1764 | issue = 12 | pages = 1811–22 | date = December 2006 | pmid = 17118725 | pmc = 1853258 | doi = 10.1016/j.bbapap.2006.10.003 }}</ref> Similar to electron-capture dissociation, ETD induces fragmentation of cations (e.g. [[peptide]]s or [[protein]]s) by transferring [[electron]]s to them. It was invented by [[Donald F. Hunt]], [[Joshua Coon]], John E. P. Syka and Jarrod Marto at the [[University of Virginia]].<ref>{{US patent reference | number = 7534622 | y = 2009 | m = 05 | d = 19 | inventor = Donald F. Hunt, Joshua J. Coon, John E.P. Syka, Jarrod A. Marto | title = Electron transfer dissociation for biopolymer sequence mass spectrometric analysis}}</ref>
+ETD does not use free electrons but employs radical anions (e.g. [[anthracene]] or [[azobenzene]]) for this purpose:
+:<math chem>[\ce M + n\ce H]^{n+} + \ce{A^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* + \ce{A -> fragments}</math>
+where A is the anion.<ref name="pmid10360331">{{cite journal | vauthors = McLuckey SA, Stephenson JL | title = Ion/ion chemistry of high-mass multiply charged ions | journal = Mass Spectrometry Reviews | volume = 17 | issue = 6 | pages = 369–407 | year = 1998 | pmid = 10360331 | doi = 10.1002/(SICI)1098-2787(1998)17:6<369::AID-MAS1>3.0.CO;2-J | bibcode = 1998MSRv...17..369M | url = https://zenodo.org/record/1235512 }}</ref>
+ETD cleaves randomly along the peptide backbone (c and z ions) while side chains and modifications such as phosphorylation are left intact. The technique only works well for higher charge state ions (z>2), however relative to [[collision-induced dissociation]] (CID), ETD is advantageous for the fragmentation of longer peptides or even entire proteins. This makes the technique important for [[top-down proteomics]]. Much like ECD, ETD is effective for peptides with [[posttranslational modification|modifications]] such as phosphorylation.<ref name="pmid17287358">{{cite journal | vauthors = Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF | title = Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 7 | pages = 2193–8 | date = February 2007 | pmid = 17287358 | pmc = 1892997 | doi = 10.1073/pnas.0607084104 | bibcode = 2007PNAS..104.2193C }}</ref>
+Electron-transfer and higher-energy collision dissociation (EThcD) is a combination ETD and HCD where the peptide precursor is initially subjected to an ion/ion reaction with [[fluoranthene]] anions in a [[linear ion trap]], which generates c- and z-ions.<ref name="pmid15210983"/><ref>{{cite journal | vauthors = Frese CK, Altelaar AF, van den Toorn H, Nolting D, Griep-Raming J, Heck AJ, Mohammed S | title = Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry | journal = Analytical Chemistry | volume = 84 | issue = 22 | pages = 9668–73 | date = November 2012 | pmid = 23106539 | doi = 10.1021/ac3025366 }}</ref> In the second step HCD all-ion fragmentation is applied to all ETD derived ions to generate b- and y- ions prior to final analysis in the orbitrap analyzer.<ref name="pmid17721543"/> This method employs dual fragmentation to generate ion- and thus data-rich MS/MS spectra for peptide sequencing and [[Post-translational modification|PTM]] localization.<ref>{{cite journal | vauthors = Frese CK, Zhou H, Taus T, Altelaar AF, Mechtler K, Heck AJ, Mohammed S | title = Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD) | journal = Journal of Proteome Research | volume = 12 | issue = 3 | pages = 1520–5 | date = March 2013 | pmid = 23347405 | pmc = 3588588 | doi = 10.1021/pr301130k }}</ref>
+====Negative electron transfer dissociation====
+Fragmentation can also occur with a deprotonated species, in which an electron is transferred from the species to an cationic reagent in a negative electron transfer dissociation (NETD):<ref name="pmid15907703">{{cite journal | vauthors = Coon JJ, Shabanowitz J, Hunt DF, Syka JE | title = Electron transfer dissociation of peptide anions | journal = Journal of the American Society for Mass Spectrometry | volume = 16 | issue = 6 | pages = 880–2 | date = June 2005 | pmid = 15907703 | doi = 10.1016/j.jasms.2005.01.015 | doi-access = free }}</ref>
+:<math chem>[\ce M-n\ce H]^{n-} + \ce{A+ ->} \left[ [\ce M-n\ce H]^{(n+1)-} \right]^* + \ce{A -> fragments}</math>
+Following this transfer event, the electron deficient anion undergoes internal rearrangement and [[fragmentation (mass spectrometry)|fragment]]s. NETD is the ion/ion analogue of [[electron-detachment dissociation]] (EDD).
+NETD is compatible with fragmenting [[peptide]] and [[proteins]] along the backbone at the C<sub>α</sub>-C bond. The resulting fragments are usually a<sup>•</sup>- and x-type product ions.
+====Electron-detachment dissociation====
+Electron-detachment dissociation (EDD) is a method for fragmenting anionic species in mass spectrometry.<ref>{{cite journal |vauthors=Budnik BA, Haselmann KF, Zubarev RA |title=Electron detachment dissociation of peptide di-anions: an electron–hole recombination phenomenon |journal=Chemical Physics Letters |volume=342 |issue=3–4 |pages=299–302  |year=2001 |doi=10.1016/S0009-2614(01)00501-2|bibcode = 2001CPL...342..299B }}</ref> It serves as a negative counter mode to electron capture dissociation. Negatively charged ions are activated by irradiation with [[electrons]] of moderate kinetic energy.  The result is ejection of electrons from the parent [[Ionic compound|ionic]] molecule, which causes dissociation via recombination.
+====Charge transfer dissociation====
+Reaction between positively charged peptides and cationic reagents,<ref>{{cite journal | vauthors = Chingin K, Makarov A, Denisov E, Rebrov O, Zubarev RA | title = Fragmentation of positively-charged biological ions activated with a beam of high-energy cations | journal = Analytical Chemistry | volume = 86 | issue = 1 | pages = 372–9 | date = January 2014 | pmid =  24236851| doi = 10.1021/ac403193k }}</ref> also known as charge transfer dissociation (CTD),<ref>{{cite journal | vauthors = Hoffmann WD, Jackson GP | title = Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations | journal = Journal of the American Society for Mass Spectrometry | volume = 25 | issue = 11 | pages = 1939–43 | date = November 2014 | pmid =  25231159| doi = 10.1007/s13361-014-0989-6 | bibcode = 2014JASMS..25.1939H | s2cid = 1400057 }}</ref> has recently been demonstrated as an alternative high-energy fragmentation pathway for low-charge state (1+ or 2+) peptides. The proposed mechanism of CTD using helium cations as the reagent is:
+:<math chem>\ce{{[{M}+H]^1+} + He+ ->} \left[ \ce{[{M}+H]^2+} \right]^* + \ce{He^0 -> fragments}</math>
+Initial reports are that CTD causes backbone C<sub>α</sub>-C bond cleavage of peptides and provides a<sup>•</sup>- and x-type product ions.
+===Photodissociation===
+The energy required for dissociation can be added by [[photon]] absorption, resulting in ion [[photodissociation]] and represented by
+:<chem>{AB+} + \mathit{h\nu} -> {A} + B+</chem>
+where <math>h\nu</math> represents the photon absorbed by the ion. Ultraviolet lasers can be used, but can lead to excessive fragmentation of biomolecules.<ref name="pmid16401510">{{cite book | vauthors = Morgan JW, Hettick JM, Russell DH | title = Peptide sequencing by MALDI 193-nm photodissociation TOF MS | volume = 402 | pages = 186–209 | year = 2005 | pmid = 16401510 | doi = 10.1016/S0076-6879(05)02006-9 | series = Methods in Enzymology | isbn = 9780121828073 | chapter = Peptide Sequencing by MALDI 193‐nm Photodissociation TOF MS }}</ref>
+====Infrared multiphoton dissociation====
+[[Infrared]] photons will heat the ions and cause dissociation if enough of them are absorbed. This process is called [[infrared multiphoton dissociation]] (IRMPD) and is often accomplished with a [[carbon dioxide laser]] and an ion trapping mass spectrometer such as a [[Fourier transform ion cyclotron resonance|FTMS]].<ref name="pmid7526742">{{cite journal | vauthors = Little DP, Speir JP, Senko MW, O'Connor PB, McLafferty FW | title = Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing | journal = Analytical Chemistry | volume = 66 | issue = 18 | pages = 2809–15 | date = September 1994 | pmid = 7526742 | doi = 10.1021/ac00090a004 }}</ref>
+====Blackbody infrared radiative dissociation====
+[[Blackbody radiation]] can be used for photodissociation in a technique known as blackbody infrared radiative dissociation (BIRD).<ref name="pmid16525512">{{cite journal | vauthors = Schnier PD, Price WD, Jockusch RA, Williams ER | title = Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase | journal = Journal of the American Chemical Society | volume = 118 | issue = 30 | pages = 7178–89 | date = July 1996 | pmid = 16525512 | pmc = 1393282 | doi = 10.1021/ja9609157 }}</ref> In the BIRD method, the entire mass spectrometer vacuum chamber is heated to create [[infrared]] light. BIRD uses this radiation to excite increasingly more energetic [[Molecular vibration|vibrations]] of the ions, until a bond breaks, creating fragments.<ref name="pmid16525512"/><ref name="pmid14732935">{{cite journal | vauthors = Dunbar RC | title = BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications | journal = Mass Spectrometry Reviews | volume = 23 | issue = 2 | pages = 127–58 | year = 2004 | pmid = 14732935 | doi = 10.1002/mas.10074 | bibcode = 2004MSRv...23..127D }}</ref> This is similar to [[infrared multiphoton dissociation]] which also uses infrared light, but from a different source.<ref name="pmid15481084"/> BIRD is most often used with [[Fourier transform ion cyclotron resonance]] mass spectrometry.
+===Surface induced dissociation===
+With surface-induced dissociation (SID), the fragmentation is a result of the collision of an ion with a surface under high vacuum.<ref name=Grill2001>{{Cite journal| last1 = Grill | first1 =  Verena | year = 2001 | title = Collisions of ions with surfaces at chemically relevant energies: Instrumentation and phenomena | journal = Review of Scientific Instruments | volume = 72 | page = 3149 | doi = 10.1063/1.1382641 | last2 = Shen | first2 = Jianwei | last3 = Evans | first3 = Chris | last4 = Cooks | first4 = R. Graham | name-list-style = vanc | issue = 8|bibcode = 2001RScI...72.3149G }}</ref><ref name=Mabud1985>{{Cite journal| last = Mabud | first =  M. | year = 1985 | title = Surface-induced dissociation of molecular ions | journal = International Journal of Mass Spectrometry and Ion Processes | volume = 67 | pages = 285–294 | doi = 10.1016/0168-1176(85)83024-X | issue = 3|bibcode = 1985IJMSI..67..285M }}</ref> Today, SID is used to fragment a wide range of ions. Years ago, it was only common to use SID on lower mass, singly charged species because ionization methods and mass analyzer technologies weren't advanced enough to properly form, transmit, or characterize ions of high m/z. Over time, self-assembled monolayer surfaces (SAMs) composed of CF3(CF2)10CH2CH2S on gold have been the most prominently used collision surfaces for SID in a tandem spectrometer. SAMs have acted as the most desirable collision targets due to their characteristically large effective masses for the collision of incoming ions. Additionally, these surfaces are composed of rigid fluorocarbon chains, which don't significantly dampen the energy of the projectile ions. The fluorocarbon chains are also beneficial because of their ability to resist facile electron transfer from the metal surface to the incoming ions.<ref name="Surface-Induced Dissociation: An Eﬀ">{{cite journal |last1=Stiving |first1=Alyssa |last2=VanAernum |first2=Zachary |last3=Busch |first3=Florian |last4=Harvey |first4=Sophie |last5=Sarni |first5=Samantha |last6=Wysocki |first6=Vicki |title=Surface-Induced Dissociation: An Eﬀective Method for Characterization of Protein Quaternary Structure |journal=Analytical Chemistry |date=9 November 2018 |volume=91 |issue=1 |pages=190–191 |doi=10.1021/acs.analchem.8b05071 |pmc=6571034 |pmid=30412666 }}</ref> SID's ability to produce subcomplexes that remain stable and provide valuable information on connectivity is unmatched by any other dissociation technique. Since the complexes produced from SID are stable and retain distribution of charge on the fragment, this produces a unique, spectra which the complex centers around a narrower m/z distribution. The SID products and the energy at which they form are reflective of the strengths and topology of the complex. The unique dissociation patterns help discover the Quaternary structure of the complex. The symmetric charge distribution and dissociation dependence are unique to SID and make the spectra produced distinctive from any other dissociation technique.<ref name="Surface-Induced Dissociation: An Eﬀ"/>
+The SID technique is also applicable to ion-mobility mass spectrometry (IM-MS). Three different methods for this technique include analyzing the characterization of topology, intersubunit connectivity, and the degree of unfolding for protein structure. Analysis of protein structure unfolding is the most commonly used application of the SID technique. For Ion-mobility mass spectrometry (IM-MS), SID is used for dissociation of the source activated precursors of three different types of protein complexes: C-reactive protein (CRP), transthyretin (TTR), and concanavalin A (Con A). This method is used to observe the unfolding degree for each of these complexes. For this observation, SID showed the precursor ions' structures that exist before the collision with the surface. IM-MS utilizes the SID as a direct measure of the conformation for each proteins' subunit.<ref>{{Cite journal|last1=Quintyn|first1=Royston S.|last2=Zhou|first2=Mowei|last3=Yan|first3=Jing|last4=Wysocki|first4=Vicki H.|date=2015-12-01|title=Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes|journal=Analytical Chemistry|volume=87|issue=23|pages=11879–11886|doi=10.1021/acs.analchem.5b03441|pmid=26499904|issn=0003-2700}}</ref>
+Fourier-transform ion cyclotron resonance (FTICR) are able to provide ultrahigh resolution and high mass accuracy to instruments that take mass measurements. These features make FTICR mass spectrometers a useful tool for a wide variety of applications such as several dissociation experiments<ref>{{Cite journal|last1=Laskin|first1=Julia|last2=Futrell|first2=Jean H.|date=2005|title=Activation of large lons in FT-ICR mass spectrometry|journal=Mass Spectrometry Reviews|volume=24|issue=2|pages=135–167|doi=10.1002/mas.20012|pmid=15389858|issn=0277-7037|bibcode=2005MSRv...24..135L|url=https://zenodo.org/record/1229281}}</ref> such as collision-induced dissociation (CID, electron transfer dissociation (ETD),<ref>{{Cite journal|last1=Kaplan|first1=Desmond A.|last2=Hartmer|first2=Ralf|last3=Speir|first3=J. Paul|last4=Stoermer|first4=Carsten|last5=Gumerov|first5=Dmitry|last6=Easterling|first6=Michael L.|last7=Brekenfeld|first7=Andreas|last8=Kim|first8=Taeman|last9=Laukien|first9=Frank|last10=Park|first10=Melvin A.|date=2008|title=Electron transfer dissociation in the hexapole collision cell of a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer|journal=Rapid Communications in Mass Spectrometry|volume=22|issue=3|pages=271–278|doi=10.1002/rcm.3356|pmid=18181247|issn=0951-4198|bibcode=2008RCMS...22..271K}}</ref> and others. In addition, surface-induced dissociation has been implemented with this instrument for the study of fundamental peptide fragmentation. Specifically, SID has been applied to the study of energetics and the kinetics of gas-phase fragmentation within an ICR instrument.<ref>{{Cite journal|last=Laskin|first=Julia|date=June 2015|title=Surface-Induced Dissociation: A Unique Tool for Studying Energetics and Kinetics of the Gas-Phase Fragmentation of Large Ions|journal=European Journal of Mass Spectrometry|volume=21|issue=3|pages=377–389|doi=10.1255/ejms.1358|pmid=26307719|s2cid=19837927|issn=1469-0667}}</ref> This approach has been used to understand the gas-phase fragmentation of protonated peptides, odd-electron peptide ions, non-covalent ligand-peptide complexes, and ligated metal clusters.
+==Quantitative proteomics==
+[[Quantitative proteomics]] is used to determine the relative or absolute amount of [[protein]]s in a sample.<ref>{{cite journal | vauthors = Ong SE, Mann M | title = Mass spectrometry-based proteomics turns quantitative | journal = Nature Chemical Biology | volume = 1 | issue = 5 | pages = 252–62 | date = October 2005 | pmid = 16408053 | doi = 10.1038/nchembio736 }}</ref><ref name="pmid17668192">{{cite journal | vauthors = Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B | title = Quantitative mass spectrometry in proteomics: a critical review | journal = Analytical and Bioanalytical Chemistry | volume = 389 | issue = 4 | pages = 1017–31 | date = October 2007 | pmid = 17668192 | doi = 10.1007/s00216-007-1486-6 | doi-access = free }}</ref><ref name="pmid=22665296">{{cite book | vauthors = Nikolov M, Schmidt C, Urlaub H | chapter = Quantitative mass spectrometry-based proteomics: an overview | volume = 893 | pages = 85–100 | year = 2012 | pmid = 22665296 | doi = 10.1007/978-1-61779-885-6_7 | series = Methods in Molecular Biology | isbn = 978-1-61779-884-9 | title = Quantitative Methods in Proteomics | hdl = 11858/00-001M-0000-0029-1A75-8 }}</ref> Several quantitative proteomics methods are based on tandem mass spectrometry. MS/MS has become a benchmark procedure for the structural elucidation of complex biomolecules.<ref name="Maher S, Jjunju FP, Taylor S 2015 113–135">{{cite journal |vauthors = Maher S, Jjunju FP, Taylor S | title = 100 years of mass spectrometry: Perspectives and future trends |journal=Rev. Mod. Phys. |volume=87 |issue=1 |pages=113–135 |year=2015 |doi= 10.1103/RevModPhys.87.113 |bibcode=2015RvMP...87..113M}}</ref>
+One method commonly used for quantitative proteomics is isobaric tag labeling. Isobaric tag labeling enables simultaneous identification and quantification of proteins from multiple samples in a single analysis. To quantify proteins, [[peptides]] are labeled with chemical tags that have the same structure and nominal mass, but vary in the distribution of heavy isotopes in their structure. These tags, commonly referred to as tandem mass tags, are designed so that the mass tag is cleaved at a specific linker region upon higher-energy collisional-induced dissociation (HCD) during tandem mass spectrometry yielding reporter ions of different masses. Protein quantitation is accomplished by comparing the intensities of the reporter ions in the MS/MS spectra. Two commercially available isobaric tags are iTRAQ and TMT reagents.
+===Isobaric tags for relative and absolute quantitation (iTRAQ)===
+[[Image:Isobaric labeling.png|right|thumb|300px|Isobaric labeling for tandem mass spectrometry: proteins are extracted from cells, digested, and labeled with tags of the same mass. When fragmented during MS/MS, the reporter ions show the relative amount of the peptides in the samples.]]
+An [[isobaric tag for relative and absolute quantitation]] (iTRAQ) is a reagent for tandem mass spectrometry that is used to determine the amount of proteins from different sources in a single experiment.<ref name="pmid15385600">{{cite journal | vauthors = Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ | title = Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents | journal = Molecular & Cellular Proteomics | volume = 3 | issue = 12 | pages = 1154–69 | date = December 2004 | pmid = 15385600 | doi = 10.1074/mcp.M400129-MCP200 | doi-access = free }}</ref><ref name="pmid16574745">{{cite journal | vauthors = Zieske LR | title = A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies | journal = Journal of Experimental Botany | volume = 57 | issue = 7 | pages = 1501–8 | year = 2006 | pmid = 16574745 | doi = 10.1093/jxb/erj168 | doi-access = free }}</ref><ref name="pmid17162667">{{cite journal | vauthors = Gafken PR, Lampe PD | title = Methodologies for characterizing phosphoproteins by mass spectrometry | journal = Cell Communication & Adhesion | volume = 13 | issue = 5–6 | pages = 249–62 | year = 2006 | pmid = 17162667 | pmc = 2185548 | doi = 10.1080/15419060601077917 }}</ref>
+It uses stable [[Isotopic labeling|isotope labeled]] molecules that can form a [[covalent bond]] with the [[N-terminus]] and [[side chain]] [[amine]]s of proteins. The iTRAQ reagents are used to label peptides from different samples that are pooled and analyzed by [[liquid chromatography]] and tandem mass spectrometry. The fragmentation of the attached tag generates a low molecular mass reporter ion that can be used to relatively quantify the peptides and the proteins from which they originated.
+===Tandem mass tag (TMT)===
+A [[tandem mass tag]] (TMT) is an isobaric mass tag chemical label used for protein quantification and identification.<ref name="pmid12713048">{{cite journal | vauthors = Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C | title = Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS | journal = Analytical Chemistry | volume = 75 | issue = 8 | pages = 1895–904 | date = April 2003 | pmid = 12713048 | doi = 10.1021/ac0262560 }}</ref> The tags contain four regions: mass reporter, cleavable linker, mass normalization, and protein reactive group. TMT reagents can be used to simultaneously analyze 2 to 11 different peptide samples prepared from cells, tissues or biological fluids. Three types of TMT reagents are available with different chemical reactivities: (1) a reactive NHS ester functional group for labeling primary amines (TMTduplex, TMTsixplex, TMT10plex plus TMT11-131C), (2) a reactive iodoacetyl functional group for labeling free sulfhydryls (iodoTMT) and (3) reactive alkoxyamine functional group for labeling of carbonyls (aminoxyTMT).
+==Applications ==
+===Peptides===
+[[Image:PeptideMSMS.jpg|right|thumb|300px|Chromatography trace (top) and tandem mass spectrum (bottom) of a peptide.]]
+Tandem mass spectrometry can be used for [[protein sequencing]].<ref name="AngelAryal2012">{{cite journal | vauthors = Angel TE, Aryal UK, Hengel SM, Baker ES, Kelly RT, Robinson EW, Smith RD | title = Mass spectrometry-based proteomics: existing capabilities and future directions | journal = Chemical Society Reviews | volume = 41 | issue = 10 | pages = 3912–28 | date = May 2012 | pmid = 22498958 | doi = 10.1039/c2cs15331a | pmc=3375054}}</ref> When intact proteins are introduced to a mass analyzer, this is called "[[top-down proteomics]]" and when proteins are digested into smaller [[peptides]] and subsequently introduced into the mass spectrometer, this is called "[[bottom-up proteomics]]". [[Shotgun proteomics]] is a variant of bottom up proteomics in which proteins in a mixture are digested prior to separation and tandem mass spectrometry.
+Tandem mass spectrometry can produce a [[peptide sequence tag]] that can be used to identify a peptide in a protein database.<ref name="pmid17492750">{{cite journal | vauthors = Hardouin J | title = Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry | journal = Mass Spectrometry Reviews | volume = 26 | issue = 5 | pages = 672–82 | year = 2007 | pmid = 17492750 | doi = 10.1002/mas.20142 | bibcode = 2007MSRv...26..672H }}</ref><ref name="pmid16196103">{{cite journal | vauthors = Shadforth I, Crowther D, Bessant C | title = Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines | journal = Proteomics | volume = 5 | issue = 16 | pages = 4082–95 | date = November 2005 | pmid = 16196103 | doi = 10.1002/pmic.200402091 }}</ref><ref name="pmid8710858">{{cite journal | vauthors = Mørtz E, O'Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M | title = Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 93 | issue = 16 | pages = 8264–7 | date = August 1996 | pmid = 8710858 | pmc = 38658 | doi = 10.1073/pnas.93.16.8264 | bibcode = 1996PNAS...93.8264M }}</ref> A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum.<ref name="pmid6525415">{{cite journal | vauthors = Roepstorff P, Fohlman J | title = Proposal for a common nomenclature for sequence ions in mass spectra of peptides | journal = Biomedical Mass Spectrometry | volume = 11 | issue = 11 | pages = 601 | date = November 1984 | pmid = 6525415 | doi = 10.1002/bms.1200111109 }}</ref> Peptide fragment ions are indicated by a, b, or c if the charge is retained on the [[N-terminus]] and by x, y or z if the charge is maintained on the [[C-terminus]]. The subscript indicates the number of amino acid residues in the fragment. Superscripts are sometimes used to indicate neutral losses in addition to the backbone fragmentation, * for loss of ammonia and ° for loss of water. Although peptide backbone cleavage is the most useful for sequencing and peptide identification other fragment ions may be observed under high energy dissociation conditions. These include the side chain loss ions d, v, w and ammonium ions<ref>{{cite journal|last1=Johnson|first1=Richard S.|last2=Martin|first2=Stephen A.|last3=Biemann|first3=Klaus|authorlink3 = Klaus Biemann| name-list-style = vanc |title=Collision-induced fragmentation of (M + H)+ ions of peptides. Side chain specific sequence ions|journal=International Journal of Mass Spectrometry and Ion Processes|date=December 1988|volume=86|pages=137–154|doi=10.1016/0168-1176(88)80060-0|bibcode=1988IJMSI..86..137J}}</ref><ref>{{cite journal | vauthors = Falick AM, Hines WM, Medzihradszky KF, Baldwin MA, Gibson BW | title = Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry | journal = Journal of the American Society for Mass Spectrometry | volume = 4 | issue = 11 | pages = 882–93 | date = November 1993 | pmid = 24227532 | doi = 10.1016/1044-0305(93)87006-X | doi-access = free }}</ref> and additional sequence-specific fragment ions associated with particular amino acid residues.<ref>{{cite journal|last1=Downard|first1=Kevin M.|last2=Biemann|first2=Klaus |authorlink2 = Klaus Biemann| name-list-style = vanc |title=Methionine specific sequence ions formed by the dissociation of protonated peptides at high collision energies|journal=Journal of Mass Spectrometry|date=January 1995|volume=30|issue=1|pages=25–32|doi=10.1002/jms.1190300106|bibcode=1995JMSp...30...25D}}</ref>
+===Oligosaccharides===
+[[Oligosaccharide]]s may be sequenced using tandem mass spectrometry in a similar manner to peptide sequencing.<ref name="Zaia2004">{{cite journal|vauthors=Zaia J|year=2004|title=Mass spectrometry of oligosaccharides|journal=Mass Spectrometry Reviews|volume=23|issue=3|pages=161–227|bibcode=2004MSRv...23..161Z|doi=10.1002/mas.10073|pmid=14966796}}</ref> Fragmentation generally occurs on either side of the [[glycosidic bond]] (b, c, y and z ions) but also under more energetic conditions through the sugar ring structure in a cross-ring cleavage (x ions). Again trailing subscripts are used to indicate position of the cleavage along the chain. For cross ring cleavage ions the nature of the cross ring cleavage is indicated by preceding superscripts.<ref>{{Cite journal|author1=Bruno Domon|author2=Catherine E Costello|year=1988|title=A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates|journal=Glycoconj. J.|volume=5|issue=4|pages=397–409|doi=10.1007/BF01049915}}</ref><ref name="pmid10973004">{{cite journal|vauthors=Spina E, Cozzolino R, Ryan E, Garozzo D|date=August 2000|title=Sequencing of oligosaccharides by collision-induced dissociation matrix-assisted laser desorption/ionization mass spectrometry|journal=Journal of Mass Spectrometry|volume=35|issue=8|pages=1042–8|bibcode=2000JMSp...35.1042S|doi=10.1002/1096-9888(200008)35:8<1042::AID-JMS33>3.0.CO;2-Y|pmid=10973004}}</ref>
+===Oligonucleotides===
+Tandem mass spectrometry has been applied to [[DNA sequencing|DNA]] and [[RNA sequencing]].<ref name="BanoubNewton2005">{{cite journal | vauthors = Banoub JH, Newton RP, Esmans E, Ewing DF, Mackenzie G | title = Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids | journal = Chemical Reviews | volume = 105 | issue = 5 | pages = 1869–915 | date = May 2005 | pmid = 15884792 | doi = 10.1021/cr030040w }}</ref><ref name="ThomasAkoulitchev2006">{{cite journal | vauthors = Thomas B, Akoulitchev AV | title = Mass spectrometry of RNA | journal = Trends in Biochemical Sciences | volume = 31 | issue = 3 | pages = 173–81 | date = March 2006 | pmid = 16483781 | doi = 10.1016/j.tibs.2006.01.004 }}</ref> A notation for gas-phase fragmentation of [[oligonucleotide]] ions has been proposed.<ref name=Wu2004>{{Cite journal | vauthors = Wu J, McLuckey SA | author-link2 = Scott A. McLuckey | year = 2004 | title = Gas-phase fragmentation of oligonucleotide ions | journal = International Journal of Mass Spectrometry | volume = 237 | pages = 197–241 | doi = 10.1016/j.ijms.2004.06.014 | issue = 2–3 |bibcode = 2004IJMSp.237..197W }}</ref>
+===Newborn screening===
+{{Main|Newborn screening}}
+Newborn screening is the process of testing newborn babies for treatable [[genetic disorder|genetic]], [[endocrinology|endocrinologic]], [[inborn error of metabolism|metabolic]] and [[hematology|hematologic]] diseases.<ref name="pmid17679658">{{cite journal | vauthors = Tarini BA | title = The current revolution in newborn screening: new technology, old controversies | journal = Archives of Pediatrics & Adolescent Medicine | volume = 161 | issue = 8 | pages = 767–72 | date = August 2007 | pmid = 17679658 | doi = 10.1001/archpedi.161.8.767 | doi-access = free }}</ref><ref name="pmid17402600">{{cite journal | vauthors = Kayton A | title = Newborn screening: a literature review | journal = Neonatal Network | volume = 26 | issue = 2 | pages = 85–95 | year = 2007 | pmid = 17402600 | doi = 10.1891/0730-0832.26.2.85 }}</ref> The development of tandem mass spectrometry screening in the early 1990s led to a large expansion of potentially detectable [[congenital metabolic disease]]s that affect blood levels of organic acids.<ref name="pmid14578311">{{cite journal | vauthors = Chace DH, Kalas TA, Naylor EW | title = Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns | journal = Clinical Chemistry | volume = 49 | issue = 11 | pages = 1797–817 | date = November 2003 | pmid = 14578311 | doi = 10.1373/clinchem.2003.022178 | doi-access = free }}</ref>
+== Limitation ==
+Tandem mass spectrometry cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell. Theses limitations are primarily due to a combination of inefficient ion production and ion losses within the instruments due to chemical noise sources of solvents.<ref>{{Cite journal|last=Angel|first=Thomas E.|last2=Aryal|first2=Uma K.|last3=Hengel|first3=Shawna M.|last4=Baker|first4=Erin S.|last5=Kelly|first5=Ryan T.|last6=Robinson|first6=Errol W.|last7=Smith|first7=Richard D.|date=2012-05-21|title=Mass spectrometry based proteomics: existing capabilities and future directions|journal=Chemical Society Reviews|volume=41|issue=10|pages=3912–3928|doi=10.1039/c2cs15331a|issn=0306-0012|pmc=3375054|pmid=22498958}}</ref>
+== Future outlook ==
+Tandem mass spectrometry will be a useful tool for protein characterization, nucleoprotein complexes, and other biological structures. However, some challenges left such as analyzing the characterization of the proteome quantitatively and qualitatively.<ref>{{Cite journal|last=Han|first=Xuemei|last2=Aslanian|first2=Aaron|last3=Yates|first3=John R.|date=October 2008|title=Mass Spectrometry for Proteomics|journal=Current Opinion in Chemical Biology|volume=12|issue=5|pages=483–490|doi=10.1016/j.cbpa.2008.07.024|issn=1367-5931|pmc=2642903|pmid=18718552}}</ref>
+== See also ==
+*[[Accelerator mass spectrometry]]
+*[[Cross section (physics)]]
+*[[Mass-analyzed ion-kinetic-energy spectrometry]]
+*[[Unimolecular ion decomposition]]
+== References ==
+==Bibliography==
+*{{Cite book|author-link1 = Scott A. McLuckey | vauthors = McLuckey SA, Busch KL, Glish GL |title=Mass spectrometry/mass spectrometry: techniques and applications of tandem mass spectrometry |publisher=VCH Publishers |location=New York, N.Y |year=1988 |isbn=978-0-89573-275-0}}
+*{{Cite book | author-link1 = Scott A. McLuckey | vauthors = McLuckey SA, Glish GL |title=Mass Spectrometry/Mass Spectrometry: Techniques and Applications of Tandem |publisher=John Wiley & Sons |location=Chichester |isbn=978-0-471-18699-1}}
+*{{Cite book | vauthors = McLafferty FW | author-link = Fred McLafferty |title=Tandem mass spectrometry |publisher=Wiley |location=New York |year=1983 |isbn=978-0-471-86597-1}}
+*{{cite book | vauthors = Sherman NE, Kinter M |title=Protein sequencing and identification using tandem mass spectrometry |publisher=John Wiley |location=New York |year=2000 |isbn=978-0-471-32249-8}}
+== External links ==
+* [http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm An Introduction to Mass Spectrometry by Dr Alison E. Ashcroft] -->
 [[Kategorie:Hmotnostní spektrometrie]]