Mass Analyzers used in Mass Spectrometry, Chemistry tutorial


The different parts of the mass spectrometer will be looked individually to comprehend the different features of the different components and the benefits of one feature over the other.

Sample Introduction:

The method of sample introduction to the ionization source often based on the ionization method being used and also the kind of complexity of the sample. The sample can be inserted directly to the ion source or can undergo some kind of chromatography en route to the ionization source. The latter process of sample introduction generally comprises the mass spectrometer being coupled directly to the high pressure liquid chromatography (HPLC), gas chromatography (GC) or capillary electrophoresis (CE) separation column, and therefore the sample is separated into a series of components which then enter the mass spectrometer sequentially for the individual analysis.

Methods of Sample Ionization:

Most of the ionization methods are available and each has its own benefits and demerits. The ionization method to be used based on the kind of sample under investigation and the mass spectrometer available.

a) Electron Impact Ionization (EI):

The vapor of the sample is bombarded by a stream of high energy electrons. The energy transferred from such electrons to the molecules of the sample causes the molecules of the sample (M) to form molecular ions initially. These are the radical cations. These then decompose to smaller fragments.

1883_Electron Impact Ionisation.jpg

Fig: Electron Impact Ionization

b) Chemical Ionization (CI):

Chemical ionization (CI) is a softer method than EI, ions being generated via collisions between sample molecules and ions produced by reagent gas like methane or ammonia. Three phases are involved for methane, for illustration:

i) Reagent gas ionized via EI: CH4 + e- → CH4+ + 2e-

ii) Secondary ion formation: CH4+ + CH4 → CH5+ + CH3

iii) Formation of molecular species: CH5+ + M → MH+ + CH4

compared to EI, there is much less fragmentation, however molecular species, MH+, which is one mass unit more than the relative molecular mass (RMM) of the analyte is made.

c) Fast Atom Bombardment (FAB):

FAB gives an efficient means to analyze polar, ionic, thermally labile and high molecular weight compounds which are not amenable to normal EI/CI analysis. This has found extreme utility in the analysis of polar biomolecules and natural products. FAB experiments are routinely conducted up to 1000 amu, having higher masses needing additional effort. In the FAB experiment, a sample which has been dissolved in an appropriate matrix is inserted to the mass spectrometer and bombarded having 8-15keV Cs+ ions. Following ionization, the chosen positive or negative ions are extracted, accelerated and then mass analyzed. The FAB mass spectrum is characterized via peaks corresponding to matrix cluster ions, analyted ions, ions representing impurities and ions of other matrix modifiers (example: trifluoroacetic acid) which were added in an attempt to increase the analyted ion abundance.

Successful ionization of FAB is totally dependent on the matrix chosen for the analysis.  The successful matrix should meet up several needs. The main requirement is that the sample should be soluble in the matrix. Moreover, the matrix should be a low volatile solvent that will not rapidly evaporate in the high vacuum system of the mass spectrometer. Therefore, the matrix or sample will maintain its liquid nature in the vacuum system. Some of the successful matrices that have been broadly employed include the glycerol, thioglycerol, nitrobenzyl alcohol, 18-crown ether, 2-nitrophenyloctyl ether, diethanolamine, sulfolane and triethanolamine.

d) Electrospray Ionization:

Electrospray Ionization (ESI) is one of the Atmospheric Pressure Ionization (API) methods and is compatible to the analysis of polar molecules ranging from less than 100 Da to more than 1,000,000 Da in the molecular weight.

Throughout standard electrospray ionization, the sample is dissolved in a polar, volatile solvent and pumped via a narrow, stainless steel capillary (75-150 µi.d) at a flow rate of between 1 µl/min and 1 ml/min.

A high voltage of around 3 or 4kV is applied to the tip of the capillary, which is placed within the ionization source of the mass spectrometer, and as an effect of this strong electric field, the sample emerging from the tip is dispersed to an aerosol of highly charged droplets, a method that is aided through a co-axially introduced nebulising gas flowing around the outside of the capillary. This gas, generally nitrogen, helps to direct the spray emerging from the capillary tip towards the mass spectrometer. The charged droplets reduce in size via solvent evaporation, assisted through a warm flow of nitrogen known as the drying gas which passes across the front of the ionization source. Ultimately charged sample ions, free from solvent, are discharged from the droplets, some of which pass via a sampling cone or orifice to an intermediate vacuum region, and from there via a small aperture into the analyzer of the mass spectrometer, that is held under high vacuum. The lens voltages are optimized individually for each and every sample.

e) Desorption Techniques:

Desorption methods are mainly utilized for solid samples which can be deposited on the tip of a heat capable probe that is then inserted to the sample inlet via vacuum locks. Molecules are ionized via the application of a high potential gradient (field desorption, FD) or via focusing a pulsed laser beam onto the surface of the sample. In matrix-assisted laser desorption (MALDI) the sample is mixed by a compound capable of absorbing energy from the laser and that results in desorption of protonated sample molecules. These methods are very soft, provide little fragmentation and are particularly helpful for compounds having a high RMM. 

Mass Analyzers:

The major function of the mass analyzer is to separate, or resolve the ions made in the ionization source of the mass spectrometer according to their mass-charge (m/z) ratio. There are a number of mass analyzers presently available examples: quadrupoles, time-of-flight, magnetic sectors, Fourier transform and quadrupole ion traps.

Such mass analyzers have various features comprising the m/z range covered, the mass accuracy and achievable resolution. The compatibility of various analyzers having different ionization methods differs. For illustration, all the analyzers listed above can be employed in conjunction by Electrospray ionization, while MALDI is not generally coupled to a quadrupole analyzer.

a) Magnetic Sector:

In a magnetic sector instrument, the ions produced are pushed out of the source through a repelled potential of similar charge as the ion itself. They are then accelerated in an electric field of ca 3-8kV and travel via an electrostatic field region in such a way that they are forced to fall into a narrow range of kinetic energies prior to entering the field of the circular magnet. They then adopt a flight path via the magnetic field based on their mass-charge (m/z) ratio; the large ions are deflected less via the magnetic field:

m/z = H2r2/2v


H = Magnetic field strength

r = Radius of the circular path in which the ion travels and 

V = Accelerating voltage

At a specific value for H and V, only ions of a specific mass adopt a flight path which lets them to pass via the collector slit and be detected. If the magnetic field strength is varied, ions across a broad mass range can be detected via the analyzer; a typical sweep time for the magnetic field across a mass range of 1000 is 5-10 s although faster speeds are needed if high-resolution chromatography is being employed in conjunction by the mass spectrometry. The accelerating voltage can as well be varied whereas the magnetic field is held constant, in order to produce separation of ions on the basis of their kinetic energies.

b) Quadrupole Mass Analyzer:

This comprises of a set of four parallel metal rods positioned very closely together, however leaving a small space via the centre. Ions are accelerated to the space between the rods at one end and a DC potential and high frequency RF signal is applied across the opposite pairs of rods.  This result in ions of one particular m/z value passing straight via the space to a detector at the other end whereas all others spiral applied to the rods, ions having different m/z ratios can be allowed to reach the detector in turn. 

c) Ion Trap Mass Analyzer:

The ion trap is a modified version of quadrupole analyzer by a circular polarizable rod and end caps enclosing a central cavity that is capable to hold ions in stable circular trajectories before allowing them to pass to the detector in order of increasing m/z value. A specific feature of quadrupole and ion trap analyzers is their capability to scan via a broad range of masses very fast, making them ideal for monitoring the chromatographic peaks.

d) Tandem Mass Analyzers:

These incorporate some mass analyzers in series. The analyzers don't necessarily have to be the similar kind, in which case the instrument is a hybrid one. More popular tandem mass spectrometers comprise those of the quadrupole-quadrupole, magnetic sector-quadrupole, and more recently, the quadrupole-time-of-flight geometries. This lets ions chosen from the first analyzer to undergo collision induced dissociation (CID) having inert gas molecules contained in a collision cell generating new ions which can then be separated via the next analyzer. The method, known as tandem mass spectrometry, MS-MS is employed in the study of decomposition pathways, particularly for molecular ions generated via soft ionization method. Collision-induced reactions having reactive gases and different scan modes are as well used in these investigations. The other mass analyzers comprise Orbitrap, FT-ICR and Time-of-Flight analyzers.

Whenever charged particles move in the electric and magnetic fields, the given two laws apply:

F = Q(E + v x B), (Lorentz force Law)

F = ma = m (dv/dt) (Newton's second law of motion)


F = Force applied to the ion 

m = Mass of the particle

a = Acceleration

Q = Electric charge

E = Electric field

v x B = Cross product of the ion's velocity and magnetic field

This differential equation is the classic equation of motion for charged particles. Altogether with the particle's initial conditions, it totally finds out the particle's motion in space and time in terms of m/Q. Therefore mass spectrometers could be thought of as 'mass-to-charge spectrometers'. Whenever presenting data in a mass spectrum, it is common to use the dimensionless m/z that represents the dimensionless quantity formed by dividing the mass number of the ion by its charge number.

Joining the two previous equation results:

 (m/Q) a = E + v x B

This differential equation is the classic equation of motion of a charged particle in vacuum. Altogether with the particle's initial conditions it finds out the particle's motion in space and time. It instantly reveals that the two particles having the same m/Q ratio behave in the similar manner. This is why the mass-charge ratio is a significant physical quantity in those scientific fields where charged particles interact by magnetic or electric fields.

The IUPAC suggested symbol for mass is 'm'.  The IUPAC recommended symbol for charge is 'Q'; though, 'q' is as well very common. Charge is a scalar property, meaning that it can be either positive (+ symbol) or negative (- symbol). At times, though, the sign of the charge is indicated indirectly.  Coulomb is the SI unit of charge; though, other units are not uncommon.

The SI unit of physical quantity m/Q is kilograms per coulomb.

[m/Q] = Kg/C

The above units and notation are widely used whenever dealing with the physics of mass spectrometry; though, the unit less m/z notation is employed for the independent variable in a mass spectrum. This notation eases data interpretation as it is numerically more associated to the unified atomic mass unit of the analyte. The 'm' in m/z is representative of molecular or atomic mass and 'z' is representative of the number of elementary charges taken out by the ion. Therefore an ion of 1000 Da carrying two charges will be noticed at m/z 500. Such notations are closely associated via the unified atomic mass unit and the elementary charge.

However it is rarely done, the numerical conversion factor from SI units (kg/C) to m/z notation is:

(1000 g/Kg) x e x NA


NA = 6.022 x 1023 mol-1

e = 1.602 x 10-19 C

Detection and Recording of Sample Ions:

The detector supervise the ion current, amplifies it and the signal is then transmitted to the data system where it is recorded in the form of a mass spectra. The m/z values of ions are plotted against their intensities to exhibit the number of components in the sample, the molecular weight of each and every component, and the relative abundance of the different components in the sample.

The kind of detector is supplied to suit the kind of analyzer. The more common ones are the photomultiplier, the electron multiplier and the micro-channel plate detectors.

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