Tandem mass spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. 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.
Tandem mass spectrometry includes triple quadrupole mass spectrometer (qqq), quad time of flight (Q-tof), and hybrid mass spectrometer
Triple quadrupole mass spectrometer (QQQ)
Tandem mass spectrometry that the first and third quadrupole work as a mass filter. When analytes pass the second quadrupole, the fragmentation proceeds through collision with gas. Usually used for the pharmaceutical industry.
Quadrupole time of flight (Q-tof)
Q-tof mass spectrometer combines TOF and quadrupole instruments, which cause high mass accuracy for product ions, accurate quantitation capability, and fragmentation experiment applicability. This is a method of mass spectrometry that ion fragmentation (m/z) ratio determined through a time of flight measurement.
hybrid mass spectrometer
hybrid mass spectrometer consists of more than two mass analyzers.
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.
Tandem in space
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.
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
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. Trapping instruments can perform multiple steps of analysis, which is sometimes referred to as MSn (MS to the n). 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.
Tandem in space MS/MS modes
When tandem MS is performed with an in space design, the instrument must operate in one of a variety of modes. There are a number of different tandem MS/MS experimental setups and each mode has its own applications and provides different information. Tandem MS in space uses the coupling of two instrument components which measure the same mass spectrum range but with a controlled fractionation between them in space, while tandem MS in time involves the use of an ion trap.
There are four main scan experiments possible using MS/MS: precursor ion scan, product ion scan, neutral loss scan, and selected reaction monitoring.
For a precursor ion scan, the product ion is selected in the second mass analyzer, and the precursor masses are scanned in the first mass analyzer. Note that precursor ion is synonymous with parent ion and product ion with daughter ion; however the use of these anthropomorphic terms is discouraged.
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. 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.
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.
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. 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 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.
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. 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) and (ii) ion trap-type (in which precursor ions are first trapped, and then fragmented).
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, it happens in the HCD cell (in some instruments named "ion routing multipole"). HCD is a trap-type fragmentation that has been shown to have beam-type characteristics.
Electron capture and transfer methods
The energy released when an electron is transferred to or captured by a multiply charged ion can induce fragmentation.
Electron capture dissociation
for a multiply protonated molecule M.
Electron transfer dissociation
Adding an electron through an ion-ion reaction is called electron transfer dissociation (ETD). 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.
where A is the anion.
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.
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. 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. This method employs dual fragmentation to generate ion- and thus data-rich MS/MS spectra for peptide sequencing and PTM localization.
Negative electron transfer dissociation
Fragmentation can also occur with a deprotonated species, in which an electron is transferred from the species to an cationic reagent in a negative electron transfer dissociation (NETD):
Electron-detachment dissociation (EDD) is a method for fragmenting anionic species in mass spectrometry. 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.
Charge transfer dissociation
Reaction between positively charged peptides and cationic reagents, also known as charge transfer dissociation (CTD), 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.
where represents the photon absorbed by the ion. Ultraviolet lasers can be used, but can lead to excessive fragmentation of biomolecules.
Infrared multiphoton dissociation
Infrared photons will heat the ions and cause dissociation if enough of them are absorbed. This process is called infrared multiphoton dissociation (IRMPD) and is often accomplished with a carbon dioxide laser and an ion trapping mass spectrometer such as a FTMS.
Blackbody infrared radiative dissociation
Blackbody radiation can be used for photodissociation in a technique known as blackbody infrared radiative dissociation (BIRD). 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. This is similar to infrared multiphoton dissociation which also uses infrared light, but from a different source. BIRD is most often used with Fourier transform ion cyclotron resonance mass spectrometry.
Surface induced dissociation
With surface-induced dissociation (SID), the fragmentation is a result of the collision of an ion with a surface under high vacuum. 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. 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.
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.
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 such as collision-induced dissociation (CID, electron transfer dissociation (ETD), 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. This approach has been used to understand the gas-phase fragmentation of protonated peptides, odd-electron peptide ions, non-covalent ligand-peptide complexes, and ligated metal clusters.
Quantitative proteomics is used to determine the relative or absolute amount of proteins in a sample. Several quantitative proteomics methods are based on tandem mass spectrometry. MS/MS has become a benchmark procedure for the structural elucidation of complex biomolecules.
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.
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. 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.
Tandem mass tag (TMT)
A tandem mass tag (TMT) is an isobaric mass tag chemical label used for protein quantification and identification. The tags contain four regions: mass reporter, cleavable linker, mass normalization, and protein reactive group. TMT reagents can be used to simultaneously analyze 2 to 11 different peptide samples prepared from cells, tissues or biological fluids. Three types of TMT reagents are available with different chemical reactivities: (1) a reactive NHS ester functional group for labeling primary amines (TMTduplex, TMTsixplex, TMT10plex plus TMT11-131C), (2) a reactive iodoacetyl functional group for labeling free sulfhydryls (iodoTMT) and (3) reactive alkoxyamine functional group for labeling of carbonyls (aminoxyTMT).
Tandem mass spectrometry can be used for protein sequencing. When intact proteins are introduced to a mass analyzer, this is called "top-down proteomics" and when proteins are digested into smaller peptides and subsequently introduced into the mass spectrometer, this is called "bottom-up proteomics". Shotgun proteomics is a variant of bottom up proteomics in which proteins in a mixture are digested prior to separation and tandem mass spectrometry.
Tandem mass spectrometry can produce a peptide sequence tag that can be used to identify a peptide in a protein database. A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum. 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 and additional sequence-specific fragment ions associated with particular amino acid residues.
Oligosaccharides may be sequenced using tandem mass spectrometry in a similar manner to peptide sequencing. 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.
Newborn screening is the process of testing newborn babies for treatable genetic, endocrinologic, metabolic and hematologic diseases. 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.
Tandem mass spectrometry cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell. Theses limitations are primarily due to a combination of inefficient ion production and ion losses within the instruments due to chemical noise sources of solvents.
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.
- Accelerator mass spectrometry
- Cross section (physics)
- Mass-analyzed ion-kinetic-energy spectrometry
- Unimolecular ion decomposition
- IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "tandem mass spectrometer". doi:10.1351/goldbook.T06250
- 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. doi:10.1016/1044-0305(92)87078-D.
- 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.
- IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "transient (chemical) species". doi:10.1351/goldbook.T06451
- 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. doi:10.1016/1044-0305(95)00626-5. PMID 24203235.
- Wells JM, McLuckey SA (2005). "Collision‐Induced Dissociation (CID) of Peptides and Proteins". Collision-induced dissociation (CID) of peptides and proteins. Methods in Enzymology. 402. pp. 148–85. doi:10.1016/S0076-6879(05)02005-7. ISBN 9780121828073. PMID 16401509.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. 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. 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.
- Morgan JW, Hettick JM, Russell DH (2005). "Peptide Sequencing by MALDI 193‐nm Photodissociation TOF MS". Peptide sequencing by MALDI 193-nm photodissociation TOF MS. Methods in Enzymology. 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.
- 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.
- 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: 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.
- 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.
- 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.
- 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. 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.
- 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.
- 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.
- 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.
- 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, Biemann K (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. doi:10.1016/1044-0305(93)87006-X. PMID 24227532.
- 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.
- 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:10.1891/0730-0822.214.171.124. PMID 17402600.
- 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.
- 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.
- 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. 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.