University of Vermont

CHEM 223: Mass Spectrometry

Chem 223 Syllabus Spring 2016
Chem 223

Spring 2016 - Course Syllabus & Overview

Class meets:

8:30-9:20 AM Mon., Wed. & Fri., Old Mill Annex (OMANEX) A202, January 20 - May 4, 2016.

Material to be covered in CHEM 223:

The purpose of CHEM 223 is to look "under the hood" of the mass spectrometer.

  • The majority of the CHEM 223 course will address how various types of mass spectrometers work and what are the components that make up a mass spectrometer. The primary areas to be covered in detail are
    • Methods to "ionize" or add a charge to a molecule
    • Analyzer types that separate charged molecules
    • Fragmentation of charged molecules
    • Fundamentals of charged molecules (exact mass and isotopic distribution)
    • Tandem mass spectrometry
    • Collisionally-induced dissociation and fragmentation of charged molecules
  • Other areas that will be covered are
    • vacuum systems
    • detector systems
  • Focus will be primarily on organic compounds and biologically relevant and important molecules.
    • Proteomics and protein and peptide analysis by mass spectrometry will be discussed specifically


No single text has been written that really covers mass spectrometry, but some texts are better than others. One problem is that published material becomes old within about 5 years of publication. Another problem is that most books are shallow in key areas. They are good surveys, but do not cover the details of the field in adequate depth for this course.

  • One book that is a reasonable introductory source and is useful to have is Edmond De Hoffmann & Vincent Stroobant, Mass Spectrometry: Principles and Applications,, 3rd ed., John Wiley, 2007
    • De Hoffmann is available on-line in paperback from a variety of sources including Amazon.Com
    • De Hoffmann is in Bailey-Howe (QD96.M3 H6413 2007).
  • Other sources are
    • Jürgen H Gross, Mass Spectrometry: A Textbook, 2nd ed., Springer-Verlag, 2011.
      • Not available in Bailey-Howe
      • Can be ordered on Amazon
    • J.Throck Watson & O. David Sparkman, Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th ed., John Wiley, 2007.
      • Watson & Sparkman is in Bailey-Howe (QC454.M3 W38 2007).
    • C. Dass, Fundamentals of Contemporary Mass Spectrometry, Wiley-Interscience, 2007. Somewhat shallow and expensive. Available from Amazon.Com


Dwight Matthews 656-8114
Cook Building - Room A121
Office hours: Scheduled per student need

How the course grade is determined:

There will be three tests throughout the semester as indicated on the schedule. All tests are take-home tests over a weekend. The last test will be handed out by 4/29/16 and is due back on 5/6/16.

The grade will be based upon the cumulative test points.

Course format:

  • The course covers introductory basic material about different types of mass spectrometers and their components.  There is no such thing as a single mass spectrometer in mass spectrometry.  There is a wide range of different instruments with different methods of producing ions, separating ions, and measuring ions.  The hope is that every student taking the course will have a good working knowledge of the fundamentals of mass spectrometry instrumentation when these lectures are complete.  This portion of the course is directed towards satisfying analytical chemistry graduate student requirements.
  • Lectures in the latter part of the course are directed towards proteomics and biological applications of mass spectrometry. This part of the course is directed towards graduate students in the biomedical sciences. However, because the biomedical applications of mass spectrometry are probably the most important applications, this information is also important to analytical chemistry students.
  • Each day's lecture notes will be available on line as a PDF file via the link shown on the left.
  • See the "Mass spec links" on the left for useful web site links about mass spectrometry.
    • Any student who finds either a web site that I do not have listed that is useful (and is not a commercial site pushing the benefits of a commercial product) or a relevant book at UVM that I don't have listed will receive 5 exam points added to their grade as a bonus for each web site or book that they turn in and is approved.

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