A
mass spectrometer creates charged particles (ions) from molecules. It then
analyzes those ions to provide information about the molecular weight of
the compound and its chemical structure. There are many types of mass spectrometers
and sample introduction techniques which allow a wide range of analyses.
This discussion will focus on mass spectrometry as it's used in the powerful
and widely used method of coupling Gas Chromatography (GC) with Mass Spectrometry
(MS).
Pictured above is a GC/MS instrument used in the organic teaching labs.
A
mixture of compounds to be analysed is initially injected into the GC where
the mixture is vaporized in a heated chamber. The gas mixture travels through
a GC column, where the compounds become separated as they interact with
the column. The chromatogram on the right shows peaks which result from
this separation. Those separated compounds then immediately enter the mass
spectrometer.
CH3OH+.+
2 electrons
EI Ionization usually produces singly charged
ions containing one unpaired electron. A charged molecule which remains
intact is called the molecular ion. Energy imparted by the electron
impact and, more importantly, instability in a molecular ion can cause
that ion to break into smaller pieces (fragments). The methanol ion
may fragment in various ways, with one fragment carrying the charge and
one fragment remaining uncharged. For example:
CH3OH+.(molecular
ion) CH2OH+(fragment
ion) + H.
(or) CH3OH+.(molecular
ion) CH3+(fragment
ion) + .OH
Ion Analyzer
Molecular ions and fragment ions are accelerated by manipulation of the charged particles through the mass spectrometer. Uncharged molecules and fragments are pumped away. The quadrupole mass analyzer in this example uses positive (+) and negative (-) voltages to control the path of the ions. Ions travel down the path based on their mass to charge ratio (m/z). EI ionization produces singly charged particles, so the charge (z) is one. Therefore an ion's path will depend on its mass. If the (+) and (-) rods shown in the mass spectrometer schematic were ‘fixed' at a particular rf/dc voltage ratio, then one particular m/z would travel the successful path shown by the solid line to the detector. However, voltages are not fixed, but are scanned so that ever increasing masses can find a successful path through the rods to the detector.
A simple spectrum, that of methanol, is
shown here. CH3OH+. (the
molecular ion) and fragment ions appear in this spectrum. Major peaks
are shown in the table next to the spectrum. The x-axis of
this bar graph is the increasing m/z ratio. The y-axis is the relative
abundance of each ion, which is related to the number of times an ion of
that m/z ratio strikes the detector. Assignment of relative abundance
begins by assigning the most abundant ion a relative abundance of 100%
(CH2OH+ in this spectrum). All other ions are shown as
a percentage of that most abundant ion. For example, there is approximately
64% of the ion CHO+ compared with the ion CH2OH+
in this spectrum. The y-axis may also be shown as abundance (not
relative). Relative abundance is a way to directly compare spectra
produced at different times or using different instruments.
EI ionization introduces a great deal of energy into molecules. It is known as a "hard" ionization method. This is very good for producing fragments which generate information about the structure of the compound, but quite often the molecular ion does not appear or is a smaller peak in the spectrum.
Of course, real analyses are performed on compounds far more complicated than methanol. Spectra interpretation can become complicated as initial fragments undergo further fragmentation, and as rearrangements occur. However, a wealth of information is contained in a mass spectrum and much can be determined using basic organic chemistry "common sense".
Following is some general information which will aid EI mass spectra interpretation:
Molecular ion (M .+):If the molecular ion appears, it will be the highest mass in an EI spectrum (except for isotope peaks discussed below). This peak will represent the molecular weight of the compound. Its appearance depends on the stability of the compound. Double bonds, cyclic structures and aromatic rings stabilize the molecular ion and increase the probability of its appearance.
Reference Spectra: Mass spectral patterns are reproducible. The mass spectra of many compounds have been published and may be used to identify unknowns. Instrument computers generally contain spectral libraries which can be searched for matches.
Fragmentation:General rules of fragmentation exist and are helpful to predict or interpret the fragmentation pattern produced by a compound. Functional groups and overall structure determine how some portions of molecules will resist fragmenting, while other portions will fragment easily. A detailed discussion of those rules is beyond the scope of this introduction, and further information may be found in your organic textbook or in mass spectrometry reference books. A few brief examples by functional group are described (see examples).
Isotopes:Isotopes occur in compounds analyzed by mass spectrometry in the same abundances that they occur in nature. A few of the isotopes commonly encountered in the analyses of organic compounds are below along with an example of how they can aid in peak identification.
Relative
Isotope Abundance of Common Elements:
| Element | Isotope | Relative
Abundance |
Isotope | Relative
Abundance |
Isotope | Relative
Abundance |
| Carbon | 12C | 100 | 13C | 1.11 | ||
| Hydrogen | 1H | 100 | 2H | .016 | ||
| Nitrogen | 14N | 100 | 15N | .38 | ||
| Oxygen | 16O | 100 | 17O | .04 | 18O | .20 |
| Sulfur | 32S | 100 | 33S | .78 | 34S | 4.40 |
| Chlorine | 35Cl | 100 | 37Cl | 32.5 | ||
| Bromine | 79Br | 100 | 81Br | 98.0 |
Methyl Bromide: An example of how isotopes can aid in peak identification.
The ratio of
peaks containing 79Br and its isotope 81Br (100/98)
confirms the presence of bromine in the compound.
Sample introduction/ionization method:
| Ionization
method |
Typical
Analytes |
Sample
Introduction |
Mass
Range |
Method
Highlights |
| Electron Impact (EI) | Relatively
small volatile |
GC or
liquid/solid probe |
to
1,000 Daltons |
Hard method
versatile provides structure info |
| Chemical Ionization (CI) | Relatively
small volatile |
GC or
liquid/solid probe |
to
1,000 Daltons |
Soft method
molecular ion peak [M+H]+ |
| Electrospray (ESI) | Peptides
Proteins nonvolatile |
Liquid
Chromatography or syringe |
to
200,000 Daltons |
Soft method
ions often multiply charged |
| Fast Atom Bombardment (FAB) | Carbohydrates
Organometallics Peptides nonvolatile |
Sample mixed
in viscous matrix |
to
6,000 Daltons |
Soft method
but harder than ESI or MALDI |
| Matrix Assisted Laser Desorption
(MALDI) |
Peptides
Proteins Nucleotides |
Sample mixed
in solid matrix |
to
500,000 Daltons |
Soft method
very high mass |
Mass Analyzers:
| Analyzer | System Highlights |
| Quadrupole | Unit mass resolution, fast scan, low cost |
| Sector (Magnetic and/or Electrostatic) | High resolution, exact mass |
| Time-of-Flight (TOF) | Theoretically, no limitation for m/z maximum, high throughput |
| Ion Cyclotron Resonance (ICR) | Very high resolution, exact mass, perform ion chemistry |
Linked Systems:
| GC/MS: | Gas chromatography coupled to mass spectrometry |
| LC/MS: | Liquid chromatography coupled to electrospray ionization mass spectrometry |
Useful tools such as an exact mass calculator and a spectrum generator can be found in the MS Tools section of Scientific Instrument Services webpage.
The JEOL Mass Spectrometry website contains tutorials, reference data and links to other sites.
More general information and tutorials can be found in Scimedia, an educational resource.
At the University of Arizona, the Wysocki Research Group studies surface-induced dissociation (SID) tandem mass spectrometry.
Many more interesting and useful links can be found by following the site links in the above references.
If you have comments or suggestions,
email me at breci@u.arizona.edu