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g faraday cups and ion to photon detectors are also used because the number of ions leaving the mass analyzer at a particular instant is typically quite small considerable amplification is often necessary to get a signal microchannel plate detectors are commonly used in modern commercial instruments 39 in ftms and orbitraps the detector consists of a pair of metal surfaces within the mass analyzer ion trap region which the ions only pass near as they oscillate no direct current is produced only a weak ac image current is produced in a circuit between the electrodes other inductive detectors have also been used 40 tandem mass spectrometry edit tandem mass spectrometry for biological molecules using esi or maldi a tandem mass spectrometer is one capable of multiple rounds of mass spectrometry usually separated by some form of molecule fragmentation for example one mass analyzer can isolate one peptide from many entering a mass spectrometer a collision cell then stabilizes the peptide ions while they collide with a gas causing them to fragment by collision induced dissociation cid a further mass analyzer then sorts the fragments produced from the peptides tandem ms can also be done in a single mass analyzer over time as in a quadrupole ion trap there are various methods for fragmenting molecules for tandem ms including collision induced dissociation cid electron capture dissociation ecd electron transfer dissociation etd infrared multiphoton dissociation irmpd blackbody infrared radiative dissociation bird electron detachment dissociation edd and surface induced dissociation sid an important application using tandem mass spectrometry is in protein identification 41 tandem mass spectrometry enables a variety of experimental sequences many commercial mass spectrometers are designed to expedite the execution of such routine sequences as selected reaction monitoring precursor ion scanning product ion scanning and neutral loss scanning 42 in selected reaction monitoring the first analyzer allows only a single mass through and the second analyzer monitors for multiple user defined fragment ions over longer dwell times than could be achieved in a full scan this increases sensitivity in product ion scans the first mass analyzer is fixed to select a particular precursor ion parent while the second is scanned to find all the fragments products or daughter ions to which it can be fragmented in the collision cell in precursor ion scans the second mass analyzer is fixed to select a particular fragment ion daughter while the first is scanned to find all possible precursor ions that could give rise to this fragment in neutral loss scans the two mass analyzers are scanned in parallel but separated by the mass of a molecular subunit of interest to the analyst ions are detected if they lose that fixed mass during fragmentation this can be used to look for any chemical that is capable of losing a particular neutral group for example a sugar residue together neutral loss and precursor ion scans can be used to hunt for chemicals with particular motifs another type of tandem mass spectrometry used for radiocarbon dating is accelerator mass spectrometry which uses very high voltages usually in the mega volt range to accelerate negative ions into a type of tandem mass spectrometer the metlin metabolite and chemical entity database 43 44 45 46 47 is the largest repository of experimental tandem mass spectrometry data acquired from standards the tandem mass spectrometry data on over 960 000 molecular standards as of october 2025 43 46 is provided to facilitate the identification of chemical entities from tandem mass spectrometry experiments 48 in addition to the identification of known molecules it is also useful for identifying unknowns using its similarity searching analysis 49 all tandem mass spectrometry data comes from the experimental analysis of standards at multiple collision energies and in both positive and negative ionization modes 43 common mass spectrometer configurations and techniques edit when a specific combination of source analyzer and detector becomes conventional in practice a compound acronym may arise to designate it succinctly one example is maldi tof which refers to a combination of a matrix assisted laser desorption ionization source with a time of flight mass analyzer other examples include inductively coupled plasma mass spectrometry icp ms accelerator mass spectrometry thermal ionization mass spectrometry tims and spark source mass spectrometry certain applications of mass spectrometry have developed monikers that although strictly speaking would seem to refer to a broad application in practice have come instead to connote a specific or a limited number of instrument configurations an example of this is isotope ratio mass spectrometry which refers in practice to the use of a limited number of sector based mass analyzers this name is used to refer to both the application and the instrument used for the application separation techniques combined with mass spectrometry edit an important enhancement to the mass resolving and mass determining capabilities of mass spectrometry is using it in tandem with chromatographic and other separation techniques gas chromatography edit a gas chromatograph right directly coupled to a mass spectrometer left main article gas chromatography mass spectrometry a common combination is gas chromatography mass spectrometry gc ms or gc ms in this technique a gas chromatograph is used to separate different compounds this stream of separated compounds is fed online into the ion source a metallic filament to which voltage is applied this filament emits electrons which ionize the compounds the ions can then further fragment yielding predictable patterns intact ions and fragments pass into the mass spectrometer s analyzer and are eventually detected 50 however the high temperatures 300 c used in the gc ms injection port and oven can result in thermal degradation of injected molecules thus resulting in the measurement of degradation products instead of the actual molecule s of interest 51 liquid chromatography edit main article liquid chromatography mass spectrometry indianapolis museum of art conservation scientist performing liquid chromatography mass spectrometry similarly to gas chromatography ms gc ms liquid chromatography mass spectrometry lc ms or lc ms separates compounds chromatographically before they are introduced to the ion source and mass spectrometer it differs from gc ms in that the mobile phase is liquid usually a mixture of water and organic solvents instead of gas most commonly an electrospray ionization source is used in lc ms other popular and commercially available lc ms ion sources are atmospheric pressure chemical ionization and atmospheric pressure photoionization there are also some newly developed ionization techniques like laser spray capillary electrophoresis mass spectrometry edit main article capillary electrophoresis mass spectrometry capillary electrophoresis mass spectrometry ce ms is a technique that combines the liquid separation process of capillary electrophoresis with mass spectrometry 52 ce ms is typically coupled to electrospray ionization 53 ion mobility edit main article ion mobility spectrometry mass spectrometry ion mobility spectrometry mass spectrometry ims ms or imms is a technique where ions are first separated by drift time through some neutral gas under an applied electrical potential gradient before being introduced into a mass spectrometer 54 drift time is a measure of the collisional cross section relative to the charge of the ion the duty cycle of ims the time over which the experiment takes place is longer than most mass spectrometric techniques such that the mass spectrometer can sample along the course of the ims separation this produces data about the ims separation and the mass to charge ratio of the ions in a manner similar to lc ms 55 the duty cycle of ims is short relative to liquid chromatography or gas chromatography separations and can thus be coupled to such techniques producing triple modalities such as lc ims ms 56 data and analysis edit mass spectrum of a peptide showing the isotopic distribution data representations edit see also mass spectrometry data format mass spectrometry produces various types of data the most common data representation is the mass spectrum certain types of mass spectrometry data are best represented as a mass chromatogram types of chromatograms include selected ion monitoring sim total ion current tic and selected reaction monitoring among many others other types of mass spectrometry data are well represented as a three dimensional contour map in this form the mass to charge m z is on the x axis intensity the y axis and an additional experimental parameter such as time is recorded on the z axis data analysis edit mass spectrometry data analysis is specific to the type of experiment producing the data general subdivisions of data are fundamental to understanding any data many mass spectrometers work in either negative ion mode or positive ion mode it is very important to know whether the observed ions are negatively or positively charged this is often important in determining the neutral mass but it also indicates something about the nature of the molecules different types of ion source result in different arrays of fragments produced from the original molecules an electron ionization source produces many fragments and mostly single charged 1 radicals odd number of electrons whereas an electrospray source usually produces non radical quasimolecular ions that are frequently multiply charged tandem mass spectrometry purposely produces fragment ions post source and can drastically change the sort of data achieved by an experiment knowledge of the origin of a sample can provide insight into the component molecules of the sample and their fragmentations a sample from a synthesis manufacturing process will probably contain impurities chemically related to the target component a crudely prepared biological sample will probably contain a certain amount of salt which may form adducts with the analyte molecules in certain analyses results can also depend heavily on sample preparation and how it was run introduced an important example is the issue of which matrix is used for maldi spotting since much of the energetics of the desorption ionization event is controlled by the matrix rather than the laser power sometimes samples are spiked with sodium or another ion carrying species to produce adducts rather than a protonated species mass spectrometry can measure molar mass molecular structure and sample purity each of these questions requires a different experimental procedure therefore adequate definition of the experimental goal is a prerequisite for collecting the proper data and successfully interpreting it interpretation of mass spectra edit main article mass spectrum analysis since the precise structure or peptide sequence of a molecule is deciphered through the set of fragment masses the interpretation of mass spectra requires combined use of various techniques usually the first strategy for identifying an unknown compound is to compare its experimental mass spectrum against a library of mass spectra if no matches result from the search then manual interpretation 57 or software assisted interpretation of mass spectra must be performed computer simulation of ionization and fragmentation processes occurring in mass spectrometer is the primary tool for assigning structure or peptide sequence to a molecule an a priori structural information is fragmented in silico and the resulting pattern is compared with observed spectrum such simulation is often supported by a fragmentation library 58 that contains published patterns of known decomposition reactions software taking advantage of this idea has been developed for both small molecules and proteins analysis of mass spectra can also be spectra with accurate mass a mass to charge ratio value m z with only integer precision can represent an immense number of theoretically possible ion structures however more precise mass figures significantly reduce the number of candidate molecular formulas a computer algorithm called formula generator calculates all molecular formulas that theoretically fit a given mass with specified tolerance a recent technique for structure elucidation in mass spectrometry called precursor ion fingerprinting identifies individual pieces of structural information by conducting a search of the tandem spectra of the molecule under investigation against a library of the product ion spectra of structurally characterized precursor ions 59 particularly unstable ions may disintegrate while passing through the analyzer if it undergoes the reaction m z m z other parts when entering the analyzer it would undergo a circular motion of radius r v m z b e displaystyle r tfrac v m z be this would then show up in the resulting spectrogram as a peak that is apparently made by an ion with m z m 2 m z displaystyle m z tfrac m 2 m z since there is no actual ion with mass m displaystyle m this is called an abnormal peak or a metastable ion peak in general a meta stable ion peak is a broad peak centered at a highly non integer value of m z displaystyle m z the existence of a metastable ion peak at m 2 m z displaystyle tfrac m 2 m z is strong evidence that two ions of masses m z m z displaystyle m z m z are in fact related by the reaction m z m z other parts 11 sec 3 5 applications edit noaa particle analysis by laser mass spectrometry aerosol mass spectrometer aboard a nasa wb 57 high altitude research aircraft mass spectrometry has both qualitative and quantitative uses these include identifying unknown compounds determining the isotopic composition of elements in a molecule and determining the structure of a compound by observing its fragmentation other uses include quantifying the amount of a compound in a sample or studying the fundamentals of gas phase ion chemistry the chemistry of ions and neutrals in a vacuum ms is now commonly used in analytical laboratories that study physical chemical or biological properties of a great variety of compounds quantification can be relative analyzed relative to a reference sample or absolute analyzed using a standard curve method 60 as an analytical technique it possesses distinct advantages such as increased sensitivity over most other analytical techniques because the analyzer as a mass charge filter reduces background interference excellent specificity from characteristic fragmentation patterns to identify unknowns or confirm the presence of suspected compounds information about molecular weight information about the isotopic abundance of elements temporally resolved chemical data a few of the disadvantages of the method is that it often fails to distinguish between optical and geometrical isomers and the positions of substi...