Mass spectrometry breaks molecules into fragments using high-energy electrons. The masses of the fragments and their relative abundances provide information about molecular weight, structure, and functional groups. Key principles for interpreting mass spectra include identifying the parent ion peak from molecular weight, observing isotope effects, and examining fragmentation patterns according to the nitrogen rule and common losses of simple groups like methyl or ethyl.

1. BASIC PRINCIPLES IN
INTERPRETATION OF MASS
SPECTRA
KOMMINENI.VIDYACHOWDHARY
VAAGDEVI PHARMACY COLLEGE
BOLLIKUNTA,WARANGAL

2. MASS SPECTROMETRY
Mass spectrometry is the most accurate method for
determining the molecular mass of the compound and
its elemental composition.
It is also called as positive ion spectra or line spectra.

3. Introduction
• Mass spectrometry (Mass Spec or MS) uses high energy
electrons to break a molecule into fragmentation.
• A beam of high-energy electrons breaks the molecule apart.
• The masses of the fragments and their relative abundance
reveal information about the structure of the molecule.
• Separation and analysis of the fragments provides information
about:
– Molecular weight
– Structure

4. General approach for acquiring
information about a sample
• degree of unsaturation
• Structures and functional groups Connectivity of
structures
• Reference spectra and comparison to possible
structures where unique identification is not
possible

5. GENERAL RULES FOR INTERPRETATION OF
MASS SPECTRA
.In order to interpret the mass spectrum , one should attain
an understanding of the ionisation process.
.To observe fragmentation pattern.
1.The exact molecular weight: The molecular weight of a
pure compound from the identification of the parent peak.
The molecular weight one can determine molecular
formula.
2.The isotope effects : Heavy isotopes will exhibit peaks in a
mass spectrum at m/e one or more units higher than
normal.
i.e.,there will be small peaks at M+1 and M+2.

6. The nitrogen rule
• In organic compounds , is a relationship
between the valance and the mass of the
most common isotope for most elements.
• Even elements have an even valance.
• Odd elements have an odd valance.
• This leads to the ‘nitrogen rule.’ It assumes
that we are limiting our elements to C, H,
halogens, O and N.

7. The nitrogen rule
• A compound containing only C, H, O or X
will have an even molecular weight.
A compound with an odd number of
nitrogens will have an odd molecular weight.
• A compound with an even number of
nitrogens will have an even molecular
weight.

8. Logical losses

9. General steps in
mass spectral interpretation

10. What is a mass spectrum

11. m/z ratio:
Molecular weight divided by the
Charge on this protein
All proteins are sorted based on a
mass to charge ratio (m/z)

12. RELATIVE ABUNDANCE:
• It is a method of reporting the amount of each
mass to charge measurement after assigning the
most abundant ion 100%.
• Abundance:
. The amount of an isotope of an element that
exists in nature , usually expressed as a
percentage of the total amount of all isotopes of
the element.

13. A simple mass spectrum

14. A simple mass spectrum

15. A simple mass spectrum

16. A simple mass spectrum

17. A simple mass spectrum

18. Fragmentation pattern

19. What is base peak?
• 100% abundance is called as base peak.
• M- is parent ion peak . It is all so called as
molecular ion peak.
• Molecular peak of M produced when an
electron is ejected from the molecule
M + e- M++2e-

21. Background of fragmentation
• The impact of a stream of high energy
electrons causes the molecule to lose an
electron forming a radical cation.
– A species with a positive charge and one unpaired
electron.
+ e
-
C H
H
H
H H
H
H
HC + 2 e
-
Molecular ion
M/z=16

22. Background
• The impact of the stream of high energy electrons can also
break the molecule or the radical cation into fragments.
(not detected by MS)
m/z = 29
molecular ion (M
+
) m/z = 30
+ C
H
H
H
+ H
HH C
H
H
C
H
H
H C
H
H
C
H
H
H C
H
H
+ e
-
H C
H
H
C
H
H
H
m/z = 15

23. Background
• Molecular ion (parent ion):
– The radical cation corresponding to the mass of the
original molecule
• The molecular ion is usually the highest mass in
the spectrum
– Some exceptions specific isotopes
– Some molecular ion peaks are absent.
H
H
H
HC H C
H
H
C
H
H
H

24. Background
Mass spectrum of ethanol(MW = 46)(C2H5OH)
M+

25. Background
M+
base peak
The mass spectrum of ethanol

26. Fragmentation Patterns
• The impact of the stream of high energy
electrons often breaks the molecule into
fragments, commonly a cation and a radical.
– Bonds break to give the most stable cation.
– Stability of the radical is less important.

27. Fragmentation Patterns
• Alkanes
– Fragmentation often splits off simple alkyl groups:
• Loss of methyl M+ - 15
• Loss of ethyl M+ - 29
• Loss of propyl M+ - 43
• Loss of butyl M+ - 57
– Branched alkanes tend to fragment forming the
most stable carbocations.

28. Fragmentation Patterns
• Mass spectrum of 2-methylpentane(M.w-86)

29. Example:

30. ASPIRIN (or) SALICYLICACID(m.wt-180)

31. Mass spectra of toulene:(m/z=91)

32. Conclusion
• We’ve totally left out any of the mechanisms
of ion fragmentation.
• On the other hand, the assumption was that
you were working with a GC/MS system.
• The chromatographic information will also
help solve many problems.