Mass spectrometry is a powerful analytical tool that is extensively used in fields like biotechnology, pharmaceuticals, clinical research, and environmental analysis. It works by ionizing molecule samples and then separating the ions based on their mass-to-charge ratio, which provides information about molecular structure. This information can be used to identify unknown compounds, study reaction mechanisms, and more. Mass spectrometry requires only picomolar concentrations of samples and can detect small changes in molecular structure. It has various applications in medicinal chemistry, such as determining molecular weights, monitoring chemical reactions, elucidating unknown structures, and identifying drug mechanisms of action.

1. Mass Spectrometry
applications in Medicinal
Chemistry
Shreekant Deshpande

2. Mass spectrometry is a very
powerful and versatile analytical
tool.
Extensively used in every fields to
detect one or the other things.
Here I try to give some outlines
about HOW TO extract a
INFORMATION FROM MASS
SPECTRA.

3. Overview
What is mass spectrometry?
Where are mass spectrometers used?
How does a mass spectrometer work?
What information can it provide?
Interpretation of spectra. and
Applications in medicinal chemistry.

4. What is Mass Spectrometry?
Analytical tool measuring molecular weight
(MW) of sample.
Only picomolar concentrations required.
With an high accuracy and within 5 ppm of
std. Error for small organic molecules.
For a mass of 40 kDa, there is a 4 Da error.
This means it can detect amino acid
substitutions / post-translational modifications
in biological systems.

5. Where are they used?
Biotechnology:
Analysis of proteins, peptides, oligonucleotides
Pharmaceutical:
Drugs discovery, combinatorial chemistry, pharmokinetics,
Drug metabolism
Clinical:
Neonatal screening, haemoglobin analysis, drug testing
Environmental:
Water, food, air quality
Geological:
Oil composition

6. Mass Spectrometry is also used to...
Detect and identify the use of steroids in athletes(Doping)
Ex. Sunita Rani’s case!!!
Monitor the breath of patients by anesthesiologists during
surgery.
Determine the composition of molecular species found in space
Adulteration in food stuff
Ex. Presence of pesticide in …..

7. How does a Mass
Spectrometer work?
3 fundamental parts: the ionisation source, the
analyser, the detector
Samples easier to manipulate if ionised
Separation in analyser according to mass-tocharge ratios (m/z)
Detection of separated ions with their relative
abundance
Signals sent to data system and formatted in a
m/z spectrum

9. Either directly or via chromatography for
component separation (HPLC, GC,
capillary electrophoresis)
Ionisation can be positively charged (for
proteins; Org. molecules) or negatively
charged (for saccharides and
oligonucleotides)

10. Electron Impact (EI)
Chemical Ionisation (CI)
Atmospheric Pressure Chemical Ionisation
(APCI)
Fast Atom Bombardment (FAB)
Field Desorption / Field Ionisation (FD/FI)
Electrospray Ionisation (ESI)
Matrix Assisted Laser Desorption
Ionisation (MALDI)

11. • Magnetic Sector
• Time of flight (tof)
• Quadrupole
• Quadrupole ion trap
• Fourier Transform Ion Cyclotron Resonance

12. The resolving power of analysers
The respective resolving powers correspond to the resolution typically
obtained for time-of-flight, quadrupole, and Fourier-transform mass
analyzers. Notice that the individual isotope peaks can be distinguished
at the higher resolution.

13. • Photo Multiplier
• Faraday Cup
Detector monitors ion current, amplifies it and then transmits signal to
data system

14. Mass spectrometry is a very powerful
method to analyse the structure of organic
compounds, but suffers from 3 major
limitations:
1 It is a destructive method
2 Compounds cannot be characterised without clean
samples
3 The dynamic properties of molecules can not be
detected.

15. Spectrum speaks
What Molecular ion peak tells !!
Most of the times chem. Strs. of the products are
known are presumed.
Sometime unexpected peaks will come then we’ll
scratch our head.
And we try to see +23/ +39 peaks(Na/ K adducts)
If MI is observed what else we can see for further
confirmations.
Isotope peaks
mass no- odd/even

16. m/z spectrum example

17. Natural abundance of
isotopes
Elements
Carbon
Nitrogen
Oxygen
Sulfur
Chlorine
Bromine
Relative abundance
C
14
N
16
O
32
S
35
Cl
79
Br
12
100
100
100
100
100
100
C
15
N
17
O
33
S
13
1.08
0.38
0.04
O
34
S
37
Cl
79
Br
18
0.78
3:1
1:1
0.20
3.35
32.5
98.0

18. Remember and Review!
The Rule of Thirteen – Molecular Formulas from Molecular
Mass
When a molecular mass, M+, is known, a base
formula can be generated from the following equation:
M
=
n
+
r
13
the base formula being:
CnHn
13
+r
For this formula, the HDI can be calculated from the
following formula:
HDI = ( n – r + 2 )
2

19. Interpretation
How to interpret our spectra?
•
Check the quality of the data; does the total ion spectrum look
ok?
•
Does the mass spectrum show significant peaks above the
baseline?
•
Identify any major peaks.
•
Look for telltale isotope patterns.
•
Remember the Nitrogen Rule. (The Nitrogen Rule: A neutral
compound containing an odd number of nitrogen atoms will
always have an odd molecular mass.)
•
Do the masses fit with the proposed structure?
•
Have you used the appropriate masses in your calculations?

20. Interpretation
How do I interpret my spectra?
Identify the MI
Check isotope pattern - halogens, sulphur etc.
Odd/Even Mass - Nitrogen Rule
If FAB check intensity of MI - aromatic or aliphatic
Accurate mass - calculate r + db
See neutral losses out of your mass.

Amine protecting groups
CxHyNzOn

r + db = x - 0.5y + 0.5z + 1


21. In Med. Chemistry
Accurate molecular weight measurements:
Unknown sample, Purity of sample, About other side products.
Reaction monitoring:
enzyme activity, chemical modification, protein digestion.
Structural elucidations:
Natural products, unknown products through fragmentations.
Identification of Mechanism of actions:
Both covalent n noncovalent interactions.
Active site Identifications:
Quantifying the amount of a compound in a sample using
carefully designed methods.
Impurity profiling for the bulk drugs.

22. AccuTOF-DART Technology
Its an atmospheric pressure source capable of ionizing liquid, solid, and
gas samples in real time.
Principle: on an atmospheric pressure interaction of a sample with longlived electronic excited-state atoms or molecules and atmospheric gases.
The system uses helium or nitrogen to produce metastable atoms or
molecules that interact with the analytes.
-lends to the analysis of samples
without any preparation and provides
data with accurate mass measurement.
A complete analysis can be done
within minutes by simply holding a
sample in the open gas stream.

23. The DART can even analyze samples directly on
surfaces such as concrete, currency, food, pills
and clothing.
The revolutionary DART ion source gives an
entirely new meaning to the phrase "open access".

24. Conclusion
MS is a highly applicable analytical tool in
Medicinal Chemistry.
The full structural information can get out of
single mass spectrum with min. qty. of sample.
Elemental analysis can b carried by using
HRMS.

25. In his book,
“Rays of Positive Electricity” (1913),
J.J.Thomson remarked:
“I feel sure that there are many problems in
chemistry which could be solved with far greater ease by
this than by any other method. The method is surprisingly
sensitive,……..requires an infinitesimal amount of material
and does not require this to be specially purified.”
Thank you very much