Reading Notes for Mass Spectrometry Articles


Van Bramer, S.E. An Introduction to Mass Spectrometry

This is a chapter I have written on mass spectrometry. Read this carefully.


Lambert, J.B.; Shurvell, H.F.; Lightner, D.A.; Cooks, R.G. Organic Structural Spectroscopy; Prentice-Hall: Upper Saddle River, NJ, 1998.

This section was written by R. Graham Cooks, one of the leading experts in mass spectrometry. It is very through.
  1. Chapter 13. This chapter discusses the instrumentation and basic chemistry involved in mass spectrometry. Section 1 is an introduction to mass spectrometry, section 2 discusses how samples are introduced to the instrument, section 3 is on ionization, section 4 is on mass analyzers. Read this chapter carefully.
  2. Chapter 14. This chapter discusses both unimolecular and intermolecular chemical reactions of gas phase ions. Don't forget your organic chemistry when looking at this chapter. Read section 1 carefully, sections 2, 3 and 4 discuss fragmentation observed for various functional groups, skim this and then use as a reference. Skip section 5 & 6. Section 7 provides an in depth look at ion chemistry, reading this carefully will show you how mass spectrometry demonstrates important principals of organic and physical chemistry.
  3. Chapter 15. This chapter models how to use mass spectrometry to identify a molecular structure. Read it carefully and use it as a guide when identifying unknowns and when proving your structures. Secctions 5, 6, 7 and 8 discuss some interesting applications of mass spectrometry.


Low Energy, Low Temperature Mass Spectra 6-A Synoptic View. (Maccoll, A. Org. Mass Spectrom.,21, 1986, 601-612)

This article describes experimental details and presents data for low energy, low temperature mass spectrometry. The article focuses on how additional structural information may be obtained from low energy electron ionization because the amount of fragmentation is reduced. In addition, the fragmentation that does occur is more likely to be low energy rearrangements.

This article is the basis for the Electron Ionization Energy Mass Spectrometry Experiment. Experimental data is presented for several of the compounds that we will be studying and this article should serve as a reference to judge the results of our experiment.

  1. Introduction. This paper is part of a series of articles presenting low energy EI data for different functional groups. In this article, the results from all these previous papers are summarized. The introduction addresses why low energy EI is useful, and some of the drawbacks of this technique.

  2. Experimental. This section discusses the experimental details of the experiment. Special attention is paid to calibration of the electron beam energy. Problems with publishing spectra without calibrating the electron beam are mentioned. Notice the details provided here and think about how we can obtain this information during our experiment.

  3. Results and Discussion In this section the low energy mass spectra for a variety of different compounds are analyzed. Data is presented in tabular form and in spectra. You should pay careful attention to the data for the compounds that we are studying. Don't worry about the rest of the results. Notice how the information is presented in the text. How the tables are useful for observing trends. And how the spectra are useful for observing patterns.

    The following functional groups are discussed:

    1. Alkanes
    2. Alkanols
    3. Ethers
    4. Amines
    5. Alkanals
    6. Alkanones
    7. Alkanonic acids
    8. Alkanoates

  4. Conclusions

Chemical Ionization Mass Spectrometry. I. General Introduction. (Munson, M.S.B.. J. Am. Chem. Soc.,88, 1966, 2621-2630)

This is the original journal article presenting the technique of chemical ionization. It is the basis for the Chemical Ionization Mass Spectrometry Experiment. In this technique, a reagent gas is introduced to the source region of the mass spectrometer. This reagent gas is ionized and forms highly reactive gas phase ions. These ions react with the analyte to produce adduct ions. This paper describes the experimental details and the results of this experiment. Pay close attention to the experimental details and the results for the compounds we will be studying.

  1. Introduction. This section describes the basic idea for chemical ionization. Notice Figures 1 and 2. Think about how this will relate to your experiment. Also notice which ions are produced by reactions of the methane reagent gas. What impact will this have on our mass spectra? Will this cause any problems? If so, how can we avoid them. The theory of chemical ionization is presented in terms of acid base reactions to describe the proton exchange. If you do not remember the different models for acid/base chemistry (Bronsted and Lewis) look them up in your general chemistry book.

  2. Experimental Section. This section describes the apparatus, how it was constructed, how it was run. This section contains lots of clues about how to configure our instrument to run the experiment. Make notes of the parameters that seem to be important.

  3. Spectra and Discussion. Notice how the experimental data is presented and what background information is provided. Look at the results for the compounds that we will be studying so that you may compare it with our data. What peaks do you expect to find in our samples?

  4. Analysis of Mixtures. This section discusses the possibility of analyzing mixtures of compounds with CI. You may skip this section.

  5. Other Reactant Gases. Discusses other reagent gases that may be useful.

  6. Conclusions

Basics of MS-MS (Busch, K.L. Spectroscopy, 13, 1998, 16-18)

This paper is a nice introduction to how tandem mass spectrometry experiments are used to obtain additional structural information from an unknown and to increase the selectivity of the mass spectrometer for chromatography experiments.


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Scott Van Bramer
Department of Chemistry
Widener University
Chester, PA 19013

Please send any comments, corrections, or suggestions to svanbram@science.widener.edu.

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