Mass Spectrometry

Mass Spectrometry
Mass Spectrometry
 Used to identify organic compounds
 mainly through molar mass and
identification of major fragments.
 A mass spectrometer is often used as
the “detector” for a gas
chromatograph (GC-MS)
 A mixture is separated and a total ion
chromatogram (TIC) obtained. A TIC is the
GC-MS equivalent of a gas chromatogram.
 The MS then allows identification of the
components without having to rely on a
comparison of retention times.
Mass Spectrometers
Mass Spectrometry
 Analysis time once the GC has been set
up (column chosen, gas flow set, oven
program finalized) is about 20
 Not too expensive
 Our benchtop model was $30K.
 Compounds that can be analyzed are
those that can be analyzed on a GC:
 Low to moderate boiling liquids
(and, of course, gases)
Mass Spectrometers
 analyze particles…cations!, not
 Impact from a high-energy electron
knocks an electron from the organic
compound and creates the Molecular
ion (aka parent ion)
 a cation with an unpaired electron M+•
 It has the m/z of the molecule, so the
value of m/z in most cases is the
value of the molar mass (provided z,
the charge of the cation, is +1)
Mass Spectrometers
 analyze cations, not photons
 Impact from a high-energy electron
also causes fragmentation.
 Base peak
 is the most intense m/z peak
 is the most stable fragment
 Other fragments form as well, some
from complex rearrangements
Mass Spectrometers
 The MS detects the m/z of each
fragment by directing the ionized
particles through a magnetic
 The trajectory of the ions in the magnetic
field bends as a function of the mass of the
particle and its charge:
Mass Spectrometers
 The magnetic quadrupole thus acts as
a mass filter.
 For a given magnetic field strength, light
particles are bent more and heavier
particles less.
 By changing the magnetic field strength,
m/z can be focused on the detector (an
electron multiplier) in succession and yield
a mass spectrum
 A plot of signal vs m/z
 Shimadzu
 GC
 GC-17A version 3
 Restek Rtx-XLB 30 meter fused silica
capillary column with 0.25 mm inner
diameter and a 0.25μm coating (the
liquid phase is low polarity…and
proprietary) for a column volume of
1.5 mL
 Column operates from 30° - 340°C
 Shimadzu
 MS parameters
 GCMS-QP5000
 requires an operating pressure of
approximately 2 Pa
quadruple mass filter
electron multiplier detector
turns on after 2 min to clear solvent
set up for 2 scans of 35-300 m/z per
Fragmentation Patterns Benzene Ring
Peaks at 51 and 77
are very typical of
the benzene ring.
Odd m/z suggests N
may be present.
Fragmentation Patterns - the
benzylic cation, the allylic cation
Extraneous peaks
Fragmentation Patterns Amines
Fragmentation Patterns alcohols
Alcohols can
fragment so
easily that the
M+ peak may
be missing
Fragmentation Patterns aldehydes and ketones
Fragmentation Patterns halogens
 Chlorine has 3:1 ratio of
 Look for peaks at 35 and 37
 Look for a gap of 35.
 Look for M:M+2 ratio of 3:1.
 Bromine has 1:1 ratio of
 Look for peaks at 79 and 81
 Look for a gap of 79.
 Look for M:M+2 ratio of 1:1.
 Iodine
 Look for peak at 127.
 Look for a gap of 127.
Rule of Thirteen
 Once you have the molecular weight
 Divide MW by 13 and express the result
as an integer (n) and a remainder (r).
 If your compound is a hydrocarbon, its
formula is approximated as CnHn+r.
 You may then find elements of
unsaturation from the molecular
Rule of Thirteen
 If you have hetero atoms in your
compound, adjust the formula to
 For O, add O and subtract CH4.
 For N, add N and subtract CH2.
 For Cl, add Cl and subtract either
C2H11 or C3H-1.
 Again, calculate elements of
unsaturation from the formula.
How to Analyze a Mass
 Identify the molecular ion peak, if present.
Note if the MW is odd.
 Mark the base peak and show the fragment
which gives rise to it.
 Mark significant fragment peaks and
identify the fragments giving rise to them.
 Mark peaks or gaps that indicate the
halogens, Cl (M : M+2 peaks = 3:1), Br (M :
M+2 peaks = 1:1), I (M or gap = 127).
 The mass of the compound with Br will be

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