Mass Spectrometry
Chapter 11 – Atomic mass spectrometry.
Chapter 20 – Molecular mass spectrometry.
Sections 11A-1, 11A-2
A mass spectrometer produces and separates ions based on their
mass-to-charge (m/z) ratio. A mass spectrum is a plot of relative
intensity (y-axis) versus m/z (x-axis).
If the charge of an ion is 1, then m/z = mass number of ion.
MS readily differentiates isotopes, which have different atomic
mass units (amu) or Daltons (Da).
The isotope of carbon-12 is exactly (by definition) 12 amu. So 1
dalton, or 1 amu is 1/12 of the mass of carbon-12.
The molecular mass or average atomic mass is what one obtains
from the periodic table.
The nominal mass is the integer mass number of a molecule with
the most abundant isotopes.
1
Section 20A – Molecular Mass Spectra
Molecular ion
&
Fragmentation
Section 20B – Ion sources
The formation of gaseous analyte ions can be done in many ways,
which has resulted in an explosion of applications of MS,
particularly for large molecules.
Here – a general discussion of hard and soft ionization methods
and some basics.
Electron Impact source – very common. A “hard” ion source.
M + e- (70 eV)  M.+ + 2e2
The parent or molecular ion may not be the base peak.
Consider formaldehyde
Electron impact ionization imparts so much energy, there is lots of
fragmentation, great for structure elucidation.
Can have too much of a good thing, no parent or molecular ion so
no molecular mass information robs analyst of vital information.
A gentler method of ionization is chemical ionization. Compare the
EI-MS of pentobarbital on the left with the CI-MS on the right.
3
Here CI gives fewer daughter ions, but the parent ion (M+1)+ is
detectable.
Chemical ionization works like electron impact ionization, but here
an ion, often derived from methane ionization, is used to ionize the
analyte rather than an electron, imparting less energy to the analyte
resulting in less fragmentation.
Other softer ionization methods for large molecules:
MALDI
ESI (2002 Nobel Prize in Chemistry)
4
Once the ions are formed by EI, CI, MALDI, ESI, etc. they are
separated by m/z in a mass analyzer.
Prior to discussing how a few different mass analyzers work:
1. They all require a high vacuum (low pressure) so that the
ions do not collide with one another in the mass analyzer.
5
2. The resolving power (the ability to detect ions of different
m/z ratio) must be defined.
The higher the resolving power, the better a mass spec is able to
separate two peaks with similar mass.
m is the nominal mass of the 1st
peak
Δm is the mass difference
between the 2 peaks
Mass analyzers resolution from
500  500,000
What resolution is needed to
resolve C2H4+ and CH2N+?
The simplest mass analyzer to understand is the magnetic sector
analyzer (Section 20C-3)
How does an ion with a velocity vector (v) behave in a magnetic
field (B)?
6
The definition of a
magnetic field (B):
F=vxB
The ion undergoes a
force perpinducalar to
velocity and magnetic
field vectors, and is
deflected through a
circular path with
radius r.
Ions with different m/z will be deflected with different radii of
curvature.
A little algebra and clear thinking provides the relationship
relating r to m/z
7
Variation of the magnetic field strength provides the ability to
scan the m/z range to acquire the mass spectrum.
This is more like a “mass filter”, where the mass analyzer is
used to filter all ions except those of a certain range to reach the
detector.
The most common mass analyzer in mass spectrometers is a
quadrupole, which also functions as a mass filter (Section 11B2)
The quadrupole is the smallest, most rugged, and least
expensive of mass analyzers. (ESI-MS importance)
The quadrupole also uses a magnetic field to manipulate ion
trajectories. There are 4 parallel rods, 2 rods opposite carry the
same DC voltage (i.e. + or -). In addition there is a radio
frequency oscillating AC voltage applied to both pairs of
electrodes. At a given frequency only ions of a small m/z range
can traverse the mass analyzer.
AC and DC voltages are varied such that ions of different m/z
ratio are “resonant” in the quadrupole.
8
How the quadrupole mass analyzer (filter) works: Below are 2 +
charged quadrupoles in the xz plane with cations traveling with
some kinetic energy in the z-direction. The ac voltage will have
a greater effect on ions with low m/z and lower KE. The dc
voltage keeps the ions between the rods. (If an ion strikes a rod
it is out!)
These pair of rods will act as a high pass filter, allowing ions of
higher m/z ratio to traverse the quadropole.
The opposite occurs for the pair of quadrupoles that are biased
with a – dc voltage. The dc voltage attracts the cations to the
rods. Cations with lower m/z ratio will respond more to the ac
voltage and be deflected from the rods. The (-) rods act as a low
pass filter, allowing ions of low m/z ratio to traverse the
quadruopole.
9
The small band of ions of m/z ratio that can traverse the
quadrupole is varied by adjusting ac and dc voltages.
The third and last mass analyzer to be discussed is time-of-flight
(TOF) mass analyzer (Section 11B-3).
Ions periodically produced and accelerated into TOF mass
analyzer, ideally all with the same kinetic energy. (See Figure
11-10, pp. 290).
If all ions have the same kinetic energy, ions of different masses
have different velocities.
Mass separation achieved by the time it takes for the ions to
traverse the flight tube. The main advantage: almost unlimited
m/z range, unlike quadrupole and other mass analyzers.
(MALDI-TOF)
Other mass analyzers (not discussed) include ion traps, ICR.
It is increasingly common to string two mass analyzers together
(tandem mass spectrometry or MS/MS). Section 20C-5
10
Here the mass spectrum of preselected and fragmented ions are
obtained.
Finally for MS instrumentation, ion detectors (Section 11B-1).
The electron multiplier is very common, see Figure 11-2, pp.
284.
The high amplification of the signal is a plus, but the signal
intensity can be dependent on the kinetic energy of the ion
reaching the detector.
11
The Faraday cup is inexpensive and rugged, it is not as
sensitive as an electron multiplier (no internal amplification),
but the signal is independent of ion kinetic energy.
Conclude Mass Spectrometry with applications (Section 20D).
1. Identification of pure compounds.
Molecular masses – MS is THE way to do it. Must find a
parent ion. Be careful, especially with electron impact spectra.
 Intensities of isotopic peaks at M+1, M+2, etc. (briefly
discussed below) must be consistent with the formula.
 The peak for the heaviest fragment ion should correspond
to a probable loss from M.+
Isotopic ratios. For example the M+1 peak provides
information on elemental composition.
12
Isotopic abundances: 12C = 98.93%, 13C =1.07%, 1H = 99+%,
2
H = 0.012%
For CnHm: M+1 intensity = (n x 1.08%) + (m x 0.012%)
For benzene: M+1 intensity =
For biphenyl: M+1 intensity =
13
The (M+2)+ peak is particularly useful for the
identification of compounds containing Cl, Br,
S.
Fragmentation patterns: If you are interested
get the classic book by Silverstein et al.
“Spectrometric Identification of Organic
Compounds” where MS spectral interpretation
is discussed, along with primarily IR and NMR
spectral interpretation.
There exist computerized library search systems of EI-mass
spectra.
2. Hyphenated mass spectrometry (GC-MS, LC-MS, CE-MS)
MS is a most sensitive and selective detector for separations.
The problem: chromatography is a high pressure technique, MS is
a high vacuum (very low pressure) technique.
First solved for GC-MS, now common and easy. (Section 27B-4)
Capillary columns are small enough such that the gas flow does
not overwhelm the MS vacuum system.
An entire mass spectrum is taken, for example, each second. For
a 10 minute run, 600 mass spectra obtained.
14
The chromatogram can be shown in various ways from the mass
spectra.
1. Total ion chromatogram – sum the ion abundances in each
spectrum and plot that sum as a function of time. Looks like a
“regular” chromatogram.
2. At a given time (i.e. at the top of a peak in a total ion
chromatogram), a mass spectrum can be displayed for
qualitative analysis.
3. To enhance selectivity
monitor one or a few
m/z values.
The specifics of LC-MS and CE-MS are not worth discussing
now (Ch. 28, 30, resp.). The information content is the same as
for GC-MS. Note however that LC-MS and CE-MS must
resolve more challenging technical problems since the mobile
phase is a liquid, and MS requires a gas. In addition, CE
requires the use of buffers, a further complication to couple
these 2 methods.
Quantitative Analysis
Selected ion monitoring
15
Questions/Problems
Chapter 11: 3
Chapter 20: 2, 4a, 5, 11, 12, 13, 18, 19a,b,c,e,f
16