The following list of terms is derived from common usage throughout the industry as an adjunct to the discussions in this primer and includes terms and techniques no longer in common usage.

Abundance - when viewed as similar to absorbance displayed on a UV detector the vertical increase in signal above background indicates an increased occurrence of that particular ion (when the x axis is calibrated in mass units) or total ions present (when the horizontal axis is calibrated in time or scans). The signal for all ions resulting from the fragmentation of a single analyte or compounds compared to a base peak (the relative abundance of each ion) is used to determine the fit of a fragmented pattern to a library spectrum for positive identification.

ASAP (atmospheric solids analysis probe) - based on work by Horning in the 1970s this form of sample ionization developed by McEwen and McKay uses a standard APCI plasma but forms ions by placing the sample in a heated nitrogen stream. The heat volatilizes a surprisingly large number of samples and ions are formed by charge exchange with metastable ions created by the APCI plasma. Relatively unambiguous identifications can be made of individual compounds from complex mixtures at low levels using accurate mass instruments. See also DART and DESI.

Atmospheric Pressure Ionization (API) - the term used to refer generally to techniques such as electrospray (ESI) and atmospheric pressure chemical ionization (APCI) and others that operate at atmospheric pressure.

Atmospheric Pressure Chemical Ionization (APCI) - originally called solvent-mediated electrospray it is more often successfully applied to neutral molecules that don't ionize easily directly out of solution. APCI provides a current on a sharp pin, positioned in the on-coming aerosol stream, to create a plasma of metastable ions from the solvent itself and transfer the charge from these ions to the analyte as it passes through the plasma. Heating a probe through which the LC or solvent stream passes creates the aerosol.

Atmospheric gas chromatography - developed by Charles McEwen at DuPont in 2002. Using a heated transfer line a standard GC effluent can be introduced to a standard API (or ESI/APCI) source on a mass spectrometer. This provides an easy and fast change over from ESI to GC for compounds that would be best analyzed by GC. Mode of ionization can be either APCI or APPI.

Atmospheric Pressure Photoionization (APPI) - developed in the 1980s but commercialized after 2000 when krypton gas lamps were found to generate sufficient photon energy at 10 eV (approximately) to ionize non-polar analytes such as PAHs and steroids not typically amenable to ESI and APCI ionization.

Base peak - usually the most intense peak in the spectrum to which others are compared; in ionization techniques which give extensive structural information such as EI the base peak may not be the parent or molecular ion.

Calibration - substances of known mass are introduced usually as a constant flowing stream while the mass spectrometer software acquires a signal for a given set of filtering conditions (i.e., RF/DC ratio for a quadrupole instrument). After comparing the acquired signal to a reference file, a calibration look-up table is created in the software. The calibration table is then the basis for the mass-to-charge ratios passed by the quads to be assigned a specific value. See the MS Primer sections on "Quantitation and Calibration"

CI (chemical ionization) - collisions induced at low vacuum (0.4 torr) by the introduction of a reagent for the purpose of enhancing the production of molecular ions and often sensitivity; as this is a much lower energy process than electron impact ionization fragmentation is reduced and it is often referred to as a soft ionization technique. See electron ionization.

DART (direct analysis real time) - developed by Robert Cody and others in 2002 similar to DESI in application although more closely related to APCI in function. A sample is placed on a substrate and bombarded by energized particles formed in a process similar to APCI. That is, metastable ions are formed by a plasma and transported by heated nitrogen gas directed at the target. See also McEwen's work listed under Atmospheric GC and ASAP.

DESI (desorption electrospray ionization) - first described by Graham Cooks in 2002 as a means of producing soft secondary ions from (typically) an inert substrate surface. Analogous to MALDI using an ESI probe aimed at about 50o incident angle to the surface allowing ions to chemically sputter and be admitted to the mass spectrometer. Shown to produce information directly from many polar and non-polar surface materials (skin, intact fruit for pesticide residue detection, etc) without the need for sample preparation. See also McEwen's work listed under Atmospheric GC and ASAP.

DIOS (desorption ionization on silica) - once viewed as an alternative to a preparing samples in a MALDI substrate especially for small molecules since the substrate (a bare silica surface) would not generate interfering ions. Its commercial potential in the late 1990s diminished as the difficulties of producing the plates and the surface susceptibility to contamination became apparent.

EI (electron ionization) - sometimes incorrectly referred to as "electron impact" ionization resulting from the interaction of an electron with a particle (atom or molecule); can be thought of as a ‘hard' ionization technique since sufficient energy is imparted to disrupt internal chemical bonds requiring high kcal/mol. Ionizing voltage (typically 70eV) refers to the difference in voltage causing acceleration of the electrons used to induce electron ionization. Unlike CI, EI avoids uncontrolled collisions by operating at high vacuum. The analyzer operates at even higher vacuum (10-4 to 10-6 torr).

Electrospray (ESI) - a so-called ‘soft' ionization technique. The most widely employed of the atmospheric pressure ionization (API) techniques. Commercially significant since the late 1980s the phenomenon is attributed to an excess of energy (voltages in the 3-5kV range) applied to a conductive tube (stainless steel capillary) inducing the liquid flowing inside to exceed its rayleigh limits and forming an aerosol upon exiting the tube. The resulting spray (the result of a coulombic explosion) then gives rise to ions contained in the aerosol droplets as they desolvate to approximately 10 micron radius. The ions are typically protonated and detected in the form M+H+ in positive ionization mode or M-H- in negative ion mode.

FAB (fast atom bombardment) - a so-called soft ionization technique where the result is usually an intense molecular ion with little fragmentation. The analyte is placed in a matrix (often glycerol) either flowing via LC or static on a probe and placed in the path of high energy atoms - often xenon or cesium iodide.

The technique has been effective for biomolecules up to 10,000 amu but perhaps a more important use is in conjunction with the magnetic sector mass spectrometer where exact weight can be determined such as for novel peptides. Sensitivity can be very good (low femtomol levels) and quite a lot of knowledge has been developed over the years with the technique (as static FAB). The technique can be difficult to master, the glycerol does foul the mass spectrometer source and the lower masses can be obscured by the presence of glycerol ions. This technique is little used now since the introduction of ESI.

Field Ionization (FI) - The soft ionization provided by FI leads to little or no fragmentation for a wide variety of analytes. This is particularly significant in petrochemical applications where there are limitations to the utility of other ionization techniques due to fragmentation (EI) or complex ionization characteristics (CI). A thin wire with a high applied voltage is heated in the vapor of an organic compound such as indene. The resulting structures which are deposited on the surface of the wire, dendrites, are pyrolized producing very fine conductive filaments. When a very fine point has a high potential applied to it a very intense electric field is generated at this tip providing conditions under which field ionization can take place.

Sample molecules pass in close proximity to the tips of a mass of carbon dendrites grown on the FI emitter. The FI emitter is positioned in close proximity to a pair of hollow extraction rods. The emitter is held at ground potential and a relatively high voltage (12 kV) is applied to the rods producing very high electric fields around the tips of the carbon dendrites. The GC column is positioned in close proximity and in line with the emitter wire. Under the influence of the electric fields, quantum tunneling of a valence electron from the molecule takes place to give an ion radical.

FIA (flow injection analysis) - this is the practice of introducing a sample (usually purified in an earlier step, as a fraction to remove interferences and complexity from the resulting spectrum) through the LC injector but without a column in-line. The LC acts as a sample introduction device only.

Filament - in electron ionization the filament is the source of electrons which interact with the analyte to ionize it. Typically made from a metal wire (flat or round) capable of giving off 70 eV electrons as it heats from current passing through it.

Fragment ion - an ion produced as the loss from a parent molecular ion. The sum of the dissociated fragments equals the parent and under given conditions will always fragment the same internal bonds to produce a predictable pattern (same ions and relative abundances for each). See also Product (daughter) ions resulting from specific MRM experiments.

Hybrid - usually refers to an instrument that is a combination of two different types for instance, earlier Micromass ‘hybrids' combined magnetic sector and quadrupoles. Today's QTOF is a hybrid of quadrupole and TOF.

Ion - mass spectrometers can only manipulate and therefore detect a mass when it possesses at least one charge. When only one charge is present (for instance by the loss of an electron causing the molecule to exist as a positively charged cation radical or by the addition of a proton or hydrogen to exist as a positively charged pseudo-molecular ion) we can think of it as representing the molecular weight in a low-resolution scheme.

Ion current (total ion current) - the electric current detected based on the charged particles created in the ion source. If the mass spectrometer is set to scan over a range of 100 to 500 Da the resulting total ion current will be the sum of all ions present in the source within that range at the selected time. If the instrument is set to detect only one ion (selected ion monitoring) the resulting total ion current will be the sum of only that ion at each selected instance.

Ion source - the physical space in the ion stream in front of the analyzer where the analyte is ionized. Each type of interface requires its own internal geometry for optimum results.

Isotope ratio - Although often presumed to be constant and stable, natural isotope abundance ratios show significant and characteristic variations when measured very precisely. Isotope ratio measurements are useful in a wide range of applications, for example, metabolic studies using isotopically enriched elements as tracers; climate studies using measurements of temperature-dependent oxygen and carbon isotope ratios in foraminifers; rock age dating using radiogenic isotopes of elements such as lead, neodymium or strontium; and source determinations using carbon isotope ratios (for instance to determine if a substance is naturally occurring or is a petroleum-based synthetic).

Typically, single focusing magnetic sector mass spectrometers with fixed multiple detectors (one per isotope) are used. Complex compounds are reduced to simple molecules prior to measurement, for example, organic compounds are combusted to CO2, H2O and N2.

Matrix Assisted Laser Desorption Ionization (MALDI) - first introduced in 1988 by Tanaka, Karas, and Hillenkamp, uses a laser to strike and energize a matrix containing the analyte. It has proven to be the method of choice for ionizing exceptionally large peptide and protein molecules that can then be detected intact. Commonly employed as the introduction scheme for Time of Flight (TOF) instruments.

Mass-to-charge ratio (m/z) - charged particles are represented as a ratio of their mass to their ionic charge. In literature and general use this often appears as ‘m/z' where the analyte from which the ion is derived might be labeled using atomic mass units (amu), daltons or molecular weight (mw).

Mean free path - the distance from entrance of an ion into the analyzer and detection of that ion. At operating vacuum the mean free path is relatively long considering time between collisions in rarified air versus the time needed to analysis an ion. Example:

atm (1000 torr) air contains 3 x 1022molecules/cm

chamber at 1 x 10-5torr contains 3 x 1011molecules/cm

l ¸pressure (torr) = min. mean free path (cm)

where l = 5 x 10-3cm

Molecular ion - the ion produced when a molecule gains (anion) or losses (cation) an electron. See also Pseudo-molecular ion.

Multiple Reaction Monitoring (MRM) - a specific experiment on a triple quad mass spectrometer where a parent ion is filtered in the first quad (Q1), a collision is then induced between the parent ion and a molecule (usually a gas such as argon) in the middle or ‘RF only' quad (Q2) followed by detection of a specific product ion from that collision (Q3). Used in high-throughput quantitative analyses in the pharmaceutical industry especially.

Parent ion - more properly referred to as ‘precursor'; a generally interchangeable term with ‘molecular ion'. Use of this term infers the presence of a product ion in an MRM scheme. See Product ion.

Particle beam (MAGIC, Thermabeam) - originally developed at Georgia Tech and dubbed MAGIC (monodisperse aerosol generating interface for chromatography) by Browner, The technique was later refined and is generically referred to as particle beam. The LC stream is heated and nebulized to remove the solvent. Vacuum pumps draw the solvent vapor through skimmer cones in series (usually two). The result is a "dried" particle that accelerates through the momentum separator and impacts the mass spectrometer source producing fragment ion spectra similar to traditional GC/MS. This technique is another which is now rarely used.

Probe also solids probe or direct insertion probe - a metal rod inserted into the mass spectrometer source through a vacuum lock. Samples can be applied to the tip of the probe and placed into the path of an ionizing beam. Typically used for EI and other single sample manual experiments. Samples can also be applied in an ionization enhancing matrix as in the case of FAB, See FAB.

Product ion - formerly called "daughter ions" these are the result of controlled experiments where a precursor (or ‘parent') ion and molecule collisions are intentionally induced to cause fragmentation. The collision gives rise to a product ion specific to the precursor ion and is used as a means of positive identification. See Multiple Reaction Monitoring (MRM).

Pseudo-molecular ion - usually refers to the adduction of a proton (e.g., M+H) or ion (e.g., M+NH4 derived from the ammonium salt commonly used in the mobile phase) that alters the analyte of interest in some relatively easily identifiable fashion. The charge allows manipulation by the mass spectrometer.

Quadrupole (Quad) - the underlying feature for the most prevalent type of mass spectrometer. Four rods (often no more than 1" in diameter and less than 12" long) are held parallel to each other (about 1" apart) in two collars. Filtering, or passing a given charged particle along its length, is accomplished by applying DC (direct current) and RF (radio frequency) voltage to the rods. Different masses (with associated charge) are affected by changing the RF/DC conditions. The rods are connected as paired opposites - each set alternated as the positive and negative poles by the RF source.

For a given calibrated setting, particles of corresponding mass-to-charge ratio only will pass (represented as m/z; approximately equivalent to molecular weight). The same setting will cause higher weight particles to miss the detector by passing in oblique fashion to the poles (the voltage settings having little or no effect) and lighter particles to become entrapped without reaching the exit and being detected. Quadrupoles can change and stabilize fields in <103 seconds allowing more than one molecular weight to be observed by scanning over time although fewer charged particles are therefore detected for any given molecular weight.

Resolution (10% valley method) - the minimum separation between two neighboring masses of approximately equal response for the mass spectrometer to distinguish between ions of different mass-to-charge ratio. More typically used with magnetic sectors; equal to the ratio of:

the average mass of the two particles
difference in their masses

Resolution (M/ΔM) - more commonly used as a measure where a given mass is divided by the resolution at full width half height maximum (FWHM). The preceding definition (10% method) was prevalent with magnetic sector instruments and requires the neighboring masses be of equal intensity. For instance, a typical resolution value for a quadrupole is 0.6 amu at FWHM. Measured using an acquired peak at mass-to-charge 3000 (equivalent to Daltons or amu) equals a resolution of 5000. The results of the two techniques are roughly comparable with this method typically yielding values double the valley method.

spectral peak width at 50% height

Scanning - see also selected ion monitoring, quadrupole and ion current. Control voltages (DC and RF) are adjusted by the computer over a given time to scan (detect) any charged particles in the specified range. The benefit of being able to detect more than one species is at the expense of sensitivity since some of the desired particles will undoubtedly be available to the detector while it is set to detect elsewhere in the range.

Selected ion monitoring (SIM) - also called Selected Ion Recording (SIR); refer also to quadrupole and scanning. The DC and RF voltage settings on the quadrupoles can be adjusted to pass only one charged particle (a single mass-to-charge ratio) through to the detector. The result is a dramatic decrease in noise allowing the signal to appear as a dramatic increase in sensitivity (all particles of that m/z are being detected all the time) at the expense of any other particles in the mixture being detected at all.

Thermospray - although this type of interface has been around in the literature for some time it was popularized in the early 1980s. LC solvent at approximately 1 ml/min is heated in a probe (insulated tubing approximately 1 - 2 feet long and 75 - 150 microns internal diameter) and the resulting vapor is sprayed into the mass spectrometer. Ions created by the desolvation of the aerosol droplets inside the mass spectrometer enter the analyzer (at right angles to the spray) and are affected by the lens voltages (see scanning, total ion current).

The spectra produced are termed soft ionization spectra since little meaningful fragmentation is produced. An intense molecular ion is produced and while the single ion may be little advantage in some backgrounds and mixtures it is advantageous for high molecular weight confirmation at great sensitivity and for filtering a target ion for further fragmentation (MS/MS). Literature reports low pmol sensitivity for vit D metabolites. The interface was generally chosen for highly polar applications such as metabolite work before the refinement of APCI in the early 1990s and worked poorly as organic content in the liquid increased.

This technique is no longer routinely used.

Time-of-Flight (TOF) Mass Spectrometer - a mass analyzer that separates ions of different mass-to-charge ratios by their time of travel through a field-free vacuum region after having been given the same kinetic energy. The velocity of the ions is dependent on their mass-to-charge ratio and as the ions are traveling over a fixed distance the time taken to reach the detector allows the mass-to-charge ratios to be determined with heavier ions taking longer.

Tuning - typically refers to optimizing the interface lenses and flowing gases to achieve a desired response for a specific analyte under a set of operating conditions as opposed to calibration. Calibration defines the mass acquisition and reporting function. Hardware settings of lenses and related circuits in conjunction with creation of a software lookup table sets a stable instrument's response, corrected to a list of known masses from a flowing stream of calibrant such as PEG or NaCsI.

Vacuum (torr) - equivalent to 1 mmHg (1 psi=51.7 torr=0.069 bar or atm). The analyzer portion of the mass spectrometer typically must be maintained at a minimum of 10-4 torr to allow discrete passage of the ionized particles. Pressures tending toward atmospheric cause ion-molecular interactions which can produce random results in the charged particles being detected further downstream. Under controlled conditions such collisions are induced at low vacuum (higher pressure) for techniques such as chemical ionization (CI).

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