Mass spectrometry is a versatile analytical technique used to characterize molecules through determination of molecular weight, elemental composition, and presence of functional groups. It is used for mechanistic studies of gas-phase ion chemistry, as a detector coupled to chromatography instruments, and integrated into vacuum systems. Mass spectrometry involves the steps of sample introduction, ionization, mass analysis, and ion detection/data analysis.

1. Mass Spectrometry
A truly interdisciplinary and versatile
analytical method
MS is used
• for the characterization of molecules ranging from small inorganic and
organic molecules to polymers and proteins. With MS we might be able to
determine the molecular weight of a molecule ion, the elemental
composition of a molecule ion, and the presence of certain functional
groups.
• for mechanistic studies of gas-phase (ion) chemistry. This is also relevant
for a better understanding of the chemistry in our atmosphere and in space.
• as a mass detector coupled to a GC, HPLC, capillary electrophoresis (CE),
and thermo-gravimetric analysis.
• as an integrated mass detector in many high vacuum systems.

2. Dr Paul M. Mayer
Assistant Professor
Chemistry Department
University of Ottawa
UofW seminar speaker January 2002
The Gas-phase
ion chemistry
of cluster ions

3. History of MS Instrumentation
http://masspec.scripps.edu/information/history/

4. 1899 Early Mass Spectrometry;
1956 Identifying Organic Compounds with MS;
1964 GC/MS
1966 Peptide Sequencing
1974 Extraterrestrial Mass Spectrometry
1990 Protein Structure
1991 Non-Covalent Interactions with ESI
1992 Low Level Peptide Analysis
1993 Oligonucleotide Sequencing
1993 Protein Mass Mapping/Fingerprinting
1996 MS of a Virus
1999 Desorption/Ionization on Silicon
1999 Isotope-Coded Affinity Tags
History of MS Applications

5. MS Celebrities
1st
MS
Joseph John Thomson
(1856 - 1940)
Cambridge University,
Great Britain; Nobel
Prize in Physics 1906
Ion Chemistry
Francis William Aston
(1877 - 1945)
Cambridge University,
Great Britain; Nobel Prize
in Chemistry 1922
Ion Trap Technique
Wolfgang Paul
(1913 - 1993)
University of Bonn,
Germany; Nobel
Prize in Physics 1989
ESI of Biomolecules
John B. Fenn (1917)
Virginia
Commonwealth
University, Richmond,
Virginia
Fragmentation
Mechanisms
Fred W. McLafferty
(1923)
Cornell University
Ithaca, New York
Peptide Sequencing using MS
Klaus Biemann (1926)
MIT, Cambridge,
Massachusetts
MALDI
Franz Hillenkamp (1936)
University of Münster,
Germany
Mechanisms and Applications
R. Graham Cooks (1941)
Department of Chemistry,
Purdue University
West Lafayette, Indiana
Mechanism of MALDI
& ESI
Michael Karas (1952)
University of
Frankfurt, Germany

6. A mass spectrometer is an instrument that produces ions and separates them in
the gas phase according to their mass-to-charge ratio (m/z). Today a wide
variety of mass spectrometers is available but all of these share the capability to
assign mass-to-charge values to ions, although the principles of operation and
the types of experiments that can be done on these instruments differ greatly.
Basically, a mass spectrometric analysis can be envisioned to be made up of the
following steps:
Sample Introduction → Ionization → Mass Analysis → Ion Detection/Data
Analysis
Samples may be introduced in gas, liquid or solid states. In the latter two cases
volatilization must be accomplished either prior to, or accompanying ionization.
Many ionization techniques are available to produce charged molecules in the
gas phase, ranging from simple electron (impact) ionization (EI) and chemical
ionization (CI) to a variety of desorption ionization techniques with acronyms
such as FAB (fast atom bombardment), PD (plasma desorption), ES
(electrospray) and MALD (matrix assisted laser desorption).
The following pages are in part from http://ms.mc.vanderbilt.edu/tutorials/ms/
Basic Concepts

7. Mass spectrometers are operated at reduced pressure in order to prevent
collisions of ions with residual gas molecules in the analyzer during the
flight from the ion source to the detector. The vacuum should be such that the
mean free path length of an ion, i.e., the average distance an ion travels
before colliding with another gas molecule, is longer than the distance from
the source to the detector. For example, the mean free path length of an
ion is approximately one meter at a pressure of 5x10-5
torr, i.e. about
twice the length of a quadrupole instrument.
Thus, the introduction of a sample into a mass spectrometer usually requires
crossing of a rather large pressure drop, and several means have been
devised to accomplish this.
Gas samples may be directly connected to the instrument and metered into
the instrument via a needle valve. Liquid and solid samples can be introduced
through a septum inlet or a vacuum-lock system. However, when connecting
continuous introduction techniques like gas chromatography (GC), high
performance liquid chromatography (HPLC) or capillary electrophoresis (CE),
special interfacing becomes imperative to prevent excessive gas load.
Sample Introduction

8. Organic Structural Spectroscopy by Lambert, Shurvell, Lightner

9. Ionization
The deciding criteria are often the following:
1. Physical state of the sample
2. Volatility and thermal stability of the sample
3. Type of information sought
Comparison
• EI, CI, and DI are suitable for high resolution MS;
• EI works well only for thermally stable and volatile samples;
• CI, SI, and DI cause much less fragmentation (normally no radicals are formed);
• DI and SI must be combined with tandem mass detection (MS-MS) to extract
more structural information from fragmentation;
Organic Structural Spectroscopy by Lambert, Shurvell, Lightner

10. Electron Impact Ionization (EI)
purely physical
processes!

11. The ionization energies of many compounds are on the order of 7-14 eV but
electron energies of 70 eV are often chosen for EI-MS to achieve higher signal
intensities and to avoid changes in the mass spectrum with small changes in
electron energy.
The energy domain: 1 J (kg m2
s-2
) = 6.24145 x 1018
eV
1 J mol-1
= 1.03641 x 10-5
eV
energies of chemical bonds are typically between 100 and
600 kJ mol-1
(C-H = 435 kJ mol-1
; C-O = 356 kJ mol-1, C-N
= 305 kJ mol-1
), which are equivalent to 1-6 eV
The time domain: a 70 eV electron has a velocity of about 5 x 108
cm s-1
and
transits a molecule of 1 nm length in 2 x 10-16
s, while a typical
bond vibration requires >10-12
s;
thus, the molecular conformation remains unchanged as the
electronic excitations occurs (Franck-Condon principle)
The degree of fragmentation depends on the internal energy deposition in
the molecular ion and on the resistance of the molecular structure to bond
cleavage (fragmentation).

12. Schematic representation of an electron ionization ion source. M represents neutral
molecules; e-, electrons; M+· , the molecular ion; F+, fragment ions; Vacc,
accelerating voltage; and MS, the mass spectrometer analyzer.

13. Schematic representation of an electron ionization ion source.
sample pressure in the ion source
is about 10-5
torr
about every 1/1000
molecule is ionized
only cations
the sample is heated
up until a sufficient
vapour pressure is
obtained

14. Organic Structural Spectroscopy by Lambert, Shurvell, Lightner
Advantages & Disadvantages of EI-MS

15. Contrasting degrees of fragmentation depending on the chemical structure
Radical cations of aromatic and unsaturated conjugated hydrocarbons resist
fragmentation more than radical cations of saturated hydrocarbons

16. Lowering the electron beam energy to approximately 15 eV does not
necessarily result in the observation of a molecular ion.
It does, however, change
the probability of different
fragmentation pathways.
Here, the H-rearrangement
wins at the expense of
single-bond cleavage.
CH2=CHCH2CH3
+
+ CH3COOH
CH3C=O+
+
•OCH2CH2CH2CH3

17. The Molecular Ion in EI-MS
Index of hydrogen deficiency (degree of unsaturation)
The index of hydrogen deficiency is the number of pairs of hydrogen atoms that
must be removed from the corresponding saturated formula to produce the
molecular formula of the compound of interest. The index is the sum of the
number of rings, double-bonds, and twice the number of triple bonds.
Compounds can contain C, H, N, O, halogen, and S.
Index = tetravalent (C, Si) - ½ monovalent (H, halogen) + ½ trivalent (N, P) + 1
Bivalent atoms such as O and S do not contribute.
The nitrogen rule
Molecular ions containing odd numbers of nitrogen must have an odd number m/z.
Example
The compound with the molecular formula C7H7NO has an index of ??
Note that a benzene ring counts for an index of 4, 3 double bonds and one ring!
What are possible structures?

18. The isotopic signature – recognition of elements