Tandem mass spectrometry: Difference between revisions
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{{Short description|Type of mass spectrometry}} |
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{{Use dmy dates|date=March 2020}} |
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[[Image:Q-TOF.jpg|300 px|right|thumb|A [[Quadrupole mass analyzer|quadrupole]] [[time-of-flight mass spectrometry|time-of-flight]] hybrid tandem mass spectrometer |
[[Image:Q-TOF.jpg|300 px|right|thumb|A [[Quadrupole mass analyzer|quadrupole]] [[time-of-flight mass spectrometry|time-of-flight]] hybrid tandem mass spectrometer]] |
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'''Tandem mass spectrometry''', also known as '''MS/MS''' or '''MS<sup>2</sup>''', is a technique in [[instrumental analysis]] where two or more [[mass spectrometry|mass |
'''Tandem mass spectrometry''', also known as '''MS/MS''' or '''MS<sup>2</sup>''', is a technique in [[instrumental analysis]] where two or more stages of analysis using one or more [[mass spectrometry|mass analyzer]] are performed with an additional reaction step in between these analyses to increase their abilities to [[Analytical chemistry|analyse]] chemical samples.<ref>{{GoldBookRef|title=tandem mass spectrometer|file=T06250}}</ref> A common use of tandem MS is the analysis of [[biomolecule]]s, such as [[protein]]s and [[peptide]]s. |
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The [[molecule]]s of a given sample are [[Ionization|ionized]] and the first spectrometer (designated '''MS1''') separates these [[ions]] by their [[mass-to-charge ratio]] (often given as '''m/z''' or m/Q). Ions of a particular m/z-ratio coming from MS1 are selected and then made to split into smaller [[Fragmentation (mass spectrometry)|fragment ion]]s, e.g. by [[collision-induced dissociation]], [[Gas-phase ion chemistry|ion-molecule reaction]], or [[photodissociation]]. These fragments are then introduced into the second mass spectrometer ('''MS2'''), which in turn separates the fragments by their m/z-ratio and [[Mass spectrometry#Detectors|detects]] them. The fragmentation step makes it possible to identify and separate ions that have very similar m/z-ratios in regular mass spectrometers. |
The [[molecule]]s of a given sample are [[Ionization|ionized]] and the first spectrometer (designated '''MS1''') separates these [[ions]] by their [[mass-to-charge ratio]] (often given as '''m/z''' or m/Q). Ions of a particular m/z-ratio coming from MS1 are selected and then made to split into smaller [[Fragmentation (mass spectrometry)|fragment ion]]s, e.g. by [[collision-induced dissociation]], [[Gas-phase ion chemistry|ion-molecule reaction]], or [[photodissociation]]. These fragments are then introduced into the second mass spectrometer ('''MS2'''), which in turn separates the fragments by their m/z-ratio and [[Mass spectrometry#Detectors|detects]] them. The fragmentation step makes it possible to identify and separate ions that have very similar m/z-ratios in regular mass spectrometers. |
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== Structure == |
== Structure == |
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Typical tandem mass spectrometry instrumentation setups include triple quadrupole mass spectrometer (QqQ), multi-[[sector mass spectrometer]], ion trap, quadrupole–time of flight (Q-TOF), Fourier transform ion cyclotron resonance (FT-ICR), and hybrid mass spectrometers.<ref>{{Cite journal |last1=Peters-Clarke |first1=Trenton M. |last2=Coon |first2=Joshua J. |last3=Riley |first3=Nicholas M. |date=2024-05-21 |title=Instrumentation at the Leading Edge of Proteomics |url=https://pubs.acs.org/doi/10.1021/acs.analchem.3c04497 |journal=Analytical Chemistry |language=en |volume=96 |issue=20 |pages=7976–8010 |doi=10.1021/acs.analchem.3c04497 |pmid=38738990 |issn=0003-2700}}</ref> |
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Tandem mass spectrometry includes triple quadrupole mass spectrometer (qqq), quad time of flight (Q-tof), and hybrid mass spectrometer |
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=== Triple quadrupole mass spectrometer === |
=== Triple quadrupole mass spectrometer === |
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Triple quadrupole mass spectrometers use the first and third quadrupoles as mass filters. When analytes pass the second quadrupole, the fragmentation proceeds through collision with gas. |
Triple quadrupole mass spectrometers use the first and third quadrupoles as mass filters. When analytes pass the second quadrupole, the fragmentation proceeds through collision with gas.{{cn|date=July 2024}} |
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=== Quadrupole–time of flight (Q-TOF) === |
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Q- |
Q-TOF mass spectrometer combines quadrupole and TOF instruments, which together enable fragmentation experiments that yield highly accurate mass quantitations for product ions. This is a method of mass spectrometry in which fragmented ion (''m''/''z'') ratios are determined through a time of flight measurement.{{cn|date=July 2024}} |
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=== Hybrid mass spectrometer === |
=== Hybrid mass spectrometer === |
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==Instrumentation== |
==Instrumentation== |
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[[Image:MS MS.png|thumb|right|400 px|Schematic of tandem mass spectrometry]] |
[[Image:MS MS.png|thumb|right|400 px|Schematic of tandem mass spectrometry]] |
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Multiple stages of mass analysis separation can be accomplished with individual mass spectrometer elements separated in space or using a single mass spectrometer with the MS steps separated in time. For tandem mass spectrometry in space, the different elements are often noted in a shorthand, giving the type of [[Mass spectrometry#Mass selection|mass selector]] used. |
Multiple stages of mass analysis separation can be accomplished with individual mass spectrometer elements separated in space or using a single mass spectrometer with the MS steps separated in time. For tandem mass spectrometry in space, the different elements are often noted in a shorthand, giving the type of [[Mass spectrometry#Mass selection|mass selector]] used.{{cn|date=July 2024}} |
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=== Tandem in space === |
=== Tandem in space === |
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[[File:Triple quadripole.png|thumb|right|250 px|Triple quadrupole diagram; and example of tandem mass spectrometry in space |
[[File:Triple quadripole.png|thumb|right|250 px|Triple quadrupole diagram; and example of tandem mass spectrometry in space]] |
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In tandem mass spectrometry ''in space'', the separation elements are physically separated and distinct, although there is a physical connection between the elements to maintain [[vacuum|high vacuum]]. These elements can be [[sector mass spectrometer|sectors]], [[Quadrupole mass analyzer|transmission quadrupole]], or |
In tandem mass spectrometry ''in space'', the separation elements are physically separated and distinct, although there is a physical connection between the elements to maintain [[vacuum|high vacuum]]. These elements can be [[sector mass spectrometer|sectors]], [[Quadrupole mass analyzer|transmission quadrupole]], or time-of-flight. When using multiple quadrupoles, they can act as both [[mass analyzer]]s and collision chambers.{{cn|date=July 2024}} |
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Common notation for mass analyzers is ''Q'' – |
Common notation for mass analyzers is ''Q'' – quadrupole mass analyzer; ''q'' – [[radio frequency]] collision quadrupole; ''TOF'' – [[Time-of-flight mass spectrometry|time-of-flight]] mass analyzer; ''B'' – magnetic sector, and ''E'' – electric sector. The notation can be combined to indicate various hybrid instrument, for example ''QqQ''' – [[triple quadrupole mass spectrometer]]; ''QTOF'' – quadrupole time-of-flight mass spectrometer (also ''QqTOF''); and ''BEBE'' – four-sector (reverse geometry) mass spectrometer. |
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===Tandem in time=== |
===Tandem in time=== |
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[[File:LTQ Trap And Dynodes 2.jpg|thumb|right|250 px|An ion trap mass spectrometer is an example of a tandem mass spectrometry in time instrument.]] |
[[File:LTQ Trap And Dynodes 2.jpg|thumb|right|250 px|An ion trap mass spectrometer is an example of a tandem mass spectrometry in time instrument.]] |
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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 |
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. |
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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 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.{{cn|date=July 2024}} |
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===Tandem in space MS/MS modes=== |
===Tandem in space MS/MS modes=== |
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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]]. |
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]].{{cn|date=July 2024}} |
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There are four main scan experiments possible using MS/MS: precursor ion scan, product ion scan, neutral loss scan, and selected reaction monitoring. |
There are four main scan experiments possible using MS/MS: precursor ion scan, product ion scan, neutral loss scan, and selected reaction monitoring. |
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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 |
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>{{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>{{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 | pmid = 24243061 | doi-access = free| bibcode = 1992JASMS...3..473A }}</ref> |
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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 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. |
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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 |
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>{{Cite journal| last1 = Louris | first1 = 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. |
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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| |
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| last1 = deHoffman | first1 = 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> |
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==Fragmentation== |
==Fragmentation== |
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{{Main|Fragmentation (chemistry)}} |
{{Main|Fragmentation (chemistry)}} |
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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. |
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.<ref>{{Cite journal |last=Brodbelt |first=Jennifer S. |date=2016-01-05 |title=Ion Activation Methods for Peptides and Proteins |journal=Analytical Chemistry |language=en |volume=88 |issue=1 |pages=30–51 |doi=10.1021/acs.analchem.5b04563 |issn=0003-2700 |pmc=5553572 |pmid=26630359}}</ref> |
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===In-source fragmentation=== |
===In-source fragmentation=== |
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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 |
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|pmc=8966047 |s2cid=214768212 }}</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 | s2cid = 1030006 | doi-access = | bibcode = 1996JASMS...7..150K }}</ref> |
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===Collision-induced dissociation=== |
===Collision-induced dissociation=== |
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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- |
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 = Biological Mass Spectrometry | chapter = 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 }}</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 |
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:<chem>{AB+} + M -> {A} + {B+} + M</chem> |
:<chem>{AB+} + M -> {A} + {B+} + M</chem> |
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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> |
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 |s2cid=16506573 |doi-access=free }}</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| doi-access = free }}</ref> |
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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 |
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. |
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===Electron capture and transfer methods=== |
===Electron capture and transfer methods=== |
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The energy released when an electron is transferred to or captured by a multiply charged ion can induce fragmentation. |
The energy released when an electron is transferred to or captured by a multiply charged ion can induce fragmentation.<ref>{{Cite journal |last1=Macias |first1=Luis A. |last2=Santos |first2=Inês C. |last3=Brodbelt |first3=Jennifer S. |date=2020-01-07 |title=Ion Activation Methods for Peptides and Proteins |journal=Analytical Chemistry |language=en |volume=92 |issue=1 |pages=227–251 |doi=10.1021/acs.analchem.9b04859 |issn=0003-2700 |pmc=6949381 |pmid=31665881}}</ref> |
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====Electron |
====Electron-capture dissociation==== |
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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 |
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>{{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 |
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:<math chem>[\ce M + n\ce H]^{n+} + \ce{e^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* \ce{-> fragments}</math> |
:<math chem>[\ce M + n\ce H]^{n+} + \ce{e^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* \ce{-> fragments}</math> |
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Line 70: | Line 71: | ||
for a multiply protonated molecule M. |
for a multiply protonated molecule M. |
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====Electron |
====Electron-transfer dissociation==== |
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Adding an electron through an ion-ion reaction is called [[electron |
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| doi-access = free }}</ref><ref>{{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> |
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ETD does not use free electrons but employs radical anions (e.g. [[anthracene]] or [[azobenzene]]) for this purpose: |
ETD does not use free electrons but employs radical anions (e.g. [[anthracene]] or [[azobenzene]]) for this purpose: |
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Line 77: | Line 78: | ||
:<math chem>[\ce M + n\ce H]^{n+} + \ce{A^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* + \ce{A -> fragments}</math> |
:<math chem>[\ce M + n\ce H]^{n+} + \ce{A^- ->} \left[ [\ce M + (n-1)\ce H]^{(n-1)+} \right]^* + \ce{A -> fragments}</math> |
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where A is the anion.<ref |
where A is the anion.<ref>{{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> |
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⚫ | 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 |
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⚫ | 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>{{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| doi-access = free }}</ref> |
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⚫ | 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 |
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⚫ | 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> |
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⚫ | |||
⚫ | Fragmentation can also occur with a deprotonated species, in which an electron is transferred from the species to |
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⚫ | |||
⚫ | Fragmentation can also occur with a deprotonated species, in which an electron is transferred from the species to a cationic reagent in a negative electron transfer dissociation (NETD):<ref>{{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 = | bibcode = 2005JASMS..16..880C }}</ref> |
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:<math chem>[\ce M-n\ce H]^{n-} + \ce{A+ ->} \left[ [\ce M-n\ce H]^{(n+1)-} \right]^* + \ce{A -> fragments}</math> |
:<math chem>[\ce M-n\ce H]^{n-} + \ce{A+ ->} \left[ [\ce M-n\ce H]^{(n+1)-} \right]^* + \ce{A -> fragments}</math> |
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Following this transfer event, the electron |
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). |
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NETD is compatible with fragmenting [[peptide]] and [[ |
NETD is compatible with fragmenting [[peptide]] and [[protein]]s along the backbone at the C<sub>α</sub>-C bond. The resulting fragments are usually a<sup>•</sup>- and x-type product ions. |
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====Electron-detachment dissociation==== |
====Electron-detachment dissociation==== |
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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. |
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.{{cn|date=July 2024}} |
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====Charge |
====Charge-transfer dissociation==== |
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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 |
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: |
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:<math chem>\ce{{[{M}+H]^1+} + He+ ->} \left[ \ce{[{M}+H]^2+} \right]^* + \ce{He^0 -> fragments}</math> |
:<math chem>\ce{{[{M}+H]^1+} + He+ ->} \left[ \ce{[{M}+H]^2+} \right]^* + \ce{He^0 -> fragments}</math> |
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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. |
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. |
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Line 105: | Line 106: | ||
:<chem>{AB+} + \mathit{h\nu} -> {A} + B+</chem> |
:<chem>{AB+} + \mathit{h\nu} -> {A} + B+</chem> |
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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 |
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 = Biological Mass Spectrometry | chapter = 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 }}</ref> |
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====Infrared multiphoton dissociation==== |
====Infrared multiphoton dissociation==== |
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[[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 |
[[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> |
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====Blackbody infrared radiative dissociation==== |
====Blackbody infrared radiative dissociation==== |
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[[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 |
[[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>{{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| doi-access = free }}</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.{{cn|date=July 2024}} |
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===Surface |
===Surface-induced dissociation=== |
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With surface-induced dissociation (SID), the fragmentation is a result of the collision of an ion with a surface under high vacuum.<ref |
With surface-induced dissociation (SID), the fragmentation is a result of the collision of an ion with a surface under high vacuum.<ref>{{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>{{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 CF<sub>3</sub>(CF<sub>2</sub>)<sub>10</sub>CH<sub>2</sub>CH<sub>2</sub>S 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"/> |
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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> |
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> |
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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. |
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|author-link=Julia Laskin|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.{{cn|date=July 2024}} |
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==Quantitative proteomics== |
==Quantitative proteomics== |
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[[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 |
[[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| s2cid = 32054251 }}</ref><ref>{{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>{{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| s2cid = 33009117 }}</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>{{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> |
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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. |
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.{{cn|date=July 2024}} |
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===Isobaric tags for relative and absolute quantitation (iTRAQ)=== |
===Isobaric tags for relative and absolute quantitation (iTRAQ)=== |
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[[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.]] |
[[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.]] |
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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 |
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>{{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 | s2cid = 1979097 | doi-access = free}}</ref><ref>{{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>{{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> |
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It uses stable [[Isotopic labeling|isotope labeled]] molecules that can form a [[covalent bond]] with the |
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.{{cn|date=July 2024}} |
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===Tandem mass tag (TMT)=== |
===Tandem mass tag (TMT)=== |
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A [[tandem mass tag]] (TMT) is an isobaric mass tag chemical label used for protein quantification and identification.<ref |
A [[tandem mass tag]] (TMT) is an isobaric mass tag chemical label used for protein quantification and identification.<ref>{{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. Recent developments allow up to 16 and even 18 samples (16plex or 18plex respectively) to be analyzed.<ref>{{Cite journal |last1=Li |first1=Jiaming |last2=Van Vranken |first2=Jonathan G. |last3=Pontano Vaites |first3=Laura |last4=Schweppe |first4=Devin K. |last5=Huttlin |first5=Edward L. |last6=Etienne |first6=Chris |last7=Nandhikonda |first7=Premchendar |last8=Viner |first8=Rosa |last9=Robitaille |first9=Aaron M. |last10=Thompson |first10=Andrew H. |last11=Kuhn |first11=Karsten |last12=Pike |first12=Ian |last13=Bomgarden |first13=Ryan D. |last14=Rogers |first14=John C. |last15=Gygi |first15=Steven P. |date=April 2020 |title=TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples |journal=Nature Methods |language=en |volume=17 |issue=4 |pages=399–404 |doi=10.1038/s41592-020-0781-4 |issn=1548-7105 |pmc=7302421 |pmid=32203386}}</ref><ref>{{Cite journal |last1=Li |first1=Jiaming |last2=Cai |first2=Zhenying |last3=Bomgarden |first3=Ryan D. |last4=Pike |first4=Ian |last5=Kuhn |first5=Karsten |last6=Rogers |first6=John C. |last7=Roberts |first7=Thomas M. |last8=Gygi |first8=Steven P. |last9=Paulo |first9=Joao A. |date=2021-05-07 |title=TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing |journal=Journal of Proteome Research |language=en |volume=20 |issue=5 |pages=2964–2972 |doi=10.1021/acs.jproteome.1c00168 |issn=1535-3893 |pmc=8210943 |pmid=33900084}}</ref> 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). |
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=== Multiplexed DIA (plexDIA) === |
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The progress in [[Data-independent acquisition|data independent acquisition]] (DIA) enabled multiplexed quantitative proteomics with non-isobaric mass tags and a new method called plexDIA introduced in 2021.<ref>{{cite journal |doi=10.1038/s41587-022-01389-w |biorxiv=10.1101/2021.11.03.467007 |title=Increasing the throughput of sensitive proteomics by plexDIA |date=2023 |last1=Derks |first1=Jason |last2=Leduc |first2=Andrew |last3=Wallmann |first3=Georg |last4=Huffman |first4=R. Gray |last5=Willetts |first5=Matthew |last6=Khan |first6=Saad |last7=Specht |first7=Harrison |last8=Ralser |first8=Markus |last9=Demichev |first9=Vadim |last10=Slavov |first10=Nikolai |journal=Nature Biotechnology |volume=41 |issue=1 |pages=50–59 |pmid=35835881 |pmc=9839897 }}</ref> This new approach increases the number of data points by parallelizing both samples and peptides, thus achieving multiplicative gains. It has the potential to continue scaling proteomic throughput with new mass tags and algorithms.<ref>{{Cite journal |last1=Derks |first1=Jason |last2=Slavov |first2=Nikolai |date=2023-03-03 |title=Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA |journal=Journal of Proteome Research |language=en |volume=22 |issue=3 |pages=697–705 |doi=10.1021/acs.jproteome.2c00721 |issn=1535-3893 |pmc=9992289 |pmid=36735898}}</ref><ref>{{Cite journal |last=Slavov |first=Nikolai |date=January 2022 |title=Scaling Up Single-Cell Proteomics |url=https://doi.org/10.1016/j.mcpro.2021.100179 |journal=Molecular & Cellular Proteomics |volume=21 |issue=1 |pages=100179 |doi=10.1016/j.mcpro.2021.100179 |issn=1535-9476 |pmc=8683604 |pmid=34808355}}</ref> plexDIA is applicable to both bulk<ref>{{Cite journal |last1=Wallmann |first1=Georg |last2=Leduc |first2=Andrew |last3=Slavov |first3=Nikolai |date=2023-10-06 |title=Data-Driven Optimization of DIA Mass Spectrometry by DO-MS |journal=Journal of Proteome Research |language=en |volume=22 |issue=10 |pages=3149–3158 |doi=10.1021/acs.jproteome.3c00177 |issn=1535-3893 |pmc=10591957 |pmid=37695820}}</ref> and single-cell samples and is particularly powerful for single-cell proteomics.<ref>{{Cite journal |last=Slavov |first=Nikolai |date=2021-11-05 |title=Driving Single Cell Proteomics Forward with Innovation |journal=Journal of Proteome Research |language=en |volume=20 |issue=11 |pages=4915–4918 |doi=10.1021/acs.jproteome.1c00639 |issn=1535-3893 |pmc=8571067 |pmid=34597050}}</ref><ref>{{Cite journal |last1=Gatto |first1=Laurent |last2=Aebersold |first2=Ruedi |last3=Cox |first3=Juergen |last4=Demichev |first4=Vadim |last5=Derks |first5=Jason |last6=Emmott |first6=Edward |last7=Franks |first7=Alexander M. |last8=Ivanov |first8=Alexander R. |last9=Kelly |first9=Ryan T. |last10=Khoury |first10=Luke |last11=Leduc |first11=Andrew |last12=MacCoss |first12=Michael J. |last13=Nemes |first13=Peter |last14=Perlman |first14=David H. |last15=Petelski |first15=Aleksandra A. |date=March 2023 |title=Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments |journal=Nature Methods |language=en |volume=20 |issue=3 |pages=375–386 |doi=10.1038/s41592-023-01785-3 |pmid=36864200 |pmc=10130941 |issn=1548-7105}}</ref> |
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===Peptides=== |
===Peptides=== |
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[[Image:PeptideMSMS.jpg|right|thumb|300px|Chromatography trace (top) and tandem mass spectrum (bottom) of a peptide |
[[Image:PeptideMSMS.jpg|right|thumb|300px|Chromatography trace (top) and tandem mass spectrum (bottom) of a peptide]] |
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Tandem mass spectrometry can be used for [[protein sequencing]].<ref |
Tandem mass spectrometry can be used for [[protein sequencing]].<ref>{{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.{{cn|date=July 2024}} |
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Tandem mass spectrometry can produce a [[peptide sequence tag]] that can be used to identify a peptide in a protein database.<ref |
Tandem mass spectrometry can produce a [[peptide sequence tag]] that can be used to identify a peptide in a protein database.<ref>{{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>{{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| s2cid = 38068737 }}</ref><ref>{{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| doi-access = free }}</ref> A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum.<ref>{{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.|author3 = [[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 | s2cid = 38931760 | doi-access = | bibcode = 1993JASMS...4..882F }}</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> |
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===Oligosaccharides=== |
===Oligosaccharides=== |
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[[Oligosaccharide]]s may be sequenced using tandem mass spectrometry in a similar manner to peptide sequencing.<ref |
[[Oligosaccharide]]s may be sequenced using tandem mass spectrometry in a similar manner to peptide sequencing.<ref>{{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|s2cid=206787925 }}</ref><ref>{{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> |
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===Oligonucleotides=== |
===Oligonucleotides=== |
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Tandem mass spectrometry has been applied to [[DNA sequencing|DNA]] and [[RNA sequencing]].<ref |
Tandem mass spectrometry has been applied to [[DNA sequencing|DNA]] and [[RNA sequencing]].<ref>{{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>{{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>{{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> |
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===Newborn screening=== |
===Newborn screening=== |
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{{Main|Newborn screening}} |
{{Main|Newborn screening}} |
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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 |
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>{{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 = }}</ref><ref>{{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| s2cid = 28372085 }}</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>{{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> |
||
'''<big>Small molecule analysis</big>''' |
|||
It has been shown that tandem mass spectrometry data is highly consistent across instrument and manufacturer platforms including quadrupole time-of-flight (QTOF) and Q Exactive instrumentation, especially at 20 eV.<ref>{{Cite journal |last1=Hoang |first1=Corey |last2=Uritboonthai |first2=Winnie |last3=Hoang |first3=Linh |last4=Billings |first4=Elizabeth M. |last5=Aisporna |first5=Aries |last6=Nia |first6=Farshad A. |last7=Derks |first7=Rico J. E. |last8=Williamson |first8=James R. |last9=Giera |first9=Martin |last10=Siuzdak |first10=Gary |date=2024-03-26 |title=Tandem Mass Spectrometry across Platforms |journal=Analytical Chemistry |volume=96 |issue=14 |pages=5478–5488 |language=en |doi=10.1021/acs.analchem.3c05576 |issn=0003-2700|doi-access=free |pmid=38529642 |pmc=11007677 }}</ref> |
|||
== Limitation == |
== Limitation == |
||
Tandem mass spectrometry cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell. |
Tandem mass spectrometry cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell. These 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|last1=Angel|first1=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 == |
== 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| |
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|last1=Han|first1=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 == |
== See also == |
||
*[[Accelerator mass spectrometry]] |
* [[Accelerator mass spectrometry]] |
||
*[[Cross section (physics)]] |
* [[Cross section (physics)]] |
||
*[[Mass-analyzed ion-kinetic-energy spectrometry]] |
* [[Mass-analyzed ion-kinetic-energy spectrometry]] |
||
*[[Unimolecular ion decomposition]] |
* [[Unimolecular ion decomposition]] |
||
== References == |
== References == |
||
Line 168: | Line 175: | ||
==Bibliography== |
==Bibliography== |
||
{{Refbegin}} |
{{Refbegin}} |
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*{{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, 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 | author-link1 = Scott A. McLuckey | vauthors = McLuckey SA, Glish GL |title=Mass Spectrometry/Mass Spectrometry: Techniques and Applications of Tandem | date = 18 January 1989 |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 = 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 |
* {{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}} |
||
{{Refend}} |
{{Refend}} |
||
== External links == |
== External links == |
||
* [http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm An Introduction to Mass Spectrometry by Dr Alison E. Ashcroft] |
* [http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm An Introduction to Mass Spectrometry by Dr Alison E. Ashcroft] {{Webarchive|url=https://web.archive.org/web/20200808031742/http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm |date=8 August 2020 }} |
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{{Mass spectrometry}} |
{{Mass spectrometry}} |
Latest revision as of 00:43, 3 October 2024
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more stages of analysis using one or more mass analyzer are performed with an additional reaction step in between these analyses to increase their abilities to analyse chemical samples.[1] A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides.
The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q). Ions of a particular m/z-ratio coming from MS1 are selected and then made to split into smaller fragment ions, e.g. by collision-induced dissociation, ion-molecule reaction, or photodissociation. These fragments are then introduced into the second mass spectrometer (MS2), which in turn separates the fragments by their m/z-ratio and detects them. The fragmentation step makes it possible to identify and separate ions that have very similar m/z-ratios in regular mass spectrometers.
Structure
[edit]Typical tandem mass spectrometry instrumentation setups include triple quadrupole mass spectrometer (QqQ), multi-sector mass spectrometer, ion trap, quadrupole–time of flight (Q-TOF), Fourier transform ion cyclotron resonance (FT-ICR), and hybrid mass spectrometers.[2]
Triple quadrupole mass spectrometer
[edit]Triple quadrupole mass spectrometers use the first and third quadrupoles as mass filters. When analytes pass the second quadrupole, the fragmentation proceeds through collision with gas.[citation needed]
Quadrupole–time of flight (Q-TOF)
[edit]Q-TOF mass spectrometer combines quadrupole and TOF instruments, which together enable fragmentation experiments that yield highly accurate mass quantitations for product ions. This is a method of mass spectrometry in which fragmented ion (m/z) ratios are determined through a time of flight measurement.[citation needed]
Hybrid mass spectrometer
[edit]Hybrid mass spectrometer consists of more than two mass analyzers.
Instrumentation
[edit]Multiple stages of mass analysis separation can be accomplished with individual mass spectrometer elements separated in space or using a single mass spectrometer with the MS steps separated in time. For tandem mass spectrometry in space, the different elements are often noted in a shorthand, giving the type of mass selector used.[citation needed]
Tandem in space
[edit]In tandem mass spectrometry in space, the separation elements are physically separated and distinct, although there is a physical connection between the elements to maintain high vacuum. These elements can be sectors, transmission quadrupole, or time-of-flight. When using multiple quadrupoles, they can act as both mass analyzers and collision chambers.[citation needed]
Common notation for mass analyzers is Q – quadrupole mass analyzer; q – radio frequency collision quadrupole; TOF – time-of-flight mass analyzer; B – magnetic sector, and E – electric sector. The notation can be combined to indicate various hybrid instrument, for example QqQ' – triple quadrupole mass spectrometer; QTOF – quadrupole time-of-flight mass spectrometer (also QqTOF); and BEBE – four-sector (reverse geometry) mass spectrometer.
Tandem in time
[edit]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.[3] Trapping instruments can perform multiple steps of analysis, which is sometimes referred to as MSn (MS to the n).[4] Often the number of steps, n, is not indicated, but occasionally the value is specified; for example MS3 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.[citation needed]
Tandem in space MS/MS modes
[edit]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.[citation needed]
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[5] is synonymous with parent ion[6] and product ion[7] with daughter ion;[8] however the use of these anthropomorphic terms is discouraged.[9][10]
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.[11] 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.[12]
Fragmentation
[edit]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.[13]
In-source fragmentation
[edit]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.[14] Nozzle-skimmer fragmentation refers to the purposeful induction of in-source fragmentation by increasing the nozzle-skimmer potential on usually 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.[15] Fragments observed by EISA have higher signal intensity than traditional fragments which suffer losses in the collision cells of tandem mass spectrometers.[16] 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 MS3-type of experiment.[17]
Collision-induced dissociation
[edit]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.[18][19] For example, consider
where the ion AB+ 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)[20] and (ii) ion trap-type (in which precursor ions are first trapped, and then fragmented).[21][22]
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,[23][24] it happens in the HCD cell (in some instruments named "ion routing multipole").[25] HCD is a trap-type fragmentation that has been shown to have beam-type characteristics.[26][27] 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),[28] and are typically used to facilitate small molecule identification.
Electron capture and transfer methods
[edit]The energy released when an electron is transferred to or captured by a multiply charged ion can induce fragmentation.[29]
Electron-capture dissociation
[edit]If an electron is added to a multiply charged positive ion, the Coulomb energy is liberated. Adding a free electron is called electron-capture dissociation (ECD),[30] and is represented by
for a multiply protonated molecule M.
Electron-transfer dissociation
[edit]Adding an electron through an ion-ion reaction is called electron-transfer dissociation (ETD).[31][32] Similar to electron-capture dissociation, ETD induces fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them. It was invented by Donald F. Hunt, Joshua Coon, John E. P. Syka and Jarrod Marto at the University of Virginia.[33]
ETD does not use free electrons but employs radical anions (e.g. anthracene or azobenzene) for this purpose:
where A is the anion.[34]
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 modifications such as phosphorylation.[35]
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.[31][36] 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.[23] This method employs dual fragmentation to generate ion- and thus data-rich MS/MS spectra for peptide sequencing and PTM localization.[37]
Negative electron-transfer dissociation
[edit]Fragmentation can also occur with a deprotonated species, in which an electron is transferred from the species to a cationic reagent in a negative electron transfer dissociation (NETD):[38]
Following this transfer event, the electron-deficient anion undergoes internal rearrangement and fragments. NETD is the ion/ion analogue of electron-detachment dissociation (EDD).
NETD is compatible with fragmenting peptide and proteins along the backbone at the Cα-C bond. The resulting fragments are usually a•- and x-type product ions.
Electron-detachment dissociation
[edit]Electron-detachment dissociation (EDD) is a method for fragmenting anionic species in mass spectrometry.[39] 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 molecule, which causes dissociation via recombination.[citation needed]
Charge-transfer dissociation
[edit]Reaction between positively charged peptides and cationic reagents,[40] also known as charge transfer dissociation (CTD),[41] 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:
Initial reports are that CTD causes backbone Cα-C bond cleavage of peptides and provides a•- and x-type product ions.
Photodissociation
[edit]The energy required for dissociation can be added by photon absorption, resulting in ion photodissociation and represented by
where represents the photon absorbed by the ion. Ultraviolet lasers can be used, but can lead to excessive fragmentation of biomolecules.[42]
Infrared multiphoton dissociation
[edit]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 FTMS.[43]
Blackbody infrared radiative dissociation
[edit]Blackbody radiation can be used for photodissociation in a technique known as blackbody infrared radiative dissociation (BIRD).[44] 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 vibrations of the ions, until a bond breaks, creating fragments.[44][45] This is similar to infrared multiphoton dissociation which also uses infrared light, but from a different source.[19] BIRD is most often used with Fourier transform ion cyclotron resonance mass spectrometry.[citation needed]
Surface-induced dissociation
[edit]With surface-induced dissociation (SID), the fragmentation is a result of the collision of an ion with a surface under high vacuum.[46][47] 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.[48] 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.[48]
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.[49]
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[50] such as collision-induced dissociation (CID, electron transfer dissociation (ETD),[51] 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.[52] 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.[citation needed]
Quantitative proteomics
[edit]Quantitative proteomics is used to determine the relative or absolute amount of proteins in a sample.[53][54][55] Several quantitative proteomics methods are based on tandem mass spectrometry. MS/MS has become a benchmark procedure for the structural elucidation of complex biomolecules.[56]
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.[citation needed]
Isobaric tags for relative and absolute quantitation (iTRAQ)
[edit]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.[57][58][59] It uses stable isotope labeled molecules that can form a covalent bond with the N-terminus and side chain amines 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.[citation needed]
Tandem mass tag (TMT)
[edit]A tandem mass tag (TMT) is an isobaric mass tag chemical label used for protein quantification and identification.[60] 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. Recent developments allow up to 16 and even 18 samples (16plex or 18plex respectively) to be analyzed.[61][62] 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).
Multiplexed DIA (plexDIA)
[edit]The progress in data independent acquisition (DIA) enabled multiplexed quantitative proteomics with non-isobaric mass tags and a new method called plexDIA introduced in 2021.[63] This new approach increases the number of data points by parallelizing both samples and peptides, thus achieving multiplicative gains. It has the potential to continue scaling proteomic throughput with new mass tags and algorithms.[64][65] plexDIA is applicable to both bulk[66] and single-cell samples and is particularly powerful for single-cell proteomics.[67][68]
Applications
[edit]Peptides
[edit]Tandem mass spectrometry can be used for protein sequencing.[69] 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.[citation needed]
Tandem mass spectrometry can produce a peptide sequence tag that can be used to identify a peptide in a protein database.[70][71][72] A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum.[73] 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[74][75] and additional sequence-specific fragment ions associated with particular amino acid residues.[76]
Oligosaccharides
[edit]Oligosaccharides may be sequenced using tandem mass spectrometry in a similar manner to peptide sequencing.[77] 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.[78][79]
Oligonucleotides
[edit]Tandem mass spectrometry has been applied to DNA and RNA sequencing.[80][81] A notation for gas-phase fragmentation of oligonucleotide ions has been proposed.[82]
Newborn screening
[edit]Newborn screening is the process of testing newborn babies for treatable genetic, endocrinologic, metabolic and hematologic diseases.[83][84] The development of tandem mass spectrometry screening in the early 1990s led to a large expansion of potentially detectable congenital metabolic diseases that affect blood levels of organic acids.[85]
Small molecule analysis
It has been shown that tandem mass spectrometry data is highly consistent across instrument and manufacturer platforms including quadrupole time-of-flight (QTOF) and Q Exactive instrumentation, especially at 20 eV.[86]
Limitation
[edit]Tandem mass spectrometry cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell. These limitations are primarily due to a combination of inefficient ion production and ion losses within the instruments due to chemical noise sources of solvents.[87]
Future outlook
[edit]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.[88]
See also
[edit]- Accelerator mass spectrometry
- Cross section (physics)
- Mass-analyzed ion-kinetic-energy spectrometry
- Unimolecular ion decomposition
References
[edit]- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "tandem mass spectrometer". doi:10.1351/goldbook.T06250
- ^ Peters-Clarke, Trenton M.; Coon, Joshua J.; Riley, Nicholas M. (21 May 2024). "Instrumentation at the Leading Edge of Proteomics". Analytical Chemistry. 96 (20): 7976–8010. doi:10.1021/acs.analchem.3c04497. ISSN 0003-2700. PMID 38738990.
- ^ Cody RB, Freiser BS (1982). "Collision-induced dissociation in a fourier-transform mass spectrometer". International Journal of Mass Spectrometry and Ion Physics. 41 (3): 199–204. Bibcode:1982IJMSI..41..199C. doi:10.1016/0020-7381(82)85035-3.
- ^ Cody RB, Burnier RC, Cassady CJ, Freiser BS (1 November 1982). "Consecutive collision-induced dissociations in Fourier transform mass spectrometry". Analytical Chemistry. 54 (13): 2225–2228. doi:10.1021/ac00250a021.
- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "precursor ion". doi:10.1351/goldbook.P04807
- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "parent ion". doi:10.1351/goldbook.P04406
- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "product ion". doi:10.1351/goldbook.P04864
- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "daughter ion". doi:10.1351/goldbook.D01524
- ^ Bursey, Maurice M. (1991). "Comment to readers: Style and the lack of it". Mass Spectrometry Reviews. 10 (1): 1–2. Bibcode:1991MSRv...10....1B. doi:10.1002/mas.1280100102.
- ^ Adams, J. (1992). "To the editor". Journal of the American Society for Mass Spectrometry. 3 (4): 473. Bibcode:1992JASMS...3..473A. doi:10.1016/1044-0305(92)87078-D. PMID 24243061.
- ^ Louris JN, Wright LG, Cooks RG, Schoen AE (1985). "New scan modes accessed with a hybrid mass spectrometer". Analytical Chemistry. 57 (14): 2918–2924. doi:10.1021/ac00291a039.
- ^ deHoffman E, Stroobant V (2003). Mass Spectrometry: Principles and Applications. Toronto: Wiley. p. 133. ISBN 978-0-471-48566-7.
- ^ Brodbelt, Jennifer S. (5 January 2016). "Ion Activation Methods for Peptides and Proteins". Analytical Chemistry. 88 (1): 30–51. doi:10.1021/acs.analchem.5b04563. ISSN 0003-2700. PMC 5553572. PMID 26630359.
- ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "transient (chemical) species". doi:10.1351/goldbook.T06451
- ^ Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Guijas, Carlos; Majumder, Erica L.-W.; Benton, H. Paul; Siuzdak, Gary (5 March 2019). "Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics". Analytical Chemistry. 91 (5): 3246–3253. doi:10.1021/acs.analchem.8b03126. PMC 6637741. PMID 30681830.
- ^ Xue, Jingchuan; Domingo-Almenara, Xavier; Guijas, Carlos; Palermo, Amelia; Rinschen, Markus M.; Isbell, John; Benton, H. Paul; Siuzdak, Gary (21 April 2020). "Enhanced in-Source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification". Analytical Chemistry. 92 (8): 6051–6059. doi:10.1021/acs.analchem.0c00409. PMC 8966047. PMID 32242660. S2CID 214768212.
- ^ Körner R, Wilm M, Morand K, Schubert M, Mann M (February 1996). "Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests". Journal of the American Society for Mass Spectrometry. 7 (2): 150–6. Bibcode:1996JASMS...7..150K. doi:10.1016/1044-0305(95)00626-5. PMID 24203235. S2CID 1030006.
- ^ Wells JM, McLuckey SA (2005). "Collision-Induced Dissociation (CID) of Peptides and Proteins". Biological Mass Spectrometry. Methods in Enzymology. Vol. 402. pp. 148–85. doi:10.1016/S0076-6879(05)02005-7. ISBN 9780121828073. PMID 16401509.
- ^ a b Sleno L, Volmer DA (October 2004). "Ion activation methods for tandem mass spectrometry". Journal of Mass Spectrometry. 39 (10): 1091–112. Bibcode:2004JMSp...39.1091S. doi:10.1002/jms.703. PMID 15481084.
- ^ Xia Y, Liang X, McLuckey SA (February 2006). "Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions". Analytical Chemistry. 78 (4): 1218–27. doi:10.1021/ac051622b. PMID 16478115.
- ^ March RE (1 April 1997). "An Introduction to Quadrupole Ion Trap Mass Spectrometry". Journal of Mass Spectrometry. 32 (4): 351–369. Bibcode:1997JMSp...32..351M. doi:10.1002/(sici)1096-9888(199704)32:4<351::aid-jms512>3.0.co;2-y. S2CID 16506573.
- ^ Bantscheff M, Boesche M, Eberhard D, Matthieson T, Sweetman G, Kuster B (September 2008). "Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer". Molecular & Cellular Proteomics. 7 (9): 1702–13. doi:10.1074/mcp.M800029-MCP200. PMC 2556025. PMID 18511480.
- ^ a b Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (September 2007). "Higher-energy C-trap dissociation for peptide modification analysis". Nature Methods. 4 (9): 709–12. doi:10.1038/nmeth1060. PMID 17721543. S2CID 2538231.
- ^ 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 (December 2013). "Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates". Analytical Chemistry. 85 (24): 11710–4. doi:10.1021/ac403115c. PMID 24251866.
- ^ Riley NM, Westphall MS, Coon JJ (July 2017). "Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation". Journal of Proteome Research. 16 (7): 2653–2659. doi:10.1021/acs.jproteome.7b00249. PMC 5555583. PMID 28608681.
- ^ Nagaraj N, D'Souza RC, Cox J, Olsen JV, Mann M (December 2010). "Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation". Journal of Proteome Research. 9 (12): 6786–94. doi:10.1021/pr100637q. PMID 20873877.
- ^ Jora M, Burns AP, Ross RL, Lobue PA, Zhao R, Palumbo CM, Beal PA, Addepalli B, Limbach PA (August 2018). "Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS)". Journal of the American Society for Mass Spectrometry. 29 (8): 1745–1756. Bibcode:2018JASMS..29.1745J. doi:10.1007/s13361-018-1999-6. PMC 6062210. PMID 29949056.
- ^ "Article Metrics - METLIN MS 2 molecular standards database: a broad chemical and biological resource | Nature Methods". ISSN 1548-7105.
{{cite journal}}
: Cite journal requires|journal=
(help) - ^ Macias, Luis A.; Santos, Inês C.; Brodbelt, Jennifer S. (7 January 2020). "Ion Activation Methods for Peptides and Proteins". Analytical Chemistry. 92 (1): 227–251. doi:10.1021/acs.analchem.9b04859. ISSN 0003-2700. PMC 6949381. PMID 31665881.
- ^ Cooper HJ, Håkansson K, Marshall AG (2005). "The role of electron capture dissociation in biomolecular analysis". Mass Spectrometry Reviews. 24 (2): 201–22. Bibcode:2005MSRv...24..201C. doi:10.1002/mas.20014. PMID 15389856.
- ^ a b Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (June 2004). "Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry". Proceedings of the National Academy of Sciences of the United States of America. 101 (26): 9528–33. Bibcode:2004PNAS..101.9528S. doi:10.1073/pnas.0402700101. PMC 470779. PMID 15210983.
- ^ Mikesh LM, Ueberheide B, Chi A, Coon JJ, Syka JE, Shabanowitz J, Hunt DF (December 2006). "The utility of ETD mass spectrometry in proteomic analysis". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1764 (12): 1811–22. doi:10.1016/j.bbapap.2006.10.003. PMC 1853258. PMID 17118725.
- ^ US patent 7534622, Donald F. Hunt, Joshua J. Coon, John E.P. Syka, Jarrod A. Marto, "Electron transfer dissociation for biopolymer sequence mass spectrometric analysis", issued 2009-05-19
- ^ McLuckey SA, Stephenson JL (1998). "Ion/ion chemistry of high-mass multiply charged ions". Mass Spectrometry Reviews. 17 (6): 369–407. Bibcode:1998MSRv...17..369M. doi:10.1002/(SICI)1098-2787(1998)17:6<369::AID-MAS1>3.0.CO;2-J. PMID 10360331.
- ^ Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF (February 2007). "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry". Proceedings of the National Academy of Sciences of the United States of America. 104 (7): 2193–8. Bibcode:2007PNAS..104.2193C. doi:10.1073/pnas.0607084104. PMC 1892997. PMID 17287358.
- ^ Frese CK, Altelaar AF, van den Toorn H, Nolting D, Griep-Raming J, Heck AJ, Mohammed S (November 2012). "Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry". Analytical Chemistry. 84 (22): 9668–73. doi:10.1021/ac3025366. PMID 23106539.
- ^ Frese CK, Zhou H, Taus T, Altelaar AF, Mechtler K, Heck AJ, Mohammed S (March 2013). "Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD)". Journal of Proteome Research. 12 (3): 1520–5. doi:10.1021/pr301130k. PMC 3588588. PMID 23347405.
- ^ Coon JJ, Shabanowitz J, Hunt DF, Syka JE (June 2005). "Electron transfer dissociation of peptide anions". Journal of the American Society for Mass Spectrometry. 16 (6): 880–2. Bibcode:2005JASMS..16..880C. doi:10.1016/j.jasms.2005.01.015. PMID 15907703.
- ^ Budnik BA, Haselmann KF, Zubarev RA (2001). "Electron detachment dissociation of peptide di-anions: an electron–hole recombination phenomenon". Chemical Physics Letters. 342 (3–4): 299–302. Bibcode:2001CPL...342..299B. doi:10.1016/S0009-2614(01)00501-2.
- ^ Chingin K, Makarov A, Denisov E, Rebrov O, Zubarev RA (January 2014). "Fragmentation of positively-charged biological ions activated with a beam of high-energy cations". Analytical Chemistry. 86 (1): 372–9. doi:10.1021/ac403193k. PMID 24236851.
- ^ Hoffmann WD, Jackson GP (November 2014). "Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations". Journal of the American Society for Mass Spectrometry. 25 (11): 1939–43. Bibcode:2014JASMS..25.1939H. doi:10.1007/s13361-014-0989-6. PMID 25231159. S2CID 1400057.
- ^ Morgan JW, Hettick JM, Russell DH (2005). "Peptide Sequencing by MALDI 193-nm Photodissociation TOF MS". Biological Mass Spectrometry. Methods in Enzymology. Vol. 402. pp. 186–209. doi:10.1016/S0076-6879(05)02006-9. ISBN 9780121828073. PMID 16401510.
- ^ Little DP, Speir JP, Senko MW, O'Connor PB, McLafferty FW (September 1994). "Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing". Analytical Chemistry. 66 (18): 2809–15. doi:10.1021/ac00090a004. PMID 7526742.
- ^ a b Schnier PD, Price WD, Jockusch RA, Williams ER (July 1996). "Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase". Journal of the American Chemical Society. 118 (30): 7178–89. doi:10.1021/ja9609157. PMC 1393282. PMID 16525512.
- ^ Dunbar RC (2004). "BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications". Mass Spectrometry Reviews. 23 (2): 127–58. Bibcode:2004MSRv...23..127D. doi:10.1002/mas.10074. PMID 14732935.
- ^ Grill V, Shen J, Evans C, Cooks RG (2001). "Collisions of ions with surfaces at chemically relevant energies: Instrumentation and phenomena". Review of Scientific Instruments. 72 (8): 3149. Bibcode:2001RScI...72.3149G. doi:10.1063/1.1382641.
- ^ Mabud, M. (1985). "Surface-induced dissociation of molecular ions". International Journal of Mass Spectrometry and Ion Processes. 67 (3): 285–294. Bibcode:1985IJMSI..67..285M. doi:10.1016/0168-1176(85)83024-X.
- ^ a b Stiving, Alyssa; VanAernum, Zachary; Busch, Florian; Harvey, Sophie; Sarni, Samantha; Wysocki, Vicki (9 November 2018). "Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure". Analytical Chemistry. 91 (1): 190–191. doi:10.1021/acs.analchem.8b05071. PMC 6571034. PMID 30412666.
- ^ Quintyn, Royston S.; Zhou, Mowei; Yan, Jing; Wysocki, Vicki H. (1 December 2015). "Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes". Analytical Chemistry. 87 (23): 11879–11886. doi:10.1021/acs.analchem.5b03441. ISSN 0003-2700. PMID 26499904.
- ^ Laskin, Julia; Futrell, Jean H. (2005). "Activation of large lons in FT-ICR mass spectrometry". Mass Spectrometry Reviews. 24 (2): 135–167. Bibcode:2005MSRv...24..135L. doi:10.1002/mas.20012. ISSN 0277-7037. PMID 15389858.
- ^ Kaplan, Desmond A.; Hartmer, Ralf; Speir, J. Paul; Stoermer, Carsten; Gumerov, Dmitry; Easterling, Michael L.; Brekenfeld, Andreas; Kim, Taeman; Laukien, Frank; Park, Melvin A. (2008). "Electron transfer dissociation in the hexapole collision cell of a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer". Rapid Communications in Mass Spectrometry. 22 (3): 271–278. Bibcode:2008RCMS...22..271K. doi:10.1002/rcm.3356. ISSN 0951-4198. PMID 18181247.
- ^ Laskin, Julia (June 2015). "Surface-Induced Dissociation: A Unique Tool for Studying Energetics and Kinetics of the Gas-Phase Fragmentation of Large Ions". European Journal of Mass Spectrometry. 21 (3): 377–389. doi:10.1255/ejms.1358. ISSN 1469-0667. PMID 26307719. S2CID 19837927.
- ^ Ong SE, Mann M (October 2005). "Mass spectrometry-based proteomics turns quantitative". Nature Chemical Biology. 1 (5): 252–62. doi:10.1038/nchembio736. PMID 16408053. S2CID 32054251.
- ^ Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (October 2007). "Quantitative mass spectrometry in proteomics: a critical review". Analytical and Bioanalytical Chemistry. 389 (4): 1017–31. doi:10.1007/s00216-007-1486-6. PMID 17668192.
- ^ Nikolov M, Schmidt C, Urlaub H (2012). "Quantitative Mass Spectrometry-Based Proteomics: An Overview". Quantitative Methods in Proteomics. Methods in Molecular Biology. Vol. 893. pp. 85–100. doi:10.1007/978-1-61779-885-6_7. hdl:11858/00-001M-0000-0029-1A75-8. ISBN 978-1-61779-884-9. PMID 22665296. S2CID 33009117.
- ^ Maher S, Jjunju FP, Taylor S (2015). "100 years of mass spectrometry: Perspectives and future trends". Rev. Mod. Phys. 87 (1): 113–135. Bibcode:2015RvMP...87..113M. doi:10.1103/RevModPhys.87.113.
- ^ 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 (December 2004). "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents". Molecular & Cellular Proteomics. 3 (12): 1154–69. doi:10.1074/mcp.M400129-MCP200. PMID 15385600. S2CID 1979097.
- ^ Zieske LR (2006). "A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies". Journal of Experimental Botany. 57 (7): 1501–8. doi:10.1093/jxb/erj168. PMID 16574745.
- ^ Gafken PR, Lampe PD (2006). "Methodologies for characterizing phosphoproteins by mass spectrometry". Cell Communication & Adhesion. 13 (5–6): 249–62. doi:10.1080/15419060601077917. PMC 2185548. PMID 17162667.
- ^ Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (April 2003). "Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS". Analytical Chemistry. 75 (8): 1895–904. doi:10.1021/ac0262560. PMID 12713048.
- ^ Li, Jiaming; Van Vranken, Jonathan G.; Pontano Vaites, Laura; Schweppe, Devin K.; Huttlin, Edward L.; Etienne, Chris; Nandhikonda, Premchendar; Viner, Rosa; Robitaille, Aaron M.; Thompson, Andrew H.; Kuhn, Karsten; Pike, Ian; Bomgarden, Ryan D.; Rogers, John C.; Gygi, Steven P. (April 2020). "TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples". Nature Methods. 17 (4): 399–404. doi:10.1038/s41592-020-0781-4. ISSN 1548-7105. PMC 7302421. PMID 32203386.
- ^ Li, Jiaming; Cai, Zhenying; Bomgarden, Ryan D.; Pike, Ian; Kuhn, Karsten; Rogers, John C.; Roberts, Thomas M.; Gygi, Steven P.; Paulo, Joao A. (7 May 2021). "TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing". Journal of Proteome Research. 20 (5): 2964–2972. doi:10.1021/acs.jproteome.1c00168. ISSN 1535-3893. PMC 8210943. PMID 33900084.
- ^ Derks, Jason; Leduc, Andrew; Wallmann, Georg; Huffman, R. Gray; Willetts, Matthew; Khan, Saad; Specht, Harrison; Ralser, Markus; Demichev, Vadim; Slavov, Nikolai (2023). "Increasing the throughput of sensitive proteomics by plexDIA". Nature Biotechnology. 41 (1): 50–59. bioRxiv 10.1101/2021.11.03.467007. doi:10.1038/s41587-022-01389-w. PMC 9839897. PMID 35835881.
- ^ Derks, Jason; Slavov, Nikolai (3 March 2023). "Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA". Journal of Proteome Research. 22 (3): 697–705. doi:10.1021/acs.jproteome.2c00721. ISSN 1535-3893. PMC 9992289. PMID 36735898.
- ^ Slavov, Nikolai (January 2022). "Scaling Up Single-Cell Proteomics". Molecular & Cellular Proteomics. 21 (1): 100179. doi:10.1016/j.mcpro.2021.100179. ISSN 1535-9476. PMC 8683604. PMID 34808355.
- ^ Wallmann, Georg; Leduc, Andrew; Slavov, Nikolai (6 October 2023). "Data-Driven Optimization of DIA Mass Spectrometry by DO-MS". Journal of Proteome Research. 22 (10): 3149–3158. doi:10.1021/acs.jproteome.3c00177. ISSN 1535-3893. PMC 10591957. PMID 37695820.
- ^ Slavov, Nikolai (5 November 2021). "Driving Single Cell Proteomics Forward with Innovation". Journal of Proteome Research. 20 (11): 4915–4918. doi:10.1021/acs.jproteome.1c00639. ISSN 1535-3893. PMC 8571067. PMID 34597050.
- ^ Gatto, Laurent; Aebersold, Ruedi; Cox, Juergen; Demichev, Vadim; Derks, Jason; Emmott, Edward; Franks, Alexander M.; Ivanov, Alexander R.; Kelly, Ryan T.; Khoury, Luke; Leduc, Andrew; MacCoss, Michael J.; Nemes, Peter; Perlman, David H.; Petelski, Aleksandra A. (March 2023). "Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments". Nature Methods. 20 (3): 375–386. doi:10.1038/s41592-023-01785-3. ISSN 1548-7105. PMC 10130941. PMID 36864200.
- ^ Angel TE, Aryal UK, Hengel SM, Baker ES, Kelly RT, Robinson EW, Smith RD (May 2012). "Mass spectrometry-based proteomics: existing capabilities and future directions". Chemical Society Reviews. 41 (10): 3912–28. doi:10.1039/c2cs15331a. PMC 3375054. PMID 22498958.
- ^ Hardouin J (2007). "Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry". Mass Spectrometry Reviews. 26 (5): 672–82. Bibcode:2007MSRv...26..672H. doi:10.1002/mas.20142. PMID 17492750.
- ^ Shadforth I, Crowther D, Bessant C (November 2005). "Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines". Proteomics. 5 (16): 4082–95. doi:10.1002/pmic.200402091. PMID 16196103. S2CID 38068737.
- ^ Mørtz E, O'Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M (August 1996). "Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases". Proceedings of the National Academy of Sciences of the United States of America. 93 (16): 8264–7. Bibcode:1996PNAS...93.8264M. doi:10.1073/pnas.93.16.8264. PMC 38658. PMID 8710858.
- ^ Roepstorff P, Fohlman J (November 1984). "Proposal for a common nomenclature for sequence ions in mass spectra of peptides". Biomedical Mass Spectrometry. 11 (11): 601. doi:10.1002/bms.1200111109. PMID 6525415.
- ^ Johnson RS, Martin SA, Klaus Biemann (December 1988). "Collision-induced fragmentation of (M + H)+ ions of peptides. Side chain specific sequence ions". International Journal of Mass Spectrometry and Ion Processes. 86: 137–154. Bibcode:1988IJMSI..86..137J. doi:10.1016/0168-1176(88)80060-0.
- ^ Falick AM, Hines WM, Medzihradszky KF, Baldwin MA, Gibson BW (November 1993). "Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry". Journal of the American Society for Mass Spectrometry. 4 (11): 882–93. Bibcode:1993JASMS...4..882F. doi:10.1016/1044-0305(93)87006-X. PMID 24227532. S2CID 38931760.
- ^ Downard KM, Biemann K (January 1995). "Methionine specific sequence ions formed by the dissociation of protonated peptides at high collision energies". Journal of Mass Spectrometry. 30 (1): 25–32. Bibcode:1995JMSp...30...25D. doi:10.1002/jms.1190300106.
- ^ Zaia J (2004). "Mass spectrometry of oligosaccharides". Mass Spectrometry Reviews. 23 (3): 161–227. Bibcode:2004MSRv...23..161Z. doi:10.1002/mas.10073. PMID 14966796.
- ^ Bruno Domon; Catherine E Costello (1988). "A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates". Glycoconj. J. 5 (4): 397–409. doi:10.1007/BF01049915. S2CID 206787925.
- ^ Spina E, Cozzolino R, Ryan E, Garozzo D (August 2000). "Sequencing of oligosaccharides by collision-induced dissociation matrix-assisted laser desorption/ionization mass spectrometry". Journal of Mass Spectrometry. 35 (8): 1042–8. Bibcode:2000JMSp...35.1042S. doi:10.1002/1096-9888(200008)35:8<1042::AID-JMS33>3.0.CO;2-Y. PMID 10973004.
- ^ Banoub JH, Newton RP, Esmans E, Ewing DF, Mackenzie G (May 2005). "Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids". Chemical Reviews. 105 (5): 1869–915. doi:10.1021/cr030040w. PMID 15884792.
- ^ Thomas B, Akoulitchev AV (March 2006). "Mass spectrometry of RNA". Trends in Biochemical Sciences. 31 (3): 173–81. doi:10.1016/j.tibs.2006.01.004. PMID 16483781.
- ^ Wu J, McLuckey SA (2004). "Gas-phase fragmentation of oligonucleotide ions". International Journal of Mass Spectrometry. 237 (2–3): 197–241. Bibcode:2004IJMSp.237..197W. doi:10.1016/j.ijms.2004.06.014.
- ^ Tarini BA (August 2007). "The current revolution in newborn screening: new technology, old controversies". Archives of Pediatrics & Adolescent Medicine. 161 (8): 767–72. doi:10.1001/archpedi.161.8.767. PMID 17679658.
- ^ Kayton A (2007). "Newborn screening: a literature review". Neonatal Network. 26 (2): 85–95. doi:10.1891/0730-0832.26.2.85. PMID 17402600. S2CID 28372085.
- ^ Chace DH, Kalas TA, Naylor EW (November 2003). "Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns". Clinical Chemistry. 49 (11): 1797–817. doi:10.1373/clinchem.2003.022178. PMID 14578311.
- ^ Hoang, Corey; Uritboonthai, Winnie; Hoang, Linh; Billings, Elizabeth M.; Aisporna, Aries; Nia, Farshad A.; Derks, Rico J. E.; Williamson, James R.; Giera, Martin; Siuzdak, Gary (26 March 2024). "Tandem Mass Spectrometry across Platforms". Analytical Chemistry. 96 (14): 5478–5488. doi:10.1021/acs.analchem.3c05576. ISSN 0003-2700. PMC 11007677. PMID 38529642.
- ^ Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin S.; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D. (21 May 2012). "Mass spectrometry based proteomics: existing capabilities and future directions". Chemical Society Reviews. 41 (10): 3912–3928. doi:10.1039/c2cs15331a. ISSN 0306-0012. PMC 3375054. PMID 22498958.
- ^ Han, Xuemei; Aslanian, Aaron; Yates, John R. (October 2008). "Mass Spectrometry for Proteomics". Current Opinion in Chemical Biology. 12 (5): 483–490. doi:10.1016/j.cbpa.2008.07.024. ISSN 1367-5931. PMC 2642903. PMID 18718552.
Bibliography
[edit]- McLuckey SA, Busch KL, Glish GL (1988). Mass spectrometry/mass spectrometry: techniques and applications of tandem mass spectrometry. New York, N.Y: VCH Publishers. ISBN 978-0-89573-275-0.
- McLuckey SA, Glish GL (18 January 1989). Mass Spectrometry/Mass Spectrometry: Techniques and Applications of Tandem. Chichester: John Wiley & Sons. ISBN 978-0-471-18699-1.
- McLafferty FW (1983). Tandem mass spectrometry. New York: Wiley. ISBN 978-0-471-86597-1.
- Sherman NE, Kinter M (2000). Protein sequencing and identification using tandem mass spectrometry. New York: John Wiley. ISBN 978-0-471-32249-8.
External links
[edit]- An Introduction to Mass Spectrometry by Dr Alison E. Ashcroft Archived 8 August 2020 at the Wayback Machine