Ken Busch

Every scientific discipline develops its own specialized nomenclature, and also a tendency to spawn new terms and acronyms to reflect the evolution of the science and its applications. Mass spectrometry (MS) is no different, but because modern MS is a particularly dynamic and rapidly evolving mixture of applications, instrumentation, and data interpretation, MS might be the complex exemplar for just how nomenclature develops. A list of approved terms generated with much care by a committee of the American Society for Mass Spectrometry is available (1). A new print publication, 

 (2), has recently become available and almost certainly will need to be updated regularly. The 

 by David Sparkman can be treated as a definitive source for terms in MS (3). The specialized terms in MS describe instruments, procedures, interpretations, and results. These terms are often used without definition or explanation in technical presentations that involve MS.  

The first iteration of this glossary appeared in 2002 in 

 to provide some basic guidance. Many web-based glossaries of MS terms have appeared subsequently, and most have since disappeared, casualties of the need for constant revision. The purpose of this glossary, now revised and expanded, remains to compile some of the more widely used terms that may be encountered in MS, and for which a simple definition might prove helpful to start (not end) the process of comprehension. The definitions given here are necessarily brief, definitely neither committee-derived nor authoritative, and should be sufficient to provide basic understanding. Note that each term encompasses subtle and changing shades of meaning in use; if it becomes static, then the definition is archival. While the mavens of precise and unchanging meaning debate every nuance of use, the rest of us marvel at the underlying science and how terms morph to describe it. This glossary, like the printed dictionary, will shrivel if not refreshed and renewed regularly. 

Clearly, some manner of a selection process has been exercised by this author to keep the length of this glossary within reason. Responsibility for selection and definition of these glossary terms resides solely with the author. Those in search of more authoritative and comprehensive compilations would do well to begin with references 1 or 3, or Price's archival ASMS compilation (4). Earlier IUPAC recommendations for terms for use in MS can be found in an article by J.F.J. Todd (5). Sparkman's current glossary (3) is an update of a previous version, and is expanded to contain new terms from several application areas of biological MS, terms specific to instrumental MS, and terms derived from keywords used by the American Society for Mass Spectrometry to organize abstracts and presentations for its annual meeting. Definitions for more-specialized MS terms are available in several glossaries found on the web, or the terms can be used as search string targets for a search engine. The arrangement of terms here is strictly alphabetical, in contrast to some web glossaries that separate terms within broad general areas. After all, if one has to look up the meaning of a term, it's not likely that one would know which category to start with. Many of these terms are associated with acronyms or abbreviations, which are given in parentheses. A listing of acronyms and abbreviations is regularly published in 

. Positive ions are used as the default descriptive example throughout the text.  

The accelerating voltage is applied to the source to move ions formed in the source into the mass analyzer of the instrument. This accelerating voltage can range from a few tens of volts in quadrupole mass spectrometers to several thousand volts in sector instruments or in time-of-flight mass spectrometers. The accelerating voltage establishes the velocity of the ions through the instrument via the equation equating potential energy to kinetic energy, equal to ½

In this specialized method, atomic ions are formed from the sample by charge stripping in a very high voltage source, usually coupled to a Van de Graff accelerator. AMS is used for low-level analysis of 

C isotopes in radiocarbon dating and biological tracer studies. 

The accurate mass (or exact mass) of an ion of specified isotopic composition is calculated by summation of the exact masses of the constituent atoms. Conversely, the empirical formula of an ion can be deduced from the measured accurate mass of the ion if the ion mass is low enough to limit the number of formulaic possibilities and if the exact mass value is known accurately enough. 

The analyzer is the section of the mass spectrometer in which ions (formed in the source) are differentiated on the basis of their mass-to-charge ratios. The detector of the instrument is located after the mass analyzer in a beam-type instrument.  

An aperture is a small hole through which an electron or ion beam passes that controls the path or direction of the beam. The size of the aperture is important in maintaining a focus for imaging applications. A conductance-limited aperture is also used to maintain differential pressures in various physical regions of a mass spectrometer. 

In MS, an array detector is an electronic device that detects ions arriving at different spots along the array. A film (photoplate) detector for a mass spectrograph was an early example of an array detector; the film has since been replaced by electronic devices. Advantages are derived from the fact that scanning to bring ions of different 

 values to a point detector may be avoided. 

Atmospheric pressure chemical ionization (APCI)

In this method of ionization, an aerosol of sample solution is sprayed at atmospheric pressure into a heated region in which a sharp metal pin held at high potential sustains a corona discharge. The action of the discharge on the solvent creates reagent ions that react with the neutral sample molecules to create protonated ions of the molecule. These ions then pass through a sampling aperture into the mass analyzer of the mass spectrometer. 

Atmospheric pressure photoionization (APPI)

In this method of ionization, closely related to APCI, a UV source is used to ionize either sample molecule or added donor molecules that can then react together in a variety of ion–molecule reactions. Although protonated molecules are often formed, the ionization chemistry can be modified through judicious choice of the solvents and donor molecules. 

The atomic mass unit represents the relative scale in which the mass of 

C is 12, and so on. The amu is an older unit, replaced by the unified atomic mass unit u. More recently the u has been replaced by the unit dalton (Da). 

Some APCI and electrospray source designs use a flow of what is called the auxiliary gas (or sheath gas) to help control the dispersal of droplets and aid in the reproducibility of the ionization process. 

The average mass of an ion of a known empirical formula is calculated by summing the relative average atomic mass of each atom present. For example, carbon has an average atomic mass of 12.01115 Da, hydrogen is 1.00797 Da, and so on. The average mass of the molecular ion of a chemical compound is also the mass that appears on the bottle. However, a mass spectrum actually does not contain any peak at the average mass. Instead, signals appear for ions of various isotopic compositions. The average mass corresponds to the center of the centroid signal recorded for higher mass ions at lower instrumental resolutions. 

The base peak in a mass spectrum (within the user-selected mass range) is the ion with the highest measured abundance. The relative abundance of the base peak ion is assigned a value of 100, and the abundances of all the other ions plotted in that mass spectrum are normalized to that value. The 

-axis in a mass spectrum is therefore given in terms of relative abundance. 

Beam divergence is the angular spread (usually measured in degrees) of an electron or ion beam emitted by a source. Minimized beam divergence is important in maintaining focus in imaging mass spectrometry, and in maintaining coherence of an ion beam as it transits a beam mass spectrometer. Beam density (related to beam divergence) is important in assessing space charge effects.  

In a beam mass spectrometer, an ion beam emanating from the source transits through a mass analyzer component through to the detector of the instrument. The total ion beam flight path in a mass spectrometer can be a few tens of centimeters to as long as several meters. 

This is an approach to peptide sequencing in which MS analysis of the smaller sections of sequences (as might be obtained after a digestion or degradation) provides overlapping chains of amino acids that are stitched together into the final sequence. 

Calibration is a process in which the operation of the mass spectrometer in a specified manner is adjusted and certified to produce the accurate and known ion masses in the spectrum of a standard compound. 

Charge stripping is a process by which atomic ions are transformed into a higher charge state, thereby changing their mass-to-charge ratios. Different cross-sections for charge stripping of isobaric atomic ions allow their differentiation and subsequent trace-level analysis. 

Chemical ionization is a process of ionization that involves the reaction of a reagent ion and a neutral molecule to yield a charged ionic form of the molecule. The first step in chemical ionization is creation of the reagent ion through electron ionization of the reagent gas molecules present in great excess. A stable population of reagent ions is formed through ion/molecule reactions, and these ions will eventually react with the neutral gas-phase sample molecules. In a common case, methane gas is ionized to form predominantly CH

, which then reacts with the neutral sample molecule in a process of protonation to form (M + H)

In a collision between an ion (moving with some kinetic energy imposed in a mass spectrometer by the accelerating potential) and a neutral gas molecule (as forms the basis of collision-induced dissociation), it is often convenient to adopt a frame of reference in which the neutral gas molecule is considered to be stationary, and the collision energy is the translational kinetic energy of the ion. 

In a collision between an ion and a neutral species, a portion of the ion translational energy is converted to internal energy. This internal energy causes dissociation of the ion into smaller fragment ions and can also cause changes in the ion charge. Collision-induced dissociation is also known as collisionally activated dissociation. CID is common in MS-MS experiments. 

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Here we present an updated glossary of industry terms - a handy guide for the seasoned analyst as well as those new to the field.

Ken Busch

Articles

A Mass Spectrometry Glossary