The Mass Spectrometry Primer

Understanding Mass Spectrometry

This primer covers a wide range of topics related to modern mass spectrometry practices and answers some frequently asked questions about the use and capabilities of mass spectrometers. Links are also provided to articles written for non-specialists for more in-depth reading. The first section examines who uses mass spectrometers followed by how compounds are ionized in the source to be analyzed by mass spectrometers. A description of the various types of mass spectrometers is next and a discussion of the important topics of mass accuracy and resolution - or how well we can tell differences between closely related compounds. Chemistry, sample prep and data handling are considered as well as the definition of some terms commonly in use in the most prevalent forms of MS practice today.


A Brief History of Mass Spectrometry

  • 1897 – Modern mass spectrometry (MS) is credited to the cathode-ray-tube experiments of J.J. Thomson of Manchester, England.
  • 1953 – Wolfgang Paul’s invention of the quadrupole and quadrupole ion trap earned him the Nobel Prize in physics.
  • 1968 – Malcolm Dole developed contemporary electrospray ionization (ESI) but with little fanfare. Creating an aerosol in a vacuum resulted in a vapor that was considered too difficult to be practical. Liquid can represent a volume increase of 100 to 1000 times its condensed phase (1 mL/min of water at standard conditions would develop 1 L/min of vapor).
  • 1974 – Atmospheric pressure chemical ionization (APCI) was developed by Horning based largely on gas chromatography (GC), but APCI was not widely adopted.
  • 1983 – Vestal and Blakely’s work with heating a liquid stream became known as thermospray. It became a harbinger of today’s commercially applicable instruments.
  • 1984 – Fenn’s work with ESI was published leading to his Nobel Prize-winning work published in 1988.

For more historical detail see


Who Uses MS?

Before considering mass spectrometry (MS), you should consider the type of analyses you perform and the kind of results you expect from them:

  • Do you want to analyze large molecules, like proteins and peptides, or acquire small, aqueous-molecule data?
  • Do you look for target compounds at a determined level of detail, or do you want to characterize unknown samples?
  • Are your current separations robust, or must you develop methods from complex matrixes?
  • Do you require unit mass acuracy-say, 400 MW-or accuracy to 5 ppm, as in 400.0125 MW (or 2 mDa at mass 400)?
  • Must you process hundreds of samples a day? Thousands? Tens of thousands?


The ability to determine an analyte's character increases with instrument capability.


Researchers and practitioners from various disciplines and subdisciplines within chemistry, biochemistry, and physics regularly depend on mass spectrometric analysis. Pharmaceutical industry workers involved in drug discovery and development rely on the specificity, dynamic range, and sensitivity of MS to differentiate closely related metabolites in a complex matrix and thus identify and quantify metabolites. Particularly in drug discovery, where compound identification and purity from synthesis and early pharmacokinetics are determined, MS has proved indispensable.

Biochemists expand the use of MS to protein, peptide, and oligonucleotide analysis. Using mass spectrometers, they monitor enzyme reactions, confirm amino acid sequences, and identify large proteins from databases that include samples derived from proteolytic fragments. They also monitor protein folding, carried out by means of hydrogen-deuterium exchange studies, and important protein-ligand complex formation under physiological conditions.

Clinical chemists, too, are adopting MS, replacing the less-certain results of immunoassays for drug testing and neonatal screening. So are food safety and environmental researchers. They and their allied industrial counterparts have turned to MS for some of the same reasons: PAH and PCB analysis, water quality studies, and to measure pesticide residues in foods. Determining oil composition, a complex and costly prospect, fueled the development of some of the earliest mass spectrometers and continues to drive significant advances in the technology.

Today, the MS practitioner can choose among a range of ionization techniques which have become robust and trustworthy on a variety of instruments with demonstrated capabilities.

See MS - The Practical Art, LCGC (

    • Profiles in Practice Series: Metabolism ID and Structural Characterization in Drug Discovery, Vol. 23, No. 2, February 2005
      • Why this is important: Illustrates and contrasts approaches used in metabolite identification practice as described by two leading practitioners.

    • Profiles in Practice Series: Stewards of Drug Discovery-Developing and Maintaining the Future Drug Candidates, Vol. 23, No. 4, April 2005
      • Why this is important: Compares developing and handling drug candidate compounds and libraries from the viewpoint of a large pharmaceutical company and a small specialty company.

    • Profiles in Practice Series: A Revolution in Clinical Chemistry, Vol. 23 No. 8 August 2005
      • Why this is important: Health care professionals have recently embraced MS as a means to greatly improving the accuracy, speed, and quality of patient information but it is a work-in-progress.

  • Profiles in Practice Series: Advances in Science and Geopolitical Issues (Food Safety), Vol.23 No. 10 October 2005
    • Why this is important: As instruments become more robust and sensitive, MS is changing the ways of regulated testing with far reaching global consequences.

Next >

What is MS and How does it Work? MS Primer - What is MS and How does it Work?
Common Ionization MS Primer - Common Ionization
Biomolecular Ionization Methods MS Primer - Biomolecular Ionization Methods
Alternative Ionization Means MS Primer - Alternative Ionization Means
Data Handling MS Primer - Data Handling
Mass Accuracy and Resolution MS Primer - Mass accuracy and resolution
Interpreting Mass Spectrometer Output MS Primer - Interpreting mass spectrometer output
Quantitation and Calibration MS Primer - Quantitation and Calibration
Solvents and Caveats for LC/MS MS Primer - Solvents and Caveats for LC/MS
Glossary MS Primer - Glossary
Acknowledgments MS Primer - Acknowledgments
What Types of Instruments Are Used? MS Primer - What Types of Instruments are Used?

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