Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectroscopy (MALDI-TOF-MS) is a technique that ionizes biomolecules and determines their masses. It involves mixing a sample with an ultraviolet-absorbing matrix, ionizing the mixture with a laser, accelerating the ions with an electric field, and measuring the time it takes for ions of different masses to travel a fixed distance, enabling mass detection. MALDI-TOF-MS provides highly accurate molecular weight information and has applications in disease diagnosis, quantitative analysis, and characterizing compounds attached to solid supports.

1. Matrix Assisted Laser Desorption Ionization
Mass Spectroscopy
Time Of Flight
MALDI-MS-TOF
Raj Kamal Vibhuti
Department of Microbiology
Central University of Haryana

2.  Mass Spectrometer (MS) is an extremely valuable analytical techniques in which the molecules in a test sample are
converted to gaseous ions that are subsequently separated in mass spectrometer according to their mass to charge (m/z)
ratio and detected.
 The development of two ionization techniques electrospray (ESI) and Matrix Assisted Laser Desorption/ionization
(MALDI).
 Both enabled the accurate mass determination of high molecular mass compounds as well as low molecular mass and
has revolutionized.
 Production of ion in the gas phase.
 Acceleration of the ion to a specific velocity in an electrical field.
 Separation of the ion in a mass analyzer.
 Detection of each species of a particular m/z ratio.
 The mass analyzer may separate ion either by use of magnetic and electric field.
 Alternatively the time taken for ion of different masses to travel a given distance in space is measured accurately in the
time of fight (TOF) mass spectrometer.

3. Component of a mass spectrometer
1. A high vacuum system (10-6 torr OR 1 µtorr) :- These include turbo-
molecular pumps, diffusion pumps and rotary vane pump.
2. A simple inlet :- This comprise a sample or target plate, HPLC, GC,
direct chemical ionization.
3. An ion source (To convert molecules into gas Phase Ion) :- This can be
MALDI, ESI, FAB (fast atom bombardment) etc.
4. A mass filter / Analyzer :- This can be TOF Quadrupole in trap etc.
5. A detector :- This can be conversion by one multiplier, microchannel
plate or array detector.

4. Principle of Mass Spectrometer
Any moving charged species of mass ‘m’ and velocity ‘v’ will be deflected by an applied
magnetic field.
 The magnitude of this deflection will depend on the momentum, µ of the species which
is given by equation.
µ=mv
Species with large momentum are deflected less than those with small momentum.
If a stream of atom and small molecules of identical velocity and charge but different in
mass in the gaseous phase is passed through a magnetic field , the deflection
experienced by each atom or molecules depends on its mass.
This deflection can therefore provide an accurate measure of mass.

5. TOF
Detector
LASER-LIGHT
mv2/r = zvb= Fc (Fc= zvbSinθ)
Where,
m = Mass
v = Velocity of ionized particle
r = Radius of curvature
z = charge of ion (+)
b = External magnetic field
Fc = Centripetal Force
Fc = ma2
= mv2/r
= mѠ2r (v = Ѡr)
= m(2∏ns)2
= m(2∏nrpm/60)2

6. MALDI- Matrix Assisted Laser Desorption Ionization
 MALDI-MS, 1st introduced in 1988 by Hillenkamp and Karas.
 In MALDI analysis, the analyte is 1st co-cryslallized with a large molar excess of a
matrix compound, usually an usually an ultraviolet absorbing weak organic acids after
which laser radiation of this analyte, vaporization of the matrix which carries the analyte
with it.
 The matrix therefore plays a key role by strongly absorbing the laser energy and causing
indirectly, the analyte to vaporize.
 The matrix also serves as a proton donor and receptor, activating to ionize the analyte in
both +Ve and –Ve ionization made.

8. TOF- Time Of Flight
 Time of flight analyzer which measures the time required for each ion to
travel to the end of the tube called the drift tube where they are detected.
 The time required for each ion to arrive at the detector is measured and from
this the m/z is calculated.

9. 1. Sample mixed with matrix is dried on the target
plate which is introduced into high-vacuum
chamber.
2. The camera allows viewing of the position of the
laser beam which can be tracked to optimize the
signal.
3. The sample/matrix is irradiated with laser pulses.
4. The clock is started to measure time-of-flight.
5. Ions are accelerated by the electric field to the
same kinetic energy and are separated according to
mass as they fly through the flight tube.
6. Ions strike the detector either in linear (dashed
arrow) or reflectron (full arrows) mode at different
times, depending on their m/z ratio.
7. A data system controls instrument parameters,
acquires signal versus time and processes the data.

10. Mechanism of MALDI
 MALDI provides for the non destructive vaporization and ionization of both large and
small biomolecules.
 The analyte is 1st co-crystallized with a large molar excess of a matrix compound,
usually a UV absorbing weak organic acids.
 The matrix Play a key role by strongly absorbing the laser light energy and causing,
indirectly the analyte to vaporize.
 The matrix play also serve as a proton donor and receptor, acting to ionize the analyte in
both +Ve and –Ve ionization respectively.

11. MALDI- Mass Analyzer
I. A linear time of flight (TOF)
II. TOF reflectron
III. Fourier transform mass analyzer
 TOF analysis is based on accelerating a set of ions to a detector where all of the ions are
given the same amount of energy.
 Because the ions have the same energy, yet a different mass, the ion reach the detector at
different times.
 The smaller ion reach the detector 1st because of their grater velocity while the large ion
take longer time to their larger mass.
 The analyzer is called TOF because the mass is determined from the ion’s time of flight
 The arrival time at the detector is dependent upon the mass, charge and kinetic energy
(KE) of the ion.
 Since KE is equal to ½mv² or velocity v = (2KE/m)½ ion will travel a given distance, d
within a time ‘t’ where t is dependent upon their mass to charge ratio (m/z).

12. TOF reflectron :-
In the reflector mode, the fragment that does not retain the charge (neutral, denoted by 0°) is
not deflected in the reflector but the charged fragments (•+) are deflected according to their
m/z and a spectrum of the fragment (daughter) ions is recorded, albeit of a limited m/z range
for each setting of the reflector voltages.

13. Fourier Transform Mass Analyzer :-
 The recent development of Fourier-transform ion cyclotron resonance (FT-ICR) mass
spectrometry has great potential in analysis of a wide range of biomolecules.
 It is potentially the most sensitive mass spectrometric technique and has very high mass
resolution; >106 is observable with most instruments.
 The instrument also allows tandem MS to be carried out. The ions can be generated by a
variety of techniques, such as an ESI or a MALDI source.
 FT-ICR MS is based on the principle of ions, which while orbiting in a magnetic field, are
excited by radio frequency (RF) signals. As a result, the ions produce a detectable image
current on the cell in which they are trapped.

14. Fig. - Schematic diagram of the Fourier-transform ion cyclotron resonance (FT-ICR) instrument.

15. General comparison of MALDI mass analyzers

16. Analysis of protein by MALDI-TOF-MS
 The utility of MALDI-TOF-MS for protein and peptide analyzes lies in its ability to
provide highly accurate molecular weight.
 Acquiring optimum MALDI data depends upon the choice of suitable matrixes and
solvents the functional and structural properties of the analytes.
Matrix used in MALDI-MS-TOF analysis
1. ἀ-cyno-4-hydroxycinnamic acid (CCA)- Peptides, Glycopeptides & Small proteins
2. 3,5-dimethoxy-4-hydroxycinnamic acid (SA)- Peptides & Small proteins
3. 2,5-dihydroxybenzoic acid (DHB)- Glycopeptides, Glycoproteins, Small Proteins &
Oligonucleotides (< 10bp)

17. Sample Preparation
I. Pipet 0.5 µl of sample to sample plate.
II. Pipet 0.5 µl of matrix to the sample plate.
III.Mix the sample & matrix by drawing in the out of the pipette
IV.Allow to air dry
1. For peptides, small proteins and most compound a saturated solution of CCA in
50:50 H2O:Acetonitrile (ACN) with 0.1% TFA (Trifluroacetic acid) is used.
2. For glycopeptides/proteins and small compound a saturated solution of DHB in
50:50 H2O:ACN with 0.1% TFA (Trifluroacetic acid) is used.
3. For prtein and large molecules a surated solution of SA in 50:50 H2O:ACN with
0.1% TFA (Trifluroacetic acid) is used.

19. APPLICATIONS
I. Diagnostic- MALDI a promising method for the diagnostic screening of
biological fluids (serum, cerebral spinal fluid, urine).
II. Quantitative Aspects of Matrix-assisted Laser Desorption/Ionization-
III.Characterizing Peptides and Reactions Directly from the Solid Phase-
Several reports have shown that MS can be very useful in characterizing
compounds covalently bound to solid polymeric supports subsequent to their
chemical cleavage from the resin.