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Mass Labels

While Mass Spectroscopy is not covered in our texts, other mass/density dependent technologies including X-ray Spectroscopy, Gamma Spectroscopy, & Ultrasound Analysis are covered in Guy & ffytche, An Introduction to The Principles of Medical Imaging, Imperial College Press, 2000, Chapters 4,5 & 7.

Other coverage is also found in Shung, Chapters 1, X-ray, & 2, Ultrasound, in Shung, Smith, Tsui, Principles of Medical Imaging, Academic Press, 1992.


Mass Spectroscopy/Spectrometry

  • This method uses one of several means to:
  • vaporize a sample
  • ionize &/or fragment it
  • introduce it into a low vacuum space
  • sort the fragment ions based on charge to mass ratio, m/z
  • detect the ions impinging on a charge or photosensitive device, e.g., film or photodiodes

Note that heavy isotopes yield higher m/z for a given compound, yielding multiple MS peaks with heights proportional to the abundance of the isotopes.


A Basic Mass Spectrometer Schematic

Animations of MS (& other techniques):


A More Detailed Mass Spectrometer


MS Basics & Theory

MS Basics in Denmark:

University of Calgary MS Basics:

MS Basics:

MS Basics PPTs, College of Charleston, Dept. of Chemistry: Slides/MS3/index.htm

Mass Spectrometry Bulletin:


Volatilizing & Ionizing Samples

MS methods differ with respect to complexity of the molecules that can be evaluated & with respect to the sensitivity of the methods. The more energy introduced in volatilizing & ionizing the sample the more likely molecules, especially large ones, will fragment. While smaller molecules may be introduced directly into the MS ionization chamber as pure compounds or as simplified mixtures resulting from the use of gas chromatographs upstream from the ionization chamber, this is not possible for most high polymers. The parent peak from the ion formed when the entire molecule looses only 1 electron provides molecular mass information. It is often vital to the analysis to find this peak which may only form under relatively “gentle” conditions.


Getting Polymers to Take Flight

Macromolecules may be introduced into the ionization chamber as pure materials or as simplified mixtures filtered through upstream high performance or liquid chromatographs. They may also be lifted from surfaces directly & used to examine surface compositions.

The surface itself may be modified to assist volatilization & ionizatin by absorbing much of the thermal energy of the ionization source (laser, microwave, …) &/or by capturing electrons from the macromolecules to generate ions secondarily.MALDI, matrix assisted laser desorption ionization, uses easily volatilized & ionized organics such as cinnamic acid, gentisic acid, & sinapinic acid to improve movement of macromolecules such as peptides from a surface to the ion stream. Nucleic acids may be examined similarly.


Validation Issues

Calibration for accuracy requires examination of molecules with known parent peak m/z & known fragmentation patterns. For more complex molecular mixtures it also requires inclusion of internal calibration molecules that provide reference peaks from which to mark m/z positions, e.g., digestive enzyme fragmentation peaks in protein digestion experiments. Note that MS methods may not have uniform sensitivity across the entire m/z range of interest; thus, multiple calibration or reference peaks may be needed. Fragmentation is also frequently run as a series of pulses each of which generate a set of data & noise peaks. Digital accumulation of pulse results accentuate true peaks & enhance sensitivity by increasing precision & specificity.


More Advanced Treatments of MS

Introduction to MS, Scripps:

Introduction to MALDI:

Protein MS Tools:


Double Focusing MS Schematic


Applied Biosystems 4700 Proteomics Analyzer,

MALDI -TOF/TOF™ tandem mass spectrometer


Example of MS/MS Schematic

In MS/MS the initially ionized sample is passed through a 2nd ionization stage to further fragment initially formed ions yielding more structural detail.


Proteomics & nucleic acid work often require use of MS/MS after initial MS.

Use of MALDI-TOF 1st followed by MS/MS in proteomics:

MS vs MS/MS Analysis:


Plasma Injector


The Ion Trap theory/iontrap.html


ANTARES Accelerator Mass Spectrometer


ICP-MS Detection Limits


Pesticide Analysis:

Mass Spectroscopy


Biological Mass Spectrometry:

BioMS at UMass:

Proteomics & MS:

DNA Sequencing:

Epigenotyping using MS:

Archaeometry Laboratory U. of MO Research Reactor:


Related Topics

Fragmantation patterns of organic ions:

Analytical Microscopy:


Other Mass-Dependent Methods

Crystallography: Heavy Atom Substitution:

TEM Staining:

X-ray, Ultrasound, & MRI Contrast Media