CHEM 5181

Info for homeworks
• Template for Journal Skims (.doc)
• Introduction to Igor (D. Sueper, 11-Sept-07)
• Igor Programming Conventions (v2, 20-Aug.-2009)
• Tips for Student Presentations (.pdf from 07-Sept-06)

2009 Homeworks
1. HW1: Igor & Review of Fundamentals
2. HW2: Simulation of Simple Electric Sector
3. HW3: Review of Prerequisites (not graded)
4. HW4: TOFMS Simulation: Basics and Delayed Extraction
5. HW5: Ionization Techniques

Older HW for reference
1. Mass Analysis Methods .doc OR .pdf
2. Ionization Methods
3. Homework #3: Quad Simulation - Part 1
   • 4th order Runge-Kutta Integration Method
4. Checklist for Interpretation Homeworks
5. Interpretation 1 (EC)
6. Interpretation 2 (EC)
7. Interpretation 3 (EC)
8. Interpretation 4 (MI)
9. Interpretation 5 (Frag. Mech.)
10. Chromatography Theory

1. Lab 1: MALDI-TOFMS: Pre-Lab and Lab
2. Lab 2: Electrospray MS: Pre-Lab, Lab, and Pulsar Instrument instructions
3. Lab 3: GC-MS of mixtures
4. Final Project Organization

1. Lecture Intro-1: Intro to Course and Intro to Igor
2. Lecture Intro-2: Numerical Integration in Igor
3. Lecture Intro-3: Review of Fundamentals
   • Regression Demo Program (PC Download)
   • Non-Parametric Regression Demo (Web)
   • Least Squares Polynomial Approximation Demo (Web)
   • Central Limit Theorem Demo (Web)
   • Fourier Synthesis Demo (Web)
   • Fourier Analysis Demo (Web)

Part I: MS Methods and Instrumentation

1. Mass Analyzers I: Intro to MS and Time-of-Flight MS
   • Mass Spec. Oscilloscope Simulator (PC Download)
2. Mass Analyzers II: Sector, FTICR, Orbitrap
   • Simulator of Magnetic Sector MS (PC Download)
3. Ionization I: Fundamentals of Ionization and Electron Ionization (EI)
   • Ion Optics Simulator (PC Download)
4. Ionization II: Chemical Ionization & Related Atmospheric Pressure Methods (J. Kimmel)
5. Electrospray (ESI) (S. Kato)
6. Ionization IV: Ionization Methods IV: Bombardment, MALDI and Elemental (J. Kimmel)
7. Mass Analyzers IV: Quadrupole
   • Video of Agilent Quadrupole LC-MS
   • Video of Agilent Triple Quadrupole LC-MS

Lectures from Previous Years for Reference
1. Introduction to Mass Spectrometry (Theory and Figures of Merit)
2. Mass Analyzers I (TOFMS)
3. Mass Analyzers II (Quadrupoles)
4. Review of Fundamentals & Prerequisites
5. Mass Analyzers III (Ion Traps)
6. Mass Analyzers IV (Sector, FTICR, Orbitrap)
7. Detectors, Digitizers, Signal-to-Noise
8. Ionization Techniques I (Theory, EI)
9. Ionization Techniques II (CI)
10. Ionization Techniques III (ESI, MALDI, DESI, DART, Elemental)

Part II: MS Interpretation

1. Interpretation of Mass Spectra I (Elemental Composition I)
2. Interpretation of Mass Spectra II (Elemental Composition II)
3. Interpretation of Mass Spectra III (The Molecular Ion)
4. Interpretation of Mass Spectra IV (Fragmentation Mechanisms)

Part III: Chemical Separations

1. Introduction and Theory of Chromatography
   • Chromatographic Separation Demo (Web)
2. Theory of Chromatography (Cont.)
3. Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis
4. Gas Chromatography
5. LC and HPLC
6. Ion Chromatography & Thin Layer Chromatography
7. Chromatographic Detectors

Introduction to Mass Spectrometry

1. (General, Suggested) ASMS Tutorial: What is Mass Spectrometry?
2. (General, Reference) MS Terms and Definitions Project
3. (General, Reference) "Frontiers in Mass Spectrometry" ,Special issue Chem. Rev. 101(2), 2001.
4. (General, Reference) The 'Thompson'. A Suggested Unit for Mass Spectroscopists. R. G. Cooks RG and A. L. Rockwood, Rap. Comm. Mass Spec. 5, 93, 1991. (pdf)
5. (Ion Optics, Advanced) Ion Optics in Mass Spectrometry. H. Wollnik, J. Mass. Spec., 34: 991-1006, 1999.
6. (Vacuum, Reference) Vacuum Technology, Davis, Moore, and Coplan
7. (Kinetics, Animation) Simple gas kinetic theory simulator
8. (Various Topics, Advanced) Selected Award/Plenary/Tutorial Lectures from the Annual Conferences of the American Society of Mass Spectrometry
9. (General, Reference, Hard Copy at Libraries): Encyclopedia of Mass Spectrometry

Ionization Methods

1. (General, Reference) Methods of Ion Generation M. L. Vestal, Chem. Rev., 101(2), 361, 2001.
2. (General, Reference) The Emergence of Mass Spectrometry in Biochemical Research G. Siuzdak, Proc. Natl. Acad. Sci. USA, 91(24), 11290, 1994.
3. (EI, Advanced) Fundamentals of Electron Interactions with Plasma Processing Gases, by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
4. (CI, Advanced) Chemical Ionization Mass Spectrometry. I. General Introduction. M.S.B. Munson and F.H. Field, J. Am. Chem. Soc., 2621, 1966.
5. (ESI, Advanced) Practical implications of some recent studies in electrospray ionization fundamentals. Cech and Enke, Mass Spec. Rev., 20: 362-387, 2002.
6. (ESI, Advanced) A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry P. Kebarle, J.Mass Spec.,804-817, 2000.
7. (ESI, Advanced) Electrospray: From ions in solution to ions in the gas phase, what we know now. P. Kebarle and U.H. Verkerk, Mass Spec. Rev. doi: 10.1002/mas.20247, 2009.
8. (ESI, Advanced) Some tenets pertaining to ESI-MS R. B. Cole, J. Mass Spec.,763-772,2000.
9. (ESI, Advanced) Analytical Properties of the Nanoelectrospray Ion Source M. Wilm and M. Mann, A. Chem., 1-8, 1996.
10. (MALDI & ESI, Reference) Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules. Advanced Information on the Nobel Prize in Chemistry 2002.
11. (MALDI, ESI, Suggested) MALDI & ESI lecture from Prof. Cotter
12. (MADLI, Suggested) MALDI Tutorial from Vanderbilt
13. (MALDI, Advanced) Ion formation in MALDI mass spectrometry. Zenobi and Knochenmuss, Mass. Spec. Rev., 17: 337-366, 1999.
14. (MALDI, Advanced) Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass SpectrometryV. V. Laiko, M. A. Baldwin, and A. L. Burlingame, A. Chem.,652-657, 2000.
15. (SIMS, Advanced) SIMS Tutorial On Evans Analytical Group Website
16. (DESI, Advanced) Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology Z. Takats, J. M. Wiseman, and R. G. Cooks, J. Mass Spec.,1261-1275, 2005.
17. (DART, Advanced) Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions R. B. Cody, J. A. Laramee, H. D. Durst, A. Chem., 2297-2303, 2005.
18. (Atm. Pres. Ion Sources, Advanced) Atmospheric Pressure Ion Sources. Mass Spec. Rev., doi: 10.1002/mas.20246, 2009.
19. (Elemental, Advanced) Surface Ionization Source Using Multiple Elements M. G. Inghram and W. A. Chupka Rev. Sci. Inst.,24(7), 518, 1953.
20. (Elemental, Advanced) Recent Developments in Thermal Ionization Mass Spectrometric Techniques for Isotope Analyis K.G. Heumann et al, Analyst, 1291, 1995.
21. (Elemental, Advanced) Tutorial. Glow discharge mass spectrometry: Trace element determinations in solid samples. King et al., J. Mass. Spec., 30: 1061-1075 (pdf)
22. (Elemental, Advanced) Tutorial. Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool. A. Ammann, J. Mass. Spec., 42: 419-427, 2007.

Mass Analyzers

1. (General, Suggested) Instrumentation lecture from Prof. Cotter
2. (General, Reference) Mass Spectrometry (Review) A.L. Burlingame, R. K. Boyd, and S. J. Gaskell, A. Chem,1998,68(12),647R-716R
3. (General, Advanced) Debating Resolution and Mass Accuracy. M. P. Balogh, LC-GC Europe, 17(3), 152–159 (2004)
4. (General, Reference) Mass Analysis at the Advent of the 21st Century S. A. McLuckey and J. M. Wells, Chem. Rev. 101(2), 571, 2001.
5. (Resolution, Advanced) Scaling MS Plateaus with High-Resolution FT-ICRMS. A. G. Marshall, C. L. Henderickson, and S. D.-H. Shi A. Chem, 74(9), 252A (2002)
6. (TOF, Suggested) Agilent's Tutorial on Time-of-Flight Mass Spectrometry
7. (TOF, Advanced) Tutorial. Principles and instrumentation in time-of-flight mass spectrometry. Physical and instrumental concepts. M. Guilhaus, J. Mass. Spec., Volume 30: 1519-1532, 1995. (pdf)
8. (TOF, Advanced) Perfect Timing: Time-of-flight Mass Spectrometry M. Guilaus, RCMS, 1997, 951-962
9. (TOF, Advanced) Time-of-Flight Mass Spectrometry: State of the Art in Chemical Analysis and Molecular Science C. Weickhardt, F. Moritz, and J. Grotemeyer. MS Review. 1996, 139-162.
10. (TOF, Advanced)Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Instrumentation and Applications D. C. Muddiman, R. Bakhtiar, S. A. Hofstadler, and R. D. Smith J. Chem. Ed. 74, 1288, 1997.
11. (TOF, Advanced) Orthogonal acceleration time-of-flight mass spectrometry. Guilhaus et al., Mass Spec. Rev., 19: 65-107, 2000.
12. (TOF, Advanced) Time-of-Flight Mass Spectrometer with Improved ResolutionW. C. Wiley and I. H. McLaren, Rev. Sci. Instrum. 1955, 26(12), 1150-1157.
13. (TOF, Advanced) Time-of-flight mass spectrometry (concepts, achievements, and prospects) B. A. Mamyrin, Int J Mass Spec, 2001, 251-266
14. (TOF, Advanced) Advanced Reading: On the initial velocity of ions generated by matrix-assisted laser desorption ionization and its effect on the calibration of delayed extraction time-of-flight mass spectra P. Juhasz, M. L. Vestal, and S. A. Martin, J. Am. Soc. Mass Spec 8(3),209, 1997.
15. (TOF, Animation) TOF-MS From Agilent
16. (Quad, Required) Understanding the Quadrupole Mass Filter through Computer Simulation, Steel and Henchman, J. Chem. Ed. 75:1049-1054, 1998.
17. (Quad, Suggested) Quadrupole Mass Spectrometers: An Intuitive Look at the Math. Leary and Schmidt, J. Chem. Ed. 73: 1142-1144, 1996.
18. (Ion Trap, Animations) Courtesy of Thermo Finnigan
    • 1: Damping Gas
    • 2: Ion Trapping
    • 3: Scanning of the Mass Spectrum
    • 4: Detection of the Mass Spectrum
    • 5: Entire Electrospray + Ion Trap Instrument (Finnigan ESI-LCQ)
    • MS/MS 1: Ion Elimination ("There Can Only Be One")
    • MS/MS 2: Ion Capture
    • MS/MS 3: Collision-Induced Dissociation (CID) of the Trapped Ion
19. (FTICR, Suggested) Baseline mass resolution of peptide isobars: A record for molecular mass resolution, He F, Hendrickson CL, Marshall AG, Anal. Chem. 73 (3): 647-650, 2001.
20. (FTICR, Suggested) Fourier Transform Mass Spectrometry (Tutorial) I. J. Amster, JMS, 1996, 1325-1337.
21. (FTICR, Advanced) Fourier transform ion cyclotron resonance mass spectrometry: A primer. A.G. Marshall et al., Mass Spec. Rev. 17: 1-35, 1998.
22. (Orbitrap, Advanced) The Orbitrap: a new mass spectrometer (Perspective). R.G. Cooks et al., J Mass Spec. 40: 430-443, 2005.
23. (Q-TOF, Advanced) An introduction to quadrupole–time-of-flight mass spectrometry I. V. Chernushevich, A. V. Loboda, and B. A. Thomson, JMS, 2001, 849-865
24. (MS/MS, Suggested) Lecture on MS/MS from Prof. Bob Cotter
25. (MCP, Advanced) Microchannel Plate Detectors J. L. Wiza, Nuc Inst Meth, 1979, 587-601.
26. (Aerosol, Suggested)Tutorial: Sampling and analysis of individual particles by aerosol mass spectrometry. , M.V. Johnston, J. Mass Spectrom. 35, 585–595 (2000).
27. (Aerosol, Suggested) Chemical and Microphysical Characterization of Ambient Aerosols with the Aerodyne Aerosol Mass Spectrometer. Canagaratna et al., Mass Spectrometry Reviews, in press, April 2006. PDF of accepted version and Figures
28. (Aerosol, Advanced) Special Issue of AS&T on Aerosol Mass Spectrometry
29. (Aerosol, Link to references) Publications using the Aerodyne Aerosol Mass Spectrometer (AMS)
30. (Aerosol, Link to references) Aerosol Mass Spectrometry Web Page
31. (Aerosol, Link to references) A List of Publications in Single Particle Mass Spectrometry, maintained by Prof. Tony Wexler.
32. (Aerosol, Link to references) Another List of Publications in Single Particle Mass Spectrometry, this one maintained by Prof. Murray Johnston.

MS Interpretation

1. (Online Tutorial) Intro to Interpretation, with examples and interactive quizzes. University of Arizona
2. (Online Database) NIST Chemistry Webbook
3. (Online Tool) Online Periodic Table (with isotope info)
4. (Online Tool) MS Tools from SIS
5. (Online Tool) Exact Mass and Isotope Calculator
6. (Online Tool) Elemental Composition Calculator
7. (Isotopes, Suggested) Using Punnett Squares To Facilitate Students' Understanding of Isotopic Distributions in Mass Spectrometry, L.T. Sein, J. Chem. Ed., 83: 228, 2006.
8. (Nitrogen Rule, Suggested) Molecular formulas of organic compounds: the nitrogen rule and degree of unsaturation. V. Pellegrin, J. Chem. Ed., 60(8): 626, 1983.
9. (Practice Problems) Additional interpretation problems from Lee book and their solutions
10. (Reading, Advanced) Gaseous Molecular Ions: An Introduction to Elementary Processes Induced by Ionization, by E. Illenberger, J. Momigny, Springer, 1992.
11. (CID, Suggested) The Interpretation of Collision Induced Dissociation Tandem Mass Spectra of Peptides, I.A. Papayannopoulos, Mass Spec. Reviews 14: 49-73, 1995.
12. (Proteomics, Suggested) Mass Spectrometry in Proteomics R. Aerbersold and D.R. Goodlett, Chem. Rev. 101(2), 269, 2001.
13. (Proteomics, Database) MASCOT Protein MS Database

Chromatography: General

1. Simple Chromatography Simulator
2. (General, Required)Introduction to Chromatography, Braithwaite and Smith
3. (General, Required)Theory of Chromatography, Braithwaite and Smith
4. (General, Reference) Equations for Calculation of Chromatographic Figures of Merit for Ideal and Skewed Peaks, J.P. Foley and J.G. Dorsey, Anal. Chem., 55: 730-737, 1983.
5. (General, Reference) Nomenclature for Chromatography (IUPAC Recommendations), L.S. Etre, Pure & Appl. Chem., 65(4): 819-872, 1993.
6. (General, Reference) The Birth of Partition Chromatography, L.S. Ettre, LC-GC North America, 19(5), 2001.
7. (General, Reference) M.S. Tswett and the Birth of Chromatography, L.S. Ettre, LC-GC North America, 2003.
8. (General, Reference) The Centenary of "Chromatography", L.S. Ettre, LC-GC North America, 2006.

Electric Field Driven Separations

1. (CE, Suggested) Lecture on HPLC and CE from Prof. Bob Cotter
2. (CE, Advanced) Electrokinetic Flow and Dispersion in Capillary Electrophoresis, S. Ghosal, Ann. Rev. Fluid Mech., 38: 309-338, 2006.
3. (CE, Reference) 2006 Analytical Chemistry Review on Bioanalytical Applications of Capillary Electrophoresis, James Kraly, Md. Abul Fazal, Regine M. Schoenherr, Ryan Bonn, Melissa M. Harwood, Emily Turner, Megan Jones, and Norman J. Dovichi, Anal. Chem., 78(12) pp 4097 - 4110, 2006.

LC, GC, and IC

1. (GC, Suggested) More Speed, Better Precision, Higher Sensitivity: Why Buy a New Gas Chromatograph?, Engewald and Ettre, LC-GC North America, 2004.
2. (GC, Suggested) 2006 Analytical Chemistry Review on Gas Chromatography, Gary A. Eiceman, Jorge Gardea-Torresdey, Frank Dorman, Ed Overton, A. Bhushan, and H. P. Dharmasena, Anal. Chem., 78(12) pp 3985 - 3996, 2006.
3. (GC, Reference) Fifty Years of GC Instrumentation, L.S. Ettre, LC-GC North America, 2005.
4. (GC, Suggested) Evolution of Capillary Columns for Gas Chromatography, L.S. Ettre, LC-GC North America, 10(1), 2001.
5. (LC, Suggested) Lecture on HPLC and CE from Prof. Bob Cotter
6. (LC, Reference) Csaba Horvath and the Development of the First Modern High Performance Liquid Chromatograph, L.S. Ettre, LC-GC North America, 2005.
7. (LC, Reference) Jim Waters: The Development of GPC and the First HPLC Instruments, L.S. Ettre, LC-GC North America, 2005.
8. (IC, Reference) 2006 Analytical Chemistry Review on Planar Chromatography, Joseph Sherma, Anal. Chem., 78(12) pp 3841 - 3852, 2006.
9. (Detector, Reference) The Invention, Development, and Triumph of the Flame Ionization Detector, L.S. Ettre, LC-GC North America, 30(1), 2002.

• Feedback from the Fall 2006 Students
  • Survey at the end of the course: Questions and Responses
  • Survey after 1st midterm: Questions and Responses
• Detailed Feedback from the Fall 2004 Students
• Detailed Feedback from the Fall 2003 Students
• Detailed Feedback from the Fall 2002 Students
• FCQs for Jose L. Jimenez
• FCQs for Dan Czizco

• CU MS-Facility nickname: "Q-Trap"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2
• Paper #3

MDS SCIEX/Applied Biosystems API Q-Star Pulsar

• CU MS-Facility nickname: "Pulsar" or "Q-TOF"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2
• Paper #3
• Paper #4 & Supplement
• Paper #5
• Paper #6
• Paper #7
• Paper #8
• Paper #9

Hewlett Packard (Agilent) 5988A GC/MS

• CU MS-Facility nickname: "GC/MS"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2
• Paper #3
• Paper #4
• Paper #5
• Paper #6
• Paper #7
• Paper #8
• Paper #9
• Paper #10
• Paper #11
• Paper #12

Hewlett-Packard 5989 Electrospray/MS

• CU MS-Facility nickname: "ESI"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2

Applied Biosystems Voyager-DE™ STR Biospectrometry™ Workstation - MALDI TOF-MS

• CU MS-Facility nickname: "MALDI" or "Voyager"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2
• Paper #3
• Paper #4

VG Autospec M

• CU MS-Facility nickname: "Sector" or "Autospec"
• Instrument Description
• User Interviews
• Journal papers that used this instrument
• Paper #1
• Paper #2
• Paper #3
• Paper #4
• Paper #5
• Paper #6
• Paper #7
• Paper #8
• Paper #9
• Paper #10
• Paper #11
• Paper #12

• MS and Chromatography in Biomedical Research by Prof. Bob Cotter, John Hopkins Univ.
• Mass Spectrometry by Prof. Dwight Matthews, Univ. of Vermont
• Chromatography and Separations Course by Prof. Cramer, RPI
• MS Tutorial by by Richard Caprioli and Marc Sutter, Vanderbilt Univ.

• NIST Chemistry Webbook (includes electron impact ionization positive mass spectra)
• Web elements. Contains physical and chemical data on the elements, and on-line isotope pattern calculators.
• The Base Peak Mass Spec Site
• Mass Spectrometry Links
• LC-GC. This is the best industry publication on general chromatographic techniques.
• Chromatography Resources
• Chromatography Links
• A useful table of isotopic patterns of the elements (Fig. 1 on that document)
• Aerosol Mass Spectrometry

• Analytical Chemistry
  • Analytical Chemistry Reviews (highly recommended)
• Analytical and Bioanalytical Chemistry
• Trends in Analytical Chemistry
• The Analyst

• Mass Spectrometry Reviews
• International Journal of Mass Spectrometry (Norlin Basement, QC451.I54)
• Rapid Communications in Mass Spectrometry
• Journal of the American Society for Mass Spectrometry
• European Mass Spectrometry Journal
• Journal of Mass Spectrometry

• Journal of Chromatography A
• Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences
• Biomedical Chromatography
• Journal of Separation Science
• Journal of High Resolution Chromatography

• American Society for Mass Spectrometry (ASMS)
• European Society for Mass Spectrometry (ESMS)
• International Mass Spectrometry Society (IMSS)
• Mass Spectrometry Society of Japan (MSSJ)