1. 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.

2. 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 Mass Spectroscopy/Spectrometry 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.

3. A Basic Mass Spectrometer Schematic Animations of MS (& other techniques): http://spider- dev.pharmacy.strath.ac.uk/mscpharmanal/sample.htm

4. http://www.chemistry.ccsu.edu/glago vich/teaching/472/ms/images/spectro meter.gifwww.chemistry.ccsu.edu/glago vich/teaching/472/ms/images/spectro meter.gif A More Detailed Mass Spectrometer

6. Mass Spectrometry Bulletin: http://www.rsc.org/Publishing/CurrentAwareness/msb/index.asp MS Basics: http://web.njit.edu/~hsieh/ene669/gc_ms.htmlhttp://web.njit.edu/~hsieh/ene669/gc_ms.html MS Basics in Denmark: http://130.237.33.129/klab/Kvantfysik_5A1450/var_labbar.htm MS Basics PPTs, College of Charleston, Dept. of Chemistry : http://www.cofc.edu/~chem/organic/Slides/MS1/index.htm http://www.cofc.edu/~chem/organic/Slides/MS2/index.htm http://www.cofc.edu/~chem/organic/ Slides/MS3/index.htm University of Calgary MS Basics: http://www.chem.ucalgary.ca/courses/351/Carey/ Ch13/ch13-ms.html MS Basics & Theory http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm http://www.udel.edu/chem/koh/chem333docs/MSlect1pp.pdf http://www.files.chem.vt.edu/chem-ed/crossref/ac-mass-spec.html

7. 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. Volatilizing & Ionizing Samples

8. 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. Getting Polymers to Take Flight

9. 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. Validation Issues

10. Introduction to MS, Scripps: http://masspec.scripps.edu/information/index.html More Advanced Treatments of MS http://www.psrc.usm.edu/mauritz/maldi.html Introduction to MALDI: http://prospector.ucsf.edu/ Protein MS Tools: http://winter.group.shef.ac.uk/chemputer/isotopes.html

11. http://www-methods.ch.cam.ac.uk/meth/ms/theory/sector.html Double Focusing MS Schematic

12. http://www.york.ac.uk/depts/biol/tf/analbio_ms.htm Applied Biosystems 4700 Proteomics Analyzer, MALDI -TOF/TOF™ tandem mass spectrometer

13. http://www.fastcomtec.com/ fwww/tofmas/wrecmas.htm Example of MS/MS Schematic In MS/MS the initially ionized sample is passed through a 2 nd ionization stage to further fragment initially formed ions yielding more structural detail.

14. MS vs MS/MS Analysis: http://www-helix.inrialpes.fr/article386.html Use of MALDI-TOF 1 st followed by MS/MS in proteomics: http://bmbus6.leeds.ac.uk/www/presentations/MassSpec /index.htm http://www.ionspec.com/Applications/applications_info.htm Proteomics & nucleic acid work often require use of MS/MS after initial MS.

15. www.chm.bris.ac.uk/pt/diamond/image/mwmbms.gif Plasma Injector

16. www-methods.ch.cam.ac.uk/.../ theory/iontrap.html The Ion Trap

17. http://www.ansto.gov.au/ansto/environment1/ams/index.html ANTARES Accelerator Mass Spectrometer

18. http://www.elementalanalysis.com/icp/ ICP-MS Detection Limits

19. Epigenotyping using MS: http://www.epigenome.org/index.php?page=epigenotyping1 Biological Mass Spectrometry: http://www.amolf.nl/research/biologica l_mass_spectrometry/main.html Archaeometry Laboratory U. of MO Research Reactor: http://www.missouri.edu/~rjse10/home.htm Proteomics & MS: http://www.mrc-dunn.cam.ac.uk/research/proteomes.html DNA Sequencing: http://www.cs.sunysb.edu/~skiena/648 /presentations/massspec/dna.html http://www.cs.sunysb.edu/~skiena/648 /presentations/massspec/dna.html Pesticide Analysis: http://www.epa.gov/nerlesd1/chemistry/ org-anal/reports/regmsf/regmsf.htm http://www.epa.gov/nerlesd1/chemistry/ org-anal/reports/regmsf/regmsf.htm BioMS at UMass: http://www.umass.edu/karbon13/index.htm Mass Spectroscopy Applications

20. Analytical Microscopy: http://www.nrel.gov/measurements/analytical.html Fragmantation patterns of organic ions: http://poohbah.cem.msu.edu/courses/CEM924JA/ Fan_Shuan2/organic/index.htm Related Topics

21. Crystallography: Heavy Atom Substitution: http://cns.csb.yale.edu/v1.0/tutorial/text.html TEM Staining: http://www.lehigh.edu/~ols0/tem/staining.html http://www.aecom.yu.edu/iag/samples/files/TEM.html http://www.cimc.cornell.edu/Pages/Gallery.htm http://www.pegacat.com/cbetts/phd/index.html X-ray, Ultrasound, & MRI Contrast Media Other Mass-Dependent Methods