MASS SPECTROMETRY

Introduction
The concept of mass spectrometry is relatively simple: a compound is ionized (ionization method).
The ions are separated on the basis of their mass/ or charge ratio (ion separation method), and the
number of ion representing each mass /charge unit is recored as a spectrum. For instance, in the
commonly used electron impact (EI) mode, the mass spectrometer bombards molecules in the
vapor phase with a high-energy electron beam and records the result a spectrum of positive ions,
which have been separated on the basis of mass/ charge (m/z).
To illustrate, the E1 mass spectrum of benzamide is given in figure 1.1 showing a plot of abudance
(vertical peak intensity) versus m/z. the positive ion peak at m/z 121 represents the intact molecule
(M) less on electron, which was removed by the impacting electron beam; it is designated the
molecular ion, M
-+
. The energetic molecular ion produces a series of fragment ions, some of which
are rationalized in figure 1.1.
it is routine to couple a mass spectrometer to some form of chromatograph (GC-MS) or a liquid
chromatograph (LC-MS). The mass spectrometer finds widespread use in the analysis of compounds
whose mass spectrum is known and in the analysis of completely unknown compounds. In the case
of known compounds, a computer search is conducted comparing the mass spectrum of the
compound in question with a library of mass spectra. Congruence of mass spectra is convincing
evidence for identification and is often even admissible in court. In the case of known compound,
the molecular ion, the fragmentation pattern, and evidence from other forms of spectrometry (e.g.,
IR and NMR ) can lead to the identification of a new compound. Our focus and goal in this chapter is
to develop skill in the latter use. For other applications or for more detail,
FIGURE 1.1 The EI mass spectrum of benzamide above which is fragmentation pathway to explain
some of he important ions.
*the unit of mass is the Dalton (Da), defined as of the mass of in atom of isotope
12
C, which is
arbitrarily 12.000 mass units.









1









Mass spectrometry texts and spectral compilations are listed at the end of this chapter.
1.2 INSTRUMENTATION
this past decade has been a time of rapid growth and change in instrumentation for mass
spectrometry. Instead of discussing individual instrumentation for mass spectrometry. Instead of
discussing individual instruments, the type of instrument will be broken down into (1) ionization
methods and (2) ion separation methods. In general, the method of ionization is independent of the
method of ion separation and vice versa, although there are expections. Some of the ionization
methods depend on a specific chromatographic front end (e.g., LC MS), while still others are
precluded from using chromatography for introduction of sample (e.g., FAB and MALDI). Before
delving further into instrumentation, let us make a distinction between two types of mass
spectrometers based on resolution.
the minimum requirement for the organic chemist is the ability to record the molecular
weight of the compound under examination to the nearest whole number. Thus, the spectrum
should show a peak at, say, mass 400. Which is distinguishable from a peak at mass 399 or at mass
401. In order to select possible molecular formula by measuring isotope peak intensities (see section
1.5.2.1), adjacent peaks must be cleanly separated. Arbitrarily, the valley between two such peaks
should not be more than 10% of the height of the larger peak. This degree of resolution is termed
unit resolution and can be obtained up to a mass of approximately 3000 Da on readily available
unit resolution instruments.
to determine the resolution of an instrument, consider two adjacent peaks of approximately
equal intensity. These peaks should be chosen so that the height of the valley between the peaks is
less than 10% of the intensity of the peaks,. The resolution (R) is R = M
n
(M
n
M
m
), where M
n
is the
heigher mass number of the two adjacent peaks and M
m
is the lower mass number.
There are two importantcategoris of mass spectrometers: low (unit) resolution and high resolution.
Low resolution instruments can be defined arbitrarily as theinstruments that separate unit masses
up to m/z 3000 [R = 3000 / (3000 2999) = 3000 ]. A high-resolution instruments (e.g ., R = 20,000)
can distinguish between C
16
H
26
0
2
and C
15
H
24
NO
2
[R = 250.1933/ (250.1933- 250.1807) 19857]. This
important class of mass spectrometers, which can have R as large as 100,000, can measure the mass
ofan ion with sufficient accuracy to determine is atomic composition (molecular formula).
All mass specrometers share common features. (see figure 1.2) some sort of
chromatography usually accomplishes introduction of the sample into the mass spectrometer,
although many instruments also allow for direct insertion of the sample ino the ionization chamber.
All mass spectrometers have methods for ionizing the sample and for separating the ions on the
basis of m/z. these methods are discussed in detail below. Once separated, the ions must be
detected and quantified. A typical ion collector consists of collimating slits that direct only one set of
ions at a time into the collector, where they are detected and amplified by an electron multiplier.
The method of ion detection is dependent to some extent on the method of ion separation.
nearly all mass spectrometers today are interfaced with a computer. Typically, the computer
controls the operation of the instrument including any chromatography, collets and stores the data,
and provides either graphical output (essentially a bar graph ) or tabular lists of the spectra.

FIGURE 1.2 block diagram of features of a typical mass spectrometer .
2

1.3 IONIZATION METHODS
Thelarge number of ionization methods, some of which are highly specialized, precludes complete
coverage. The mostcommon ones in the three general areas of gas-phase, desorption, and
evaporative ionization are described below.
1.3.1 Gas-Phase Ionization Methods
Gas-phase methods for generating ions for mass spectrometry are the oldest and most popular
methods. They are applicable to compounds that have a minimum vapor pressure of ca. 10
-6
Torr at
a temperature at which the compound is stable; this criterion applies to a large number of non ionic
organic molecules with MW < 1000

1.3.1.1 Electron Impact Ionization .
Electron impact (EI) is the most widely used method for generating ions for mass spectrometry.
Vapor phase sample molecules are bombarded with high-energy electrons ( generally 70 Ev), which
eject an electron from a sample molecule to produce a radical cation, known as the molecular ion.
Because the ionization potential of typical organic componds is generally less than 15 Ev, the
bombarding electrons impart 50 eV (or more) of excess energy to the newly created molecular ion,
which have bond strengths between 3 and 10 Ev.
bond breaking is usually extensive and critically, highly reproducible, and critically, highly
reproducible, and characteristic of the compound. Furthermore, this fragmentation process is also
predictable and is the source of the powerful structure elucidation potential of mass
spectrometry.often, the excess energy imparted to the molecular ion is too great,which leads to a
mass spectrum with no discernible molecular ion. Reduction of the ionization voltage is a commonly
used strategy to obtain a molecular ion; the strategy is often successful because there is greatly
reduced fragmentation. The disadvantage of this strategy is that the spectrum changes and cannot
be compered to standard literature spectra.
to many, mass spectrometry is synonymous with EI mass spectrometry. This view is
understandable for two reasons. First,historically , EI was universally available before other
ionization methods were developed. Much of the early work was EI mass spectrometry. Second the
major libraries and databases of mass spectral data, which are relied upon so heavily and cited so
often, are of EI mass spectra. Some of the readily accessible databases contain EI mass spectra of
over 390,000 compounds and they are easily searched by efficient computer algorithms. The
uniqueness of the EI mass spectrum for a given organic compound, even for stereoisomers, is an
almost certainly. This uniqueness, coupled with the great sensitivity of the method,is what makes
GC-MS such a powerful and popular analytical tool.
1.3.1.2 Chemical Ionization
electron impact ionization often leads to such extensive fragmentation that no molecular ion is
observed. One way to avoid this problem is to use soft ionization techniques, of which chemical
ionization (Cl) is the most important. In Cl sample molecules (in the vapor phase) are not subjected
to bombardment by high energy electrons. Reagent gas (usually methane,isobutane, ammonia, but
others are used) is introduced into the source,and ionized. Sample molecules collide with ionized
reagent gas molecules (CH
5
+
, C
4
H
9
+
, etc) in the relatively high-pressure CI source, and undergo
secondary ionization by proton transfer producing an [ M + 1]+ ion, by electrophilic addition
producing [M + 15]+ ,[M + 24]+,[M + 43]+ , or [M + 18 ]+ (with NH4+) ions, or by charge exchange
(rare) producing a [M]+ ion. Chemical ionization spectra sometimes have prominent [M 1]+ ions
hydride abstraction . the ions thus produced are even electron species. The excess energy
transferred to the sample molecules during the ionization phase is small. Generally less than 5 eV, so
much less fragmentation takes place. There are several important consquances, the most valuable of
which are an abudance of molecularions and greater sensitity because the total ion current is
concentrated into a few ions. There is however, less information on structure. The quasimolecular
ions are usually quite stable and they are readily detected. Oftentimes there are only one or two
fragment ions produced and sometimes there are none.
for example, the EI mass spectrum of 3, 4-dimethoxyacetophenone (figure 1.3) shows, in
addition to the molecular ion at m/z 180,numerous fragment peaks in the range of m/z 15-167:
these include the base peak at m/z 165 and prominent peaks at m/z 137 and m/z 77. The Cl mass
spectrum (methane, CH4, as reagent gas) show the quasimolecular ion ([M + 1]+ . m/z 181) as the
base peak, m/z 180 , m/z 209 ([M + 29 ]+ or M + C2H5 +), and m/z 221 ([M + 41] + or M + C2H5+).
These last two peaks are a result of electrophilic addition of carbocations and are very useful in
indentifing the molecular ion. The excess methane carrier gas is ionized by electron impact to the
primary ions CH4+ and CH3+. These react with the excess methane to give secondary ions.
CH3+ + CH4 C2H5+ and H2
CH
4
+ C
2
H
5
+
C
3
H5 + and 2H2
The energy content of the various secondary ions (from, respectively, methane, isobutene, and
ammonia ) decrease in the order : CH
5
+
> t-C
4
H
9
+
> NH
4
+
. Thus,













3