66218 - Mass Spectrometry with Exercises

Course Unit Page

  • Teacher Guido Galletti

  • Credits 6

  • SSD CHIM/01

  • Teaching Mode Traditional lectures

  • Language Italian

Academic Year 2018/2019

Learning outcomes

At the end of the course, students are able to explain electron ionization mass spectra of the principal classes of organic molecules and to recognize spectra obtained by other ionization techniques. About the instrumental part of mass spectrometry, they know: (a) the main parts of the instrument (ion sources and analyzers, detectors, vacuum pumps); (b) fundamentals of mass spectrometer functioning; (c) applications of mass spectrometry to analytical problems.

Course contents

Students are required to have a good knowledge about math, stoichiometry, fundamentals of chemistry, and organic chemistry. Foreign students should master Italian (writing, speaking and listening) at a C1-level.


The course starts with practice (24 hours - 2 CFU) and carries on with lectures (32 hours - 4 CFU), both held in the classroom. 

a) Practice (24 hours - 2 CFU).

  1. EI-MS interpretation.
  2. Interpretation of EI mass spectra. Even- and odd-electron ions. Molecular ion identification. Ion abundances. Stevenson rule with exceptions. Gamma-hydrogen rearrangement. Tropylium and aza-tropylium ions. Even-electron rule. H- and McLafferty rearrangement. Multiple rearrangements (e.g., phthalates, tributylphosphate). Examples of mass spectra of the main classes of compounds: saturated and unsaturated hydrocarbons, alcohols, carboxylic acids, esters, amines. aromatics, pyridines, pyrroles, fluorinated, chlorinated and brominated cpds. Identification of unknown compounds.
  3. Identification of unknown compounds by searching mass spectra in NIST library database (parameters used to compare the unknown spectra with the library ones).
  4. Examples of practical solutions of analytical problems through GC/MS.

b) Lectures (32 hours - 4 CFU).

  1. Students are motivated to study mass spectrometry. Application and fundamentals of mass spectrometry. Diagram of a mass spectrometer. Definition of average mass, nominal mass, monoisotopic mass, and exact mass. Isotopic ions (A+2 rule): e.g. bromobenzene.
  2. Ion sources. Electron Ionization (EI). Chemical Ionization (CI). Field Ionization (FI). Field Desorption (FD). Fast Atom Bombardment (FAB). Continuous Flow FAB. Matrix Assisted Laser Desorption Ionization (MALDI): chemical structure of principal matrixes, calibration compounds spectra, mass spectra resolution, monoisotopic masses and average masses, adduct ions, cationized ions, multicharged ions. ThermoSpray Ionization (TSP). ElectroSpray Ionization (ESI) (multicharged ions recognize and methods to calculate the number of charges). Atmospheric Pressure Chemical Ionization (APCI). Particle Beam (PB). Inductively Coupled Plasma Ionization (ICP). Examples of mass spectra are shown when necessary.
  3. Ion analyzers. Magnetic analyzer (B): equation which describes the action of a magnetic field on a moving ion, resolution, metastable ions. Electrostatic analyzer (E): equation which describes the action of an electrostatic field on a moving ion. Energy and angular dispersions. Double focusing instruments EB and BE. IKE and MIKE spectra. Resolution: definitions, high and low resolution. Linked scan B/E, B2/E, [B2(1-E)]/E2. Quadrupole analyzer (Q): equation of ion motion in a quadrupolar field, Mathieu diagram for a bi-dimensional quadrupole. Multipole radiofrequency-only guides (Multipole Rf-only guides). Tandem Mass Spectrometry (MS2) using a triple quadrupole analyzer (QQQ). Ion Trap analyzer (ITMS): equation of ion movtion, Mathieu diagram for an ion trap, ion analysis by resonant ejection i and instability ejection. MS2 and MSn in an ion trap by resonant ejection. Ion trap as a single device for both ion production and analysis. Automatic control of the filament current emission in electron ionization (automatic gain control). Time of Flight analyzer (TOF): equation of ion motion, delayed extraction (DE), reflectron, post source decay (PSD). Fundamentals of Ion Cyclotrone Resonance (ICR) and Orbitrap.
  4. Hyphenated techniques: gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS).


E. de Hoffmann, V. Stroobant, Mass Spectrometry – Principles and Applications, Third Edition, Wiley, 2007. (*)

T.A. Lee, A Beginner's Guide to Mass Spectral Interpretation, Wiley, 1998. (*)

F. W. McLafferty, F. Turecek, Interpretation of Mass Spectra, University Science Books, Fourth Edition, 1993. (°)

J. H. Gross, Mass Spectrometry – A textbook, Springer, Second Edition, 2011. (^)

J. T. Watson, O. D. Sparkman, Introduction to Mass Spectrometry – Instrumentation, Applications and Strategies for Data Interpretation, Wiley, Fourth Edition, 2007. (^)

R. E. March, J. F. J. Todd, Practical Aspects of Trapped IonMass Spectrometry, Volume V, Applications of Ion Trapping Devices, pp 491-507, CRC Press, 2010. (^)

O. D. Sparkman, Z. E. Penton, F. G. Kitson, Gas Chromatography and Mass Spectrometry – A Practical Guide, Academic Press, Second Edition, 2011. (^)

M. C. McMaster, LC/MS – A Practical User's Guide, Wiley, 2005. (^)

R. B. Cole, Electrospray and MALDI Mass Spectrometry – Fundamentals, Instrumentation, Practicalities, and Biological Applications, Wiley, Second Edition, 2010. (^)

(*) The text contains sections that students have to study to pass the exam.

(°) The text contains sections useful to pass the exam.

(^) The text is not necessary to pass the exam, but contains sections which may be useful for future focusing.

Teaching methods

The course consists of 32 hours of lectures and 24 hours of practice. The lectures provide explanations about the following topics (a) theory, instrumentation and applications of mass spectrometry (basics, mass spectrum representation, techniques for ion production and separation, detectors); (b) methods for the interpretation of mass spectra of organic compounds as obtained by electron ionization and other ionization techniques. During the practice, the students learn how to interpret EI spectra and the features of the EI spectra of the main classes of substances. They also learn the characteristics of the spectra generated by other ionization methods, such as CI, MALDI and ESI.

Assessment methods

Students are encouraged to attend practice and lectures. Small groups of students, according to an agenda to be set in due time, will deliver short presentations about topics to be decided by the teacher. Such presentations will earn the students 1/30 score.

Intermediate written test.

Two written tests are delivered to the students who attended at least 90% of the preceding practice/lectures, the first one at the end of the practice, the second one at the end of the course. Tests are not mandatory, but students are encouraged to take part. Tests are an alternative to final exams.

The first test includes a simple problem on GC/MS quantitation methods and concentration units and interpretation of EI mass spectra previously discussed. Maximum total score: 31/30.

The second test is about the lecture subjects. Maximum score: 31/30. Students who failed test 1 will have to solve the problems and the mass spectral interpretation of the first test.


A written test (corresponding to intermediate test-1) has to be passed with minimum 18/30 to immediately access to an oral examination on the lecture subjects. Both written and oral scores must be sufficient for the exam to be passed. Books, notes and cell phones are not allowed during written and oral exams.

Final score.

Test scores are weighed by the credits of the corresponding part of the course, summed, averaged and the score of the student presentation is added. A final score results which is directly entered in the student record. Honors are assigned when the final score is 31.5/30, at least. Students are failed when either intermediate test-1 or test-2 (viz. written and oral part of the official exams) are insufficient.

Results of intermediate tests 2017/2018.

Students: 60.

Participants: 51.

Pass: 45;

with 30-30+honors score: 25;

with 27-29 score: 10;

with 23-26 score: 10.


Teaching tools

Blackboard; transparencies; power-point and other similar softwares; instruments which can be studied and/or used in laboratory.

Teaching materials published on Insegnamenti On-Line (IOL) web site.

Office hours

See the website of Guido Galletti