Mass spectrometry is a technique that ionizes chemical compounds and sorts the ions based on their mass-to-charge ratio. It can be used to determine molecular weights, identify organic and inorganic compounds, and analyze complex mixtures. The key components of a mass spectrometer are an ion source that ionizes samples, a mass analyzer that separates the ions by mass, and a detector that records the results as a mass spectrum. Common applications of mass spectrometry include molecular structure determination, quantitative analysis of mixtures, and identification of unknown compounds.

1. MASS SPECTROMETRY

2. • Mass spectra is also called as positive ion spectra or line spectra
• We use electron bombardment to convert neutral charged molecules into positive charged.
• Also there is no ground or excited state like other types of spectroscopy
NaCl + e-  NaCl-
NaCl  NaCl+ + e-
• The mass spectrometer(MS) is an instrument that serves for
• establishment of the molecular weight
• structure of both inorganic and organic compounds,
• the identification and determination of analytes in complex mixtures.
• The MASS is an instrument capable of
• producing a beam of ions from sample under investigation,
• separating these ions according to their mass-to charge (m/z) ratios
• recording the relative abundances of the separated ion species as a mass spectrum.
• The ion-currents corresponding to the different species are amplified and either displayed on an
oscilloscope or a chart-recorder, or are stored in a computer.

3. Mass Spec Principles
Sample
Ionizer
+
_
Mass Analyzer Detector

4. How does a mass spectrometer work?
Create ions Separate ions Detect ions
• Ionization method
• MALDI
• Electrospray
(Proteins must be charged and dry)
• Mass analyzer
• MALDI-TOF
• MW
• Triple Quadrapole
• AA seq
• MALDI-QqTOF
• AA seq and MW
• QqTOF
• AA seq and protein modif.
• Mass spectrum
• Database analysis

5. Mass Spectrometry Needs
Ionization-how the protein is injected in to the MS machine
Separation-Mass and Charge is determined
Activation-protein are broken into smaller fragments (peptides/AAs)
Mass Determination-m/z ratios are determined for the ionized protein fragments/peptides
Mass Spectrometry Theory
In mass spectrometry, a small sample of a chemical compound is vaporized, bombarded with high energy electrons to
ionize the sample, and the ions produced are detected based on the charge to mass ratio of the ions Only the cations
are deflected by the magnetic field.
(High energy electrons)
Ionization process in mass spectrometry.
•Characterized by sharp, narrow peaks
•X-axis position indicates the m/z ratio of a given ion (for singly charged ions this corresponds to the mass of the
ion)
•Height of peak indicates the relative abundance of a given ion (not reliable for quantitation)
•Peak intensity indicates the ion’s ability to desorb or “fly” (some fly better than others)

6. MASS SPETRUM
Relative Abundance

7. INSTRUMENTATION
Components of a mass spectrometry:
1) Inlet system : introduce a very small amount of sample ( micromole or less) into the mass spectrometer, where its components
are converted to gaseous ions.
2) Ion source : converts the components of a sample into ions by bombardment with electrons, ions, molecules, or photon.
3) Mass analyzer : separates the analyte ions according to their m/z ratios.
4) Detector : converts the beam of ions into an electrical signal(currents) ; the detector output can be displayed or stored, to yield
the mass spectrum.
5) Electronics of power supply and control of the systems.
6) Vacuum systems : maintain low pressures ( 10–5 to 10–8 torr); rotary vacuum oil pump, diffusion pump, turbomolecular pump.

8. INLET SYSTEM:
• Heated inlet system: Gases and the less volatile liquids and liquids vapourized externally and the slowly introduced into the chamber
• Direct inlet system: Solids, non-volatile liquids, unstable compounds directly injected into the system
ION SOURCE:
From the inlet system the sample is introduced into ionisation chamber where a beam of electrons put across the molecule of the sample
DIFFERENT IONISATION METHODS:
• Electron Impact (EI - Hard method)
• small molecules, 1-1000 Daltons, structure
• Fast Atom Bombardment (FAB – Semi-hard)
• peptides, sugars, up to 6000 Daltons
• Electrospray Ionization (ESI - Soft)
• peptides, proteins, up to 200,000 Daltons
• Matrix Assisted Laser Desorption (MALDI-Soft)
• peptides, proteins, DNA, up to 500 kD

9. IONISATION METHODS:
Ionization
method
Typical
Analytes
Sample
Introduction
Mass
Range
Method
Highlights
Electron Impact (EI)
Relatively
small
volatile
GC or
liquid/solid
probe
to
1,000
Daltons
Hard method
versatile
provides
structure info
Chemical Ionization (CI)
Relatively
small
volatile
GC or
liquid/solid
probe
to
1,000
Daltons
Soft method
molecular ion
peak [M+H]+
Electrospray (ESI)
Peptides
Proteins
nonvolatile
Liquid
Chromatography
or syringe
to
200,000
Daltons
Soft method
ions often
multiply
charged
Fast Atom Bombardment
(FAB)
Carbohydrates
Organometallics
Peptides
nonvolatile
Sample mixed
in viscous
matrix
to
6,000
Daltons
Soft method
but harder
than ESI or
MALDI
Matrix Assisted Laser
Desorption
(MALDI)
Peptides
Proteins
Nucleotides
Sample mixed
in solid
matrix
to
500,000
Daltons
Soft method
very high
mass

10. Chemical ionisation:
• In this technique a reaction gas like methane is introduced along the sample to be analysed by mass spectrometer in the
ionisation chamber
• When the beam of electrons passed through the ionisation chamber, the reaction gas undergoes ionisation to produce ions
which react further with neutral molecules to form products
• The product so formed are reactive species and can interact with the sample molecules to produce positive ions
Matrix-assisted laser desorption ionization (MALDI)
• Analyte (protein) is mixed with large excess of matrix (small organic molecule)
• Irradiated with short pulse of laser light.
• Wavelength of laser is the same as absorbance max of matrix.
• Sample is ionized by bombarding sample with laser light
• Sample is mixed with a UV absorbant matrix (sinapinic acid for proteins, 4-hydroxycinnaminic acid for peptides)
• Light wavelength matches that of absorbance maximum of matrix so that the matrix transfers some of its energy to the
analyte (leads to ion sputtering)
• Unlike ESI, MALDI generates spectra that have just a singly charged ion
• Generally more robust that ESI (tolerates salts and nonvolatile components)
• Easier to use and maintain, capable of higher throughput
• Requires 10 mL of 1 pmol/mL sample

11. PRINCIPAL FOR MALDI-TOF MASS
Linear Time Of Flight tube
Reflector Time Of Flight tube
detector
reflector
ion source
ion source
detector
time of flight
time of flight

12. Electrospray mass spectrometry (ESI-MS)
• Liquid containing analyte is forced through a steel capillary at high voltage to electrostatically disperse analyte. Charge imparted from
rapidly evaporating liquid.
• Can be modified to “nanospray” system with flow < 1 mL/min
• Very sensitive technique, requires less than a picomole of material
• Strongly affected by salts & detergents
FAST ATOM BOMBARDMENT
• Although now considered insensitive by comparison with more recently introduced ionisation modes, FAB still has a role as a rapid, reliable
and robust technique for samples where quantity and purity are not a problem.
• The sample is first dissolved in a liquid matrix. This is typically a viscous, low vapour pressure liquid such as glycerol or 3-nitrobenzyl
alcohol. A few micro-litres of this liquid are placed on a small metal target at the end of a probe which is inserted into the mass spectrometer.
• The liquid surface is then bombarded with a beam of high kinetic energy atoms (xenon or argon) or ions (caesium). Molecules are sputtered
from the surface, enter the gas phase and ionise, either by protonation or deprotonation.
• The resulting ions tend to be stable and exhibit little fragmentation.

13. ION SEPERATOR
• It is a part of mass spectrometer which seperates the ions according to their masses. An analyser must posses the following characters
• It should have high resolution
• It must have high rate of transmission of electrons
There are different types of analysers. They are:
1. Single focusing magnetic analyser
2. Double focusing analayzer
3. Quadrapole mass spectrometer
4. Time of flight systems

14. SINGLE FOCUSING MAGNETIC ANALYZER

15. ION DETECTORS
• Farady cup or cylinder
• The electron multiplier
RESOLUTOIN AND RESOLVING POWER
• Width of peak indicates the resolution of the MS instrument
• The better the resolution or resolving power, the better the instrument and the better the mass accuracy
• Resolving power is defined as:
DM/퐌
M is the mass number of the observed mass (DM) is the difference between two masses that can be separated
The resolution is decreased due to following factors:
• Variation in accelerating voltage and magnetic field
• Poorly collimated and space charge of ion beam
• Width of ion beam as determined by the slits
• Pressure in the spectrometer.

16. TYPES OF IONS PRODUCED:
• Molecular ions
• Base peak ions
• Multiple charged ions
• Negative ions
• Rearrangement ions
• Metastable ions

17. DIFFERENT MASS ANALYZERS
• Magnetic Sector Analyzer (MSA)
• High resolution, exact mass, original MA
• QuadrupoleAnalyzer (Q)
• Low (1 amu) resolution, fast, cheap
• Time-of-Flight Analyzer (TOF)
• No upper m/z limit, high throughput
• Ion Trap Mass Analyzer (QSTAR)
• Good resolution, all-in-one mass analyzer
• Ion Cyclotron Resonance (FT-ICR)
• Highest resolution, exact mass, costly

18. DIFFERENT TYPES OF MS
• GC-MS - Gas Chromatography MS
• separates volatile compounds in gas column and Identified by mass
• LC-MS - Liquid Chromatography MS
• separates delicate compounds in HPLC column and Identified by mass
• MS-MS - Tandem Mass Spectrometry
• separates compound fragments by magnetic field and Identified by mass
• LC/LC-MS/MS-Tandem LC and Tandem MS
• Separates by HPLC, Identified by mass

19. General rules for interpretation of mass spectra
• The exact molecular weight
• Iosotope effect
• Nitrogen rule
• Ring rule
APPLICATIONS
• Molecular mass determination
• Iosotopic abundance
• Quantitative analysis of mixtures
• Distiction between trans and cis iosomer
• Determination of ionisation potential
• Bonding
• Reaction kinetics
• Impurity detection
• Identification of unknown compound
• Characterization of polymers