Glossary of Terms in Mass Spectrometry

 Acquisition Time (Mass Spectrometer Acquire Time)

The total mass spectrometer analysis time. During this time data are stored on the hard disk drive.

Array Detectors

Solid state devices which detect ions impacting over a region.

Atmospheric Pressure Chemical Ionization (APCI)

A very soft chemical ionization technique [but not as soft as electrospray ionization (ESI)] carried out in an ion source operating at atmospheric pressure. Electrons from a corona discharge initiate the process by ionizing the mobile phase vapor molecules. A reagent gas forms, which efficiently produces positive and negative ions of the analyte through a complex series of chemical reactions.

APCI is typically used to analyze small molecules with molecular weights up to about 2000 u. APCI is a very robust ionization technique. It is not affected by minor changes in most variables, such as changes in buffer or buffer strength.

Auxiliary Gas

The outer-coaxial gas (nitrogen) that assists the sheath (inner-coaxial) gas in dispersing and/or evaporating sample solution as the sample solution exits the APCI or ESI nozzle. The auxiliary gas also sweeps solvents out of the API source to help keep the interior of the ion source as dry as possible. The auxiliary gas is used especially at higher solvent flow rates.In the static NSI source, the auxiliary gas can be used to provide backpressure. The backpressure required to initiate the spray is often higher than that required to maintain the spray. (Auxiliary gas is not used with the dynamic NSI source.)

Calibration

Mass calibration: A procedure performed to ensure that the mass spectrometer mass assignments are accurate. You perform a mass calibration with a compound that has a well-known mass spectrum.

Quantitative calibration: The process of determining how the LC/MS system responds to different compounds. Quantitative calibration involves designing a processing method and performing calibration experiments with calibration standards containing known quantities of analyte.

Calibration, Mass Spectrometer

A procedure performed to ensure that the mass spectrometer mass assignments are accurate. You perform a mass calibration with a compound that has a well-known mass spectrum.

Calibrating the mass spectrometer involves setting the electron multiplier gain, calibrating mass and resolution for various scan modes, and calibrating RF voltage parameters to achieve optimum mass spectral performance.

Centroid Data

Data used to represent mass spectral peaks in terms of two parameters, the centroid (the weighted center of mass) and the intensity. The data is displayed as a bar graph. Centroid data differ from profile data. In profile data format, the mass spectral peak is represented as a series of data points, each with its own intensity value. In centroid data format, the transformed representation of this mass spectral peak consists of the centroid of this series of data points and a single intensity value that represents the sum of the intensities of the data points.

Centroiding

A method used to improve mass spectral data quality, get better mass assignments, and reduce data file size. Profile data, in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.

Charge State

The imbalance between the number of protons (in the nuclei of the atoms) and the number of electrons that a molecular species (or adduct ion) possesses. If the species possesses more protons than electrons, its charge state is positive. If it possesses more electrons than protons, its charge state is negative.

For positive ion ESI, medium to large ions frequently have charge states of greater than +1 by the addition of protons. For negative ion ESI, medium to large ions frequently have charge states of greater than -1 by the loss of protons. For positive ion APCI, ions typically have a charge state of +1 by the addition of a proton. For negative ion APCI, ions typically have a charge state of -1 by the loss of a proton or electron capture.

Chemical Ionization (CI)

The formation of new ionized species when gaseous molecules interact with ions. The process can involve transfer of an electron, proton, or other charged species between the reactants. When a positive ion results from chemical ionization, the term can be used without qualification. When a negative ion results, the term negative ion chemical ionization can be substituted.

Chemical Ionization (CI) Plasma

The collection of ions, electrons, and neutral species formed in the ion source during chemical ionization. Chemical ionization is a two-step process. First, CI reagent ions are formed in the CI plasma. Then, sample ions are formed by gas phase reactions with the CI reagent ions.

Chromatogram

The graphical representation of a chemical separation, such as liquid chromatography, obtained from an analytical instrument called a chromatograph. The result of plotting detector response versus time.

Chromatography Filter

The chromatography filter is a sophisticated noise reduction algorithm that smoothes peak profiles at low sample concentrations in chromatographic data. These peak profiles integrate more consistently than those acquired under normal data acquisition conditions.

Collision Energy

 The translational kinetic energy (TKE) of a (moving) projectile ion when it interacts with a (stationary) target neutral species, such as a collision gas molecule.  Collision energy is an important factor in the collision induced dissociation (CID) process.

 Collision-Induced Dissociation (CID)

 An ion/neutral process in which a (fast) projectile ion is dissociated as a result of interaction with neutral target species. Dissociation is brought about by the conversion of part of the translational kinetic energy of the ion into internal energy in the ion during the collision.  [Also referred to as collision-activated dissociation (CAD)]. 

 Data Systems

 Computer based instruments which process and record the detector signals as well as providing control for all the processes involved in operating the instrument.

Divert/Inject Valve

A valve on the mass spectrometer that can be plumbed as a divert valve or as a loop injector. As a loop injector, you can load the valve and then inject the contents of the valve into the ion source of the mass spectrometer. As a divert valve, the valve directs the effluent from an LC into the ion source of the mass spectrometer for the analysis of samples, or it diverts the LC effluent to a waste container.

EI (Electron Ionisation)

Ionisation in the gas phase by interaction with a beam of electrons.

Electron Multipliers or Photomultipliers

Detection of ions by production of an amplified electric current, either as a consequence of direct impact of the ion on a surface or following production of a photon from a phosphor followed by a photomultiplier tube.

Electrospray Ionization (ESI)

A type of atmospheric pressure ionization that is currently the softest ionization technique available to transform ions in solution into ions in the gas phase. The analyte solution is forced through a narrow-bore spray capillary (needle) to which a potential has been applied. The high potential causes the emerging solution to disperse into a fine spray of charged droplets. As the solvent evaporates away, the droplet size shrinks and the charge concentration on the surface increases. Eventually, the coulombic repulsion overcomes the droplet's surface tension. The droplet explodes and forms a series of smaller, lower-charged droplets. This process continues until the analyte ion escapes the droplet (ion desorption) or all of the solvent evaporates to leave the bare ion (ion evaporation). This ionization technique produces ions in multiple charge states. As a result, a mass spectrum can have multiple peaks for ions of the same mass.

Many samples that previously were unsuited for mass analysis (for example, heat-labile compounds or high molecular weight compounds) can be analyzed by the use of ESI. ESI can be used to analyze any polar compound that makes a preformed ion in solution, including adduct ions.

ESI Spray Current

The flow of charged particles in the ESI source. The voltage on the ESI spray needle supplies the potential required to ionize the particles. The ESI spray current varies; the ESI spray voltage is set. A type of electrospray ionization (ESI) that accommodates very low flow rates of sample and solvent on the order of 1 to 20 nL/min (for static nanospray) or 100 to 1000 nL/min (for dynamic nanospray). Nanospray allows for ESI analysis of very small sample volumes (approximately 1 µL). This in turn allows the use of more concentrated solutions from small amounts of sample and/or longer analysis times because of the very low flow rates.

Static nanospray permits continuous analysis of small analyte solution volumes over an extended period of time. It is particularly useful for obtaining detailed structural information using MS/MS for purified samples or those present in a simple mixture. Sample is loaded into a metal-coated glass capillary with a tip internal diameter that ranges from 1 to 4 mm. A voltage is applied to the metal coating on the tip and an air-filled syringe provides a constant backpressure to initiate and maintain electrospray. After electrospray has begun, the electric field and the solvent properties allow the flow to be self-regulated.

Dynamic nanospray employs microscale capillary columns to separate the analytes in complex mixtures. The sample is loaded onto a column using an injection valve or a gas pressure vessel. The mixture components are then eluted by a solvent gradient and pumped through the emitter.

FT (Fourier Transform)

The mathematical operation used to convert the signals detected in an ICR mass spectrometer to a set of m/z values.

Full Scan Type

A scan type that provides a full mass spectrum of each analyte or parent ion.  With the full scan type, the mass analyzer is scanned from the first mass to the last mass without interruption in a given scan time.  The full scan type can be employed in the following three cases:

• Single-stage (MS) full scan type.
• Two-stage (MS/MS) full scan type.
• Multi-stage (MS^n) full scan type. 

GC/MS (Gas Chromatography/Mass Spectrometry)

The linking of mass spectrometry to a gas chromatographic system. The gaseous effluent from a capillary GC column can be introduced directly into the mass spectrometer source.

Ionization Mode	Scan Filter Abbreviation
atmospheric pressure chemical ionization	APCI
chemical ionization	CI
electron ionization	EI
electrospray	ESI
fast atom bombardment	FAB
field desorption	FD
glow discharge	GD
matrix-assisted laser desorption/ionization	MALDI
nanospray	NSI
thermospray	TSP

 

ICP-MS (Inductively Coupled Plasma Mass Spectrometry)

 Ionization of elements in a high temperature plasma.

Ion Polarity Mode

The mass spectrometer can operate in either of two ion polarity modes: positive ion, in which positive ions are analyzed, and negative ion, in which negative ions are analyzed.

Ion Source

The source of ions (molecular ions and fragment ions, or in an MS/MS experiment, parent ions). Your mass spectrometer can employ any of several ion sources: an atmospheric pressure chemical ionization (APCI) source, an electrospray ionization (ESI) source, or a nanospray ionization (NSI) source.

Ion-Trap

Ions are pulsed into a three dimensional device where they are stored by a quadrupole field. They can then be ejected at defined m/z values by the application appropriate secondary electric fields.

Isotopes

Most elements are composed of a mixture of isotopes. These will be separated in a mass spectrometer. Atoms or molecules containing such elements will display a cluster of ions reflecting the isotopic composition.

LC/MS (Liquid Chromatography/Mass Spectrometry)

The linking of the effluent from a liquid chromatographic system to a mass spectrometer.

MSn

A term used in the case of MS/MS experiments with ion traps where product ion analysis is extended over a number of generations.

MALDI (Matrix Assisted Laser Ionisation)

Ionization by effect of illumination with a beam of laser generated light onto a matrix containing a small proportion of analyte.

Mass Analyzer

A devise that separates ionic species according to the mass-to-charge ratios of the ions.

Mass Range Chromatogram

A type of chromatogram in which all ions from one or more specified mass spectrometer mass ranges are summed and plotted as a function of time.

A plot of the ion intensity of a specified mass or masses [Y-axis] versus the corresponding scan number or time [X-axis]. The ion intensity is the sum of all ion intensities for data in a selected mass range or mass ranges of each scan.

Mass Spectrometer

An instrument that ionizes sample molecules and then separates the ions according to their mass-to-charge ratio (m/z). The resulting mass spectrum is a characteristic pattern for the identification of a molecule.

All mass spectrometers have four common components:

• A system for introducing the sample to be analyzed into the instrument
• A system for ionizing the sample
• An accelerator that directs the ions into the measuring apparatus
• A system for separating the constituent ions and recording the mass spectrum (a plot of ion abundance versus ion mass-to-charge ratio) of the sample.

Abbreviated: MS.

Mass Spectrometry

This is the technique in which an instrument is employed to produce ions from atoms or molecules (the source) which are then separated according to their charge-to-mass-ratios (the analyzer) and detected.

Mass Spectrum

A spectrum obtained when ions are separated according to their mass-to-charge ratios (m/z). A graphical representation (plot) of measured ion abundance versus mass-to-charge ratio. The mass spectrum is a characteristic pattern for the identification of a molecule and is helpful in determining the chemical composition of a sample.

m/z

Mass to charge ratio. An abbreviation used to denote the quantity formed by dividing the mass of an ion (in u) by the number of charges carried by the ion. For example, for the ion C₇H₇²⁺, m/z = 45.5.

MS/MS

Mass spectrometry / mass spectrometry or tandem mass spectrometry. An analytical technique that involves two stages of mass analysis. In the first stage, ions formed in the ion source are analyzed by an initial analyzer. In the second stage, the mass-selected ions are activated by collision with a neutral gas, and the resultant ionic fragments are mass analyzed by a second analyzer.

MS Scan Mode

The scan power equal to 1, where the scan power is the power “n” in the expression MS^n.

The MS scan mode corresponding to the one stage of mass analysis in a single-stage full scan experiment or a selected ion monitoring (SIM) experiment. 

MS/MS Scan Mode

The scan power equal to two (2), where the scan power is the power “n” in the expression MS^n. The MS/MS scan mode corresponding to the two stages of mass analysis in a two-stage full scan experiment or a selected reaction monitoring (SRM) experiment. 

Negative Ion

An atom, radical, molecule, or part of a molecule that has one or more electrons than it has protons, and thus has a negative charge. The charge state (-1, -2, -3, etc.) depends upon the number of electrons in excess of the number of protons.

NICI (Negative Ion Chemical Ionization)

Ionization as a consequence of capture of an electron in the gaseous phase.

Neutral Loss Map

The neutral loss mass is [parent mass – product mass]. 

Octapole

An octagonal array of cylindrical rods that acts as an ion transmission device. An RF voltage and dc offset voltage applied to the rods create an electrostatic field that transmits the ions along the axis of the octapole rods. (Also called an octapole rod assembly.)

Parent Ion

An electrically charged molecular species that can dissociate to form fragments. The fragments can be electrically-charged or neutral species. A parent ion can be a molecular ion or an electrically charged fragment of a molecular ion. Parent ions are produced in the API source. Also called a precursor ion.

Parent Mass

The mass-to-charge ratio of a parent ion. The location of the center of a target parent-ion peak in mass-to-charge ratio (m/z) units.

Peak Width

The distance across a peak measured at a selected peak-height level.

For chromatograms: The time in minutes between peak start and peak end using the current peak integration settings

For mass spectra: The number of mass units across a peak measured at a designated peak-height level. The peak-height level is usually specified as a percentage of the maximum peak height.

Positive Ion

An atom, radical, molecule, or part of a molecule that has one or more fewer electrons than it has protons, and thus has an electrically positive charge. The charge state (+1, +2, +3, etc.) depends upon the number of protons in excess of the number of electrons.

Product Ion

An electrically charged product of reaction of a selected parent ion. In general, product ions have a direct relationship to a particular parent ion and can correlate to a unique state of the parent ion. The reaction need not necessarily involve fragmentation. It could, for example, involve a change in the number of charges carried. Thus, all fragment ions are product ions, but not all product ions are necessarily fragment ions. Product ions are formed in the collision cell.

Formerly called a daughter ion.

Product Mass

The mass-to-charge ratio of a product ion. The location of the center of a target product-ion peak in mass-to-charge ratio (m/z) units.

Formerly called the daughter ion mass.

Profile Data

Data representing mass spectral peaks as point-to-point plots, with each point having an associated intensity value. Profile data are different from centroid data. In profile data format, the mass spectral peak is represented as a series of data points, each with its own intensity value. In centroid data format, the transformed representation of this mass spectral peak consists of the centroid of this series of data points and a single intensity value that represents the normalized sum of the intensities of the data points.

Profile Scan Data Type

A scan data type that shows the shape of the peaks in the mass spectrum. 

Quadrupole(Q)

The application of a combination of DC and AC voltages to four parallel rods creates a filter through which, on application of the appropriate voltages, only ions of any one defined m/z value can be transmitted. If only an Rf field is applied all ions are transmitted (q)

Relative Collision Energy

A measure of collision energy given as a percent of the maximum value.  The term relative collision energy is used in for two cases:  octapole region source CID and mass analyzer CID.

For octapole region ion source CID:  The relative collision energy varies from 0.1% to 100% for octapole region ion source CID.  (0 to 100% relative collision energy corresponds to 0 to-100Vdc of octapole offset voltage for positive ions and 0 to+100Vdc for negative ions.)

For mass analyzer CID:  The relative collision energy varies from 0 to 100% for mass analyzer CID.  (0 to 100% relative collision energy corresponds to 0 to 5V peak-to-peak of resonance excitation RF voltage.)

Resolution

A term which defines the performance of an analyzer. This parameter describes the degree to which two ions of adjacent m/z can be distinguished from each other with less than a defined amount of overlap. The latter is often quoted as 10% for sector instruments and 50% for quadrupoles. For isolated peaks the same term can be calculated from the width of the peak at defined heights.

Scan Event

A mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time.

Scan Power

The power n in the expression MSⁿ. The number of stages of mass analysis, expressed as MSⁿ where n is the scan power.

For example, a scan power of n = 1 corresponds to an MS¹ (or MS) scan with one stage of mass analysis. A scan power of n = 2 corresponds to an MS² (or MS/MS) scan with two stages of mass analysis. A scan power of n = 3 corresponds to an MS³ scan with three stages of mass analysis, and so on.

Scan Time

The amount of time required to accomplish one scan, from the lowest mass to the highest mass of a specified scan range. The scan can be continuous (full scan type) or it can be in segments (SIM and SRM, for example).

Selected Ion Monitoring (SIM) Scan Type

A scan type with one stage of mass analysis and in which one or more ions of particular mass-to-charge ratios are monitored.

In the SIM scan type, the ions formed in the ion source are stored in the mass analyzer.  Then, ions of interest for one or more mass-to-charge ratios are isolated and are scanned out of the mass analyzer to produce a SIM mass spectrum.  (No data are acquired for other ions as they leave the mass analyzer.)

Because only ions of selected mass-to-charge ratio are monitored, the selected ion monitoring scan mode generally provides higher sensitivity than does the full scan mode.

Sheath Gas

The inner coaxial gas (nitrogen), which is used in the API source, that helps to nebulize the sample solution into a fine mist as the sample solution exits the ESI or APCI nozzle. (Sheath gas is not used with the NSI source.)

Source CID

Ion source collision-induced dissociation (CID) is a technique for fragmenting ions in an atmospheric pressure ionization (API) source.  Either of two regions can be used for the ion source CID process:  the capillary-skimmer region and the octapole region.

Note:  Ion source CID is useful for some experiments.  However, its usefulness is limited compared to mass analyzer CID, which provides true MS/MS and MS^n capabilities.  Mass analyzer CID provides greater specificity and higher efficiency than does ion source CID.  Therefore, it is usually the method of choice.

Capillary-skimmer region ion source CID:  Ions emerge from the heated capillary and expand into the capillary-skimmer region of the API source with considerable translational kinetic energy.  This kinetic energy is further increased by applying greater than usual voltages to the heated capillary and/or tube lens, which increases the difference in potential between these components and the skimmer (which is at ground potential).  The voltages are increased sufficiently to impart enough kinetic energy to the ions so that, when they collide with solvent or air molecules (collision gas) present in the API source, the ions dissociate to form product ions.

Syringe Pump Flow Rate

The rate of flow of liquid from the syringe pump (in microliters per minute). The syringe pump flow rate can be set from the Syringe Pump page of Instrument Setup. Typical syringe pump flow rates are between 10 and 20 µL/min.

Tandem Mass Spectrometry

The use of two analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). (see MS/MS)

TOF (Time-of-Flight)

The ions formed are all accelerated by a pulsed potential down an evacuated tube (drift region) and their time of arrival at a detector is determined. This is a function of their m/z values.

Tune, Mass Spectrometer

Tuning the mass spectrometer involves optimizing voltages, currents, flows, and the like for the ion source parameters to achieve the maximum mass spectral sensitivity and proper resolution. The way the mass spectrometer is tuned affects all data acquisition. The tuning of the various parameters is often interdependent, with each parameter affecting the optimum value of other parameters.