CHEM-5181

• This is the new home for the CU-Boulder Graduate Course CHEM-5181: Mass Spectrometry, Chromatography, and Research Methods (note new name in Fall 2013). A shortcut to this page is http://tinyurl.com/CHEM-5181.
• Schedule: This course will be offered in Fall 2017 by Jose.

Course Information & Organization

• Syllabus: http://tinyurl.com/CHEM-5181-Syll

• 3 Key Electronic Resources for the Course
  • This Wiki page http://tinyurl.com/CHEM-5181
  • Piazza bulletin board for Q&A & email lists
  • Homeworks

• Other Resources:
  • Spreadsheet for time conflicts
  • Course schedule (to be updated)

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EVERYTHING AFTER THIS POINT IS FROM PRIOR OFFERINGS (for reference)
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• Textbooks (reading will be assigned from these):
  • Required: de Hoffmann & Stroobant Mass Spectrometry, Principles and Applications, 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
  • Required: McLafferty & Turecek Interpretation of Mass Spectra, 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993
  • Required: Wavemetrics Igor Pro Manuals (available as PDFs inside Igor, but printed version recommended)
  • Suggested: Travis & Kring, Labview for Everyone / Suggested: Press et al. Numerical Recipes / Suggested: Taylor, An Introduction to Error Analysis, 2nd Ed., 1996. / Suggested: Moore et al. Building Scientific Apparatus, 4th Ed., 2009. Alt. Link

Introduction & Review of Fundamentals

• Lecture Notes: Organization, Introduction & Review of Fundamentals

• Reading for Thu 28-Aug-2014
  • All readings required unless marked otherwise
  • For all the readings that include a simulation, you are required to use the simulation for a range of parameters.
  • Electric and Magnetic Fields & Forces:
    • Electric & Magnetic Fields / Magnetic Fields & Forces
    • Suggested: Electrostatics (W)
  • Kinetic Theory and Gas Properties: Kinetic Theory of Gases / Mean Free Path / Ideal Gas Law, Diffusion / (Suggested: MFP (W))
  • Probability and Statistics:
  • Basic Statistics: Statistics Demo / Central Limit Theorem
  • Suggested: Probability & Statistics (KhA)
  • Complete this Reading Quiz by 9am on Thu.

• HW for Thu 28-Aug-2014

Intro to Igor & MS Resolution

• Lecture Notes: Intro to Igor & MS Resolution

• Basic info:
  • Igor Pro graphing and programming software
  • Limitations of Igor Coursework License that we will use in the class

• Reading for Tue 2-Sep-2014 (Required unless marked otherwise)
  • On Mass Spectrometer Resolution
    • Debating Resolution and Mass Accuracy in Mass Spectrometry (for 19-Sep)
    • Suggested: 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)
  • On Igor
    • Igor: "Getting Started" section of the manual
    • Igor Programming Conventions (v3, 24-Sep-2013)
    • Unofficial Igor Programming Manual
    • Igor Quick Reference Page / Video Tutorials
    • Working with Commands
    • Programming Overview
    • User-Defined Functions
    • Debugging

• For you to do:
  • Complete this Reading Quiz by 9am on class day.
  • HW2 due Tue 2-Sep-2014

MS Analyzers: TOFMS

• Lecture Notes: Time-of-Flight

• Reading for next class:
  • Required: Sect. 2.4 (start) and 2.4.1 of de Hoffman & Stroobant on linear TOFMS
  • Required: Agilent videos: ESI TOFMS & ESI Q-TOFMS w/ MW/MS
  • Suggested, Intro: Tutorial on TOFMS (from RM Jordan, manufacturer of custom MS)
  • Suggested, Intro: TOFMS in Wikipedia
  • Suggested, Historical: ASMS poster on the Bendix TOFMS (first commercial TOFMS)
  • Suggested, Intro: Agilent's Tutorial on Time-of-Flight Mass Spectrometry
  • Suggested, Intro: 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)
• For you to do
  • HW3
  • Reading Quiz (needs to be completed at least 2 hrs before the start of class)

• Reading for 2nd Lecture
  • All of Sect. 2.4 of de Hoffman & Stroobant on TOFMS
  • Suggested: also the suggested readings for the previous lecture
  • Suggested, Advanced: Perfect Timing: Time-of-flight Mass Spectrometry M. Guilaus, RCMS, 1997, 951-962
  • Suggested, 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.
  • Suggested, 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.
  • Suggested, Advanced: Orthogonal acceleration time-of-flight mass spectrometry. Guilhaus et al., Mass Spec. Rev., 19: 65-107, 2000.
  • Suggested, Advanced: Time-of-Flight Mass Spectrometer with Improved Resolution W. C. Wiley and I. H. McLaren, Rev. Sci. Instrum. 1955, 26(12), 1150-1157.
  • Suggested, Advanced: Time-of-flight mass spectrometry (concepts, achievements, and prospects) B. A. Mamyrin, Int J Mass Spec, 2001, 251-266

• For you to do
  • HW4
  • Reading Quiz (needs to be completed at least 2 hrs before the start of class)

• Reading for 25-Sep-2014
  • Euler Method
  • Euler Method Video

MS Analyzers: Quadrupole

• Lecture Notes: Quadrupoles
  • Prop: Quadrupole

• Reading for Tue 30-Sep
  • Sect. 2.1 of de Hoffmann & Stroobant
  • Suggested, will use in HW: Understanding the Quadrupole Mass Filter through Computer Simulation, Steel and Henchman, J. Chem. Ed. 75:1049-1054, 1998.
  • (Will use in HW) Quad Simulation in Igor following Steel and Henchman. Need to understand the code and be ready answer questions about it and about how it would be modified. Investigations using the code will be the next HW.
    • IPF of quad simulation (only needed if PXP is giving you problems)
  • Agilent GC/MS Triple Quad Video
  • Suggested: Quadrupole Mass Spectrometers: An Intuitive Look at the Math. Leary and Schmidt, J. Chem. Ed. 73: 1142-1144, 1996.
  • Suggested: Linear Quadrupoles in Mass Spectrometry, D.J. Douglas, Mass Spec. Rev., 28: 937-960, 2009.
  • Suggested: An introduction to quadrupole–time-of-flight mass spectrometry I. V. Chernushevich, A. V. Loboda, and B. A. Thomson, JMS, 2001, 849-865
  • Suggested: Lecture on MS/MS from Prof. Bob Cotter

MS Analyzers: Ion Traps, FTICR, Orbitrap

• Lecture Notes: 3d & 2d Quadrupole Ion Traps, FTICR, Orbitrap

• Reading: (all required unless marked otherwise):
  • Sect. 2.2, 2.3, 2.6 & 2.7 of de Hoffmann and Stroobant 2007
  • Ion trap movies: geometry + buffer gas, trapping, scanning, ESI-IT overview, MS/MS elimination, capture, and collision-induced dissociation
    • Note: IT movies only work on PCs, find a PC to watch them if you have a Mac
  • Homemade ion trap with two spons and a wire!
  • Orbitrap animation
  • Suggested if you are curious: Short interview of Alexander Makarov (Orbitrap inventor, very commercial)
  • Introductory animation of FTICR
  • Suggested: An Introduction to Quadrupole Ion Trap Mass Spectrometry, R. Mach, J. Mass Spec., 32: 351-369, 1997.
  • 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.
  • Suggested: Fourier Transform Mass Spectrometry (Tutorial) I. J. Amster, JMS, 1996, 1325-1337.
  • Suggested: Fourier transform ion cyclotron resonance mass spectrometry: A primer. A.G. Marshall et al., Mass Spec. Rev. 17: 1-35, 1998.
  • Suggested: The Orbitrap: a new mass spectrometer (Perspective). R.G. Cooks et al., J Mass Spec. 40: 430-443, 2005.
  • Reading Quiz

Chemical Ionization (CI)

• Lecture Notes: Chemical Ionization

• Reading
  • de Hoffmann and Stroobant 2007, Sections 1.2, 1.12, 1.13, 1.16
  • PTRMS Commercial Instrument (read at least 10 pages on the site, focusing on the most relevant to the fundamentals and the course)
  • SYFT Commercial Instrument (same)
  • ToF-CIMS Commercial Instrument (same)
  • Suggested: Bertram. et al. 2011 on Aerodyne ToF-CIMS
  • Suggested: Chemical Ionization Mass Spectrometry. I. General Introduction. M.S.B. Munson and F.H. Field, J. Am. Chem. Soc., 2621, 1966. (First paper on CI)

Electrospray Ionization (ESI) & Ambient Ionization Sources

• Lecture Notes: Electrospray and its Ion Chemistry
  • Prop: ESI Source

• Reading on ESI (suggested unless marked otherwise)
  • Required: de Hoffmann and Stroobant 2007, Section 1.11
  • 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.
  • A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry P. Kebarle, J.Mass Spec.,804-817, 2000.
  • The Emergence of Mass Spectrometry in Biochemical Research G. Siuzdak, Proc. Natl. Acad. Sci. USA, 91(24), 11290, 1994.
  • Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules. Advanced Information on the Nobel Prize in Chemistry 2002.
  • Practical implications of some recent studies in electrospray ionization fundamentals. Cech and Enke, Mass Spec. Rev., 20: 362-387, 2002.
  • Some tenets pertaining to ESI-MS R. B. Cole, J. Mass Spec.,763-772,2000.
  • Analytical Properties of the Nanoelectrospray Ion Source M. Wilm and M. Mann, A. Chem., 1-8, 1996.

• Reading on Ambient Sources
  • Required: Atmospheric Pressure Ion Sources. Mass Spec. Rev., doi: 10.1002/mas.20246, 2009.
  • 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.
  • 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.

Old Materials from Here Down, for Reference

Introduction & Review of Fundamentals

• Reading on math & statistics (required unless marked otherwise):
  • Linear Regression: Regression / Non-Parametric Regression / Least Squares Polynomial Approximation / Numerical Recipes (pages 656-662 of chapter 15) / Intro to Orthogonal Distance Regression (for 10-Sep) / Orthogonal Distance Regression in Igor Manual (pages III-208 to III-212) (for 10-Sep)
  • Fourier Analysis: Fourier Analysis / Fourier Synthesis /
  • Differential Equations:
    • DEs (W)
    • Suggested: DE Videos (KhA)
    • Suggested: DE Videos (MIT OCW)

• Reading on basic physical chemistry, physics, fluids (required unless marked otherwise):
  • Reynolds Number & laminar turbulent / flow (for 5-Sep): video demo of the transition / Laminar & Turbulent flows (up to page 6) / Reynolds number (W) (until "Flow in a wide duct")

• Info for Student Presentations
  • Tips for Student Presentations
  • Template for Journal Skims (.doc)
  • Required reading: Advice to Beginning Physics Speakers, by James C. Garland, Physics Today, July 1991.

Computer Programming, Igor Pro, and Labview

Igor Pro

• Reading (required unless marked otherwise):
  • Suggested: Intro to Igor Pro (2011 lecture slides)
  • Parts of Igor that we will use and not. We have excluded some topics, either because they are too advanced, tangential to what we need, or unnecessary / confusing. Often things can be done in multiple ways, and in that case we are trying for the students to only use the simplest / least confusing / most useful method and avoid the others.
  • Suggested (very useful if no background): Computer Programming (KhA)
  • Suggested: Sign up for Igor email list (Strongly suggested for people who will use Igor in their research. Suggest "daily digest" mode to reduce the number of messages you get)
  • Suggested: Intro to Igor Programming

• Reading from Igor Users' Guide I & II (when releant for a corresponding HWs) (required unless marked otherwise):
  • Getting Help
  • The Command Window
  • Suggested: Experiments, Files, and Folders
  • Waves
  • Suggested: Data Folders
  • Tables
  • Graphs
  • Contour Plots
  • Image Plots
  • Suggested: Notebooks
  • Suggested: Annotations

Data Acquisition using Labview

• Lecture Materials:
  • Intro to PID control

• Reading:
  • Labview Skills Guide
  • Labview Basics
  • Learn Labview
  • Self-Paced Training
  • Specific reading items required for each day are listed here
  • Reading on PID

• Practice Programs:
  • Example VIs in the CHEM-5161 page
  • Example:Error Example 1 / Error Example 2 / Error Example 3 / Global Example / Simulated AI Example / Simulated AO Example
  • Program for HW #15 (Need the simulated AO, AI, and Global examples)
    • Notes: you can open just the "6008 Check.vi". If you want to see what a project is like, you can open the "6008 Check.lvproj", but that is not necessary for using the program.

Mass Analyzers

Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics

• Lecture Notes: Intro to MS, Sector MS, Resolution/Accuracy, Ion Optics
  • Resources we may use in class: MS Oscilloscope Simulator / Magnetic Sector MS Simulator / Ion Optics Simulator

• Required Reading:
  • Introduction Chapter & Sect. 2.5.1 & 2.5.2 of de Hoffman & Stroobant (for 12-Sep)
  • Intro to Chapter 2 (p. 85-90), section 2.5.3 (p. 145-146), and Appendix 1.1 & 1.2 (p. 437-438) of de Hoffman & Stroobant (for 19-Sep)
  • NR Ch 9: 9.0 Intro and 9.1 Bracketing & Bisection (p.347-354) (for 24-Sep)
  • Bisection method (Video) & Its advantages & disadvantages (Video) (for 24-Sep)
  • The Early History of MS
  • The Commercialization of MS

• Suggested Reading:
  • A century of mass spectrometry: from atoms to proteomes, Yates, Nature Methods 2011.
  • Critical Mass: a History of MS
  • ASMS Posters on the History of MS (for 19-Sep)
  • More details on the definitions (Not everyone uses the same definitions, and there is an active debate on this topic. Thus you should always be clear about which definition YOU are using). (for 19-Sep)
  • Instrumentation lecture from Prof. Cotter
  • Suggested: Chemical Reviews Issue on "Frontiers in Mass Spectrometry"
  • Suggested: Mass Analysis at the Advent of the 21st Century S. A. McLuckey and J. M. Wells, Chem. Rev. 101(2), 571, 2001.
  • Suggested: (for all of MS): Encyclopedia of Mass Spectrometry (Hard Copy at the Library]
  • Suggested: (for all of MS): The Base Peak Mass Spec Site
  • Suggested: ASMS Tutorial: What is Mass Spectrometry?
  • Suggested: MS Terms and Definitions Project
  • Suggested: The 'Thomson'. A Suggested Unit for Mass Spectroscopists. R. G. Cooks RG and A. L. Rockwood, Rap. Comm. Mass Spec. 5, 93, 1991.
  • Suggested: Selected Award/Plenary/Tutorial Lectures from the Annual Conferences of the American Society of Mass Spectrometry
  • Suggested: Ion Optics in Mass Spectrometry. H. Wollnik, J. Mass. Spec., 34: 991-1006, 1999.

Time-of-Flight (TOFMS)

• Lecture Notes: Time-of-Flight MS

• Reading for Thu 3-Oct.
  • Required: Igor Manual on Solving Ordinary-Differential Equations (ODEs) (p. III-270 to III-283)
  • Required: Runge-Kutta Method: Part I & Part II
  • Suggested: Numerical Recipes Chapter 16
  • Suggested: Wikipedia on Runge-Kutta
  • Reading Quiz (needs to be completed at least 90 min before the start of class)

• Reading for Thu 10-Oct. (Required unless marked otherwise)
  • Histograms in Igor (p. III-128 to III-136)
  • Piazza post on responses to the last reading
  • Posts from your classmates in G+ (need to +1 one and only one of the 2)
    • Suggested: look at the articles after reading the posts, and reading the abstract and looking at the rest of the figures (i.e. skimming the paper, a critical skill in drinking from the research literature firehose!)
  • Ch. 6 of McLafferty (p. 103-114)
  • Appendix E of Voyager MALDI-TOFMS User's Guide
    • Chapter 1 of the same guide is suggested if you have time
  • Reading Quiz

• Reading for Thu 17-Oct. (Required)
  • Required (for HW): Curve Fitting in Igor (III-158 to 182, rest of the chapter is suggested as needed for HW)

MS Interpretation

Intro & Elemental Composition

• Lecture Notes: Introduction to MS Interpretation & Elemental Composition 1
  • Prop: Offline NIST database

• Reading for Tue 8-Oct
  • Required: Ch. 1 and Sect. 2.1-2.4 of McLafferty & Turecek
  • Required: NIST Chemistry WebBook
  • Suggested: Example of ions in high-resolution MS of Ambient Aerosols (Fig. S-18)

• Reading & HW for Tue 15-Oct (required unless noted otherwise)
  • HW 8, due Tue: work through the 6 remaining group questions in the handouts from last time. We will discuss in class.
  • Sect. 2.5-2.8 McLafferty & Turecek
  • Periodic Table of the Isotopes (only) (the rest of this document is only suggested)
  • Multichoose combinations (this is what applies for isotopes. Note that k is # of atoms and n is # of isotopes to choose from)
  • Software Tools:
    • ChemCalc Isotopic Distribution (Online) (play with the different functions)
    • Isotopic Calculator (SIS) (same)
    • IsoPro Isotopic Distribution (PC Download, install, play with)
    • MS Tools from NIST
    • Webelements Online Periodic Table (with isotope info)
    • Exact Masses and Isotopic Abundances (SIS)
    • Suggested: NMass (very powerful, but note that it has a lot of proteomics functions that are not relevant to us)
    • Suggested: Exact Mass and Isotope Calculator
  • Suggested: Combinations videos (KA)
  • Suggested: Use of isotopes for environmental studies (the "small" isotopic fractionations that we discussed in class)
  • Suggested: Isotopic Fractionation (W). See the links these, those are the processes that cause the deviations studied by stable isotope research.
  • Suggested: Aston Nobel Prize Lecture on the Discovery of Isotopes
  • Reading Quiz
  • Suggested: Using Punnett Squares To Facilitate Students' Understanding of Isotopic Distributions in Mass Spectrometry, L.T. Sein, J. Chem. Ed., 83: 228, 2006.

The Molecular Ion

• Lecture Notes: Interpretation III: The Molecular Ion

• Reading for Tue 29-Oct (Required unless noted otherwise)
  • McLafferty and Turecek 1993, Chapter 3
  • Tutorial on interpretation (there will be a question in the reading about comparing his procedure to McLafferty. Note that I had initially assigned this reading to a previous lecture by mistake but the removed it)
  • NIST Chemistry Webbook (Explore for a few molecules, look at the MS data and its format, can it be donwloaded etc.)
  • Download, install and explore the NIST08 Demo EI MS database. The software is the same as for the full database, but this one only includes 6000 compounds instead of 240,000+. (PC-only, find a PC to run it if you have a Mac)
  • NIST MS Database (SIS) (NIST)
  • Suggested: NIST Database 2011: What's New and What Value Does it Offer (D. Sparkman) Part 1 + Part 2 + Part 3 + Part 4 + Part 5
  • Suggested: NIST MS/MS Database (esp. for Demetrios and anyone who may do MS/MS)
  • Suggested: NIST GC Database; AMDIS Program Description and AMDIS Software Demo (PC-only) (esp. for Abby and anyone who may do GC)
  • Suggested: Intro to interpretation with Quizzes (Univ. of Arizona)
  • Suggested: Molecular formulas of organic compounds: the nitrogen rule and degree of unsaturation. V. Pellegrin, J. Chem. Ed., 60(8): 626, 1983.
  • Suggested: Little MS and Sailing Blog
  • Reading Quiz

Fragmentation Mechanisms

• Lecture Notes: Interpretation IV: Fragmentation Mechanisms
  • Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 7 & 8

Postulation of Molecular Structures

• Lecture Notes: Interpretation V: Postulation of Molecular Structures
  • Required Reading: McLafferty and Turecek 1993, Chapter 5

• Old Homeworks & Additional Practice on interpretation
  • Additional Practice Problems & Their Solutions
  • HW Int1 (elemental composition)
  • HW Int2
  • HW Int3

Ionization Sources

Fundamentals & Electron Ionization (EI)

• Lecture Notes: Fundamentals & Electron Ionization
  • Prop: EI ionizer, filaments, magnets

• Reading for Tue 5-Nov
  • de Hoffmann and Stroobant 2007, Section 1.1, 1.17
  • Ion Chemistry (p. 421-427 including 'Rates of Ion-Molecule Reactions. Rest of the reading is suggested)
  • Suggested: Methods of Ion Generation M. L. Vestal, Chem. Rev., 101(2), 361, 2001.
  • Reference: Fundamentals of Electron Interactions with Plasma Processing Gases, by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
  • Reading Quiz

Other Types of Ionization: SIMS, MALDI, ICP etc.

• Lecture Notes: Ionization IV: Bombardment, MALDI and Elemental
  • Prop: MALDI plate

• Reading:
  • de Hoffmann and Stroobant 2007, Section 1.4, 1.7, 1.8, 1.9, 1.14, 1.15
  • A beginner's guide to ICPMS
  • The 30-minute guide to ICPMS
  • Tutorial. Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool. A. Ammann, J. Mass. Spec., 42: 419-427, 2007.
  • SIMS Tutorial
  • Suggested: ICP-MS Facility at CU-Boulder
  • Suggested: Surface Ionization Source Using Multiple Elements M. G. Inghram and W. A. Chupka Rev. Sci. Inst.,24(7), 518, 1953.
  • Suggested: Recent Developments in Thermal Ionization Mass Spectrometric Techniques for Isotope Analyis K.G. Heumann et al, Analyst, 1291, 1995.
  • Suggested: Tutorial. Glow discharge mass spectrometry: Trace element determinations in solid samples. King et al., J. Mass. Spec., 30: 1061-1075 (pdf)
  • Suggested: MALDI & ESI lecture from Prof. Cotter
  • Suggested: MALDI Tutorial from Vanderbilt
  • Suggested: Ion formation in MALDI mass spectrometry. Zenobi and Knochenmuss, Mass. Spec. Rev., 17: 337-366, 1999.
  • Suggested: Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry V. V. Laiko, M. A. Baldwin, and A. L. Burlingame, A. Chem.,652-657, 2000.

• Homeworks on Ionization:
  • HW5.1: ESI charge states

MS Detectors, Data Acquisition, Vacuum

MS Detectors, A/D Conversion, Signal-to-Noise

• Lecture Notes: MS Detectors, A/D, Signal-to-Noise
  • Props: EMs, MCP, EM in vacuum mount

• Reading:
  • de Hoffmann and Stroobant 2007, Chapter 3
  • Simulation of an Electron Multiplier
  • Simulation of an Analog-to-Digital Converter
  • Manual and specifications of a typical analog-to-digital converter
  • Igor Manual on FFT (p. III-237 to III-241) (Rest of the chapter is 'suggested')
  • Microchannel Plate Detectors J. L. Wiza, Nuc Inst Meth, 1979, 587-601.
  • Suggested: Numerical Recipes Chapter 12.0-12.2 on FFT

Vacuum Technology

• Props: turbo pump, diaphragm pump

• Reading:
  • Fundamentals of Vacuum Technology (Leybold)
  • Vacuum Technology, Davis, Moore, and Coplan
  • Suggested: Introduction to Vacuum Technology (Pfeiffer)
  • Suggested: Vacuum Technology Book (Pfeiffer)

Chromatography and Analytical Separations

Ion Mobility Spectrometry

• Lecture Notes: Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis

• Reading for Tue 12-Nov
  • Ion Mobility Spectrometry: A Primer
  • FAIMS & DMS Applications Overview
  • Ion Mobility - Mass Spectrometry
  • Suggested: Performance, Resolving Power, and Radial Ion Distributions of a Prototype Nanoelectrospray Ionization Resistive Glass Atmospheric Pressure Ion Mobility Spectrometer, Kwasnik et al., Anal. Chem., 2007.
  • Suggested: Ion Mobility Spectrometry, Hill et al., Anal. Chem., 1990.
  • Suggested: IMS (W)
  • Suggested: Tofwerk IMS-TOF
  • Suggested (for all of chromatography): LC-GC. The best industry publication on general chromatographic techniques.
  • Suggested: FAIMS website
  • Suggested: The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics, Lanucara et al., 2014.

Introduction and Theory of Chromatography

• Lecture Notes: Introduction and Theory of Chromatography

• Reading for Thu 14-Nov:
  • Chromatographic Separation Demo
  • Introduction to Chromatography, Braithwaite and Smith
  • Theory of Chromatography, Braithwaite and Smith
  • Suggested: A Play about the Van Deemter equation
  • Suggested: 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.
  • Suggested: Nomenclature for Chromatography (IUPAC Recommendations), L.S. Etre, Pure & Appl. Chem., 65(4): 819-872, 1993.
  • Suggested: The Birth of Partition Chromatography, L.S. Ettre, LC-GC North America, 19(5), 2001.
  • Suggested: M.S. Tswett and the Birth of Chromatography, L.S. Ettre, LC-GC North America, 2003.
  • Suggested: The Centenary of "Chromatography", L.S. Ettre, LC-GC North America, 2006.

Gas Chromatography

• Gas Chromatography
  • Prop: GC column

• Reading:
  • Suggested: More Speed, Better Precision, Higher Sensitivity: Why Buy a New Gas Chromatograph?, Engewald and Ettre, LC-GC North America, 2004.
  • 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.
  • Suggested: Fifty Years of GC Instrumentation, L.S. Ettre, LC-GC North America, 2005.
  • Suggested: Evolution of Capillary Columns for Gas Chromatography, L.S. Ettre, LC-GC North America, 10(1), 2001.
  • Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool, J. Dalluge, J. Beens, and U.A.T. Brinkman, Journal of Chromatography A, 1000, 69-108, 2003.
  • Suggested GC x GC, J.M.D. Dimandja, Anal. Chem., 76, 167A - 174A, 2004.
  • Suggested: Recent advances in comprehensive two-dimensional gas chromatography (GC x GC), T. Gorecki, O. Panic, and N. Oldridge, Journal of Liquid Chromatography & Related Technologies, 29(7-8), 1077-1104, 2006.
  • Suggested: Using Comprehensive Two-Dimensional Gas Chromatography to Study the Atmosphere, J.F. Hamilton, Journal of Chromatographic Science, 48, 274-282, 2010.

Liquid Chromatographies

• Lecture Notes: LC, HPLC, and IC, Ion Chromatography, and Thin Layer Chromatography

• Reading
  • Suggested: Lecture on HPLC and CE from Prof. Bob Cotter
  • Suggested: Csaba Horvath and the Development of the First Modern High Performance Liquid Chromatograph, L.S. Ettre, LC-GC North America, 2005.
  • Suggested: Jim Waters: The Development of GPC and the First HPLC Instruments, L.S. Ettre, LC-GC North America, 2005.
  • Suggested: 2006 Analytical Chemistry Review on Planar Chromatography, Joseph Sherma, Anal. Chem., 78(12) pp 3841 - 3852, 2006.

Chromatographic Detectors

• Lecture Notes: Chromatographic Detectors

• Reading
  • The Invention, Development, and Triumph of the Flame Ionization Detector, L.S. Ettre, LC-GC North America, 30(1), 2002.

Capillary Electrophoresis

• Capillary Electrophoresis

• Reading:
  • Suggested: Lecture on HPLC and CE from Prof. Bob Cotter
  • Suggested: Electrokinetic Flow and Dispersion in Capillary Electrophoresis, S. Ghosal, Ann. Rev. Fluid Mech., 38: 309-338, 2006.

Invited Lectures on Applications of MS & Chrom.

GCxGC-MS

• Lecture Notes by Dr. Lucas Smith, LECO Corp. (2013)
• Reading:
  • Comprehensive two-dimensional gas chromatography-mass spectrometry: A review. Mondello et al., Mass. Spec. Rev. 2008.
  • Suggested: Speciation of nitrogen-containing compounds in diesel fuel by comprehensive two-dimensional gas chromatography. Wang et al., J. Sep. Sci., 2004.

MS of Peptides and Proteins

• Lecture Notes: Mass Spectrometry of Peptides and Proteins by Prof. W. Old (2011)
• Reading:
  • Paizs and Suhai: Fragmentation Pathways of Protonated Peptides, Mass Spec. Rev., 24:508-548, 2005.
  • Suggested: Wysocki, Resing et al., 2005: Mass spectrometry of peptides and proteins
  • Suggested: The Interpretation of Collision Induced Dissociation Tandem Mass Spectra of Peptides, I.A. Papayannopoulos, Mass Spec. Reviews 14: 49-73, 1995.
  • Suggested: Mass Spectrometry in Proteomics R. Aerbersold and D.R. Goodlett, Chem. Rev. 101(2), 269, 2001.
  • Suggested: MASCOT Protein MS Database

Aerosol Mass Spectrometry

• Lecture Notes: Aerosol Mass Spectrometry by J.L. Jimenez (2010)

• Reading:
  • Tutorial: Sampling and analysis of individual particles by aerosol mass spectrometry., M.V. Johnston, J. Mass Spectrom. 35, 585–595 (2000).
  • Chemical and Microphysical Characterization of Ambient Aerosols with the Aerodyne Aerosol Mass Spectrometer. Canagaratna et al., Mass Spectrometry Reviews, 2007.
  • Video tutorial on AMS
  • Suggested: Special Issue of AS&T on Aerosol Mass Spectrometry
  • Suggested: Aerosol Mass Spectrometry Web Page
  • Reference: Publications using the Aerodyne Aerosol Mass Spectrometer (AMS)
  • Reference: A List of Publications in Single Particle Mass Spectrometry, maintained by Prof. Tony Wexler.
  • Reference: Another List of Publications in Single Particle Mass Spectrometry, this one maintained by Prof. Murray Johnston.

Isotope Ratio MS

• Reading: Isotope Ratio MS

The Flowing Afterglow

• The Flowing Afterglow and its application to Astrochemistry by Prof. Chuck dePuy (2010)

Auto-resonant MS

• Autoresonant MS (ART-MS) (Invited Lecture by Jeff Rathbone, Brooks Inc., Fall 2012)
  • IJMS paper on ART-MS
  • Web page on ART-MS product with additional information

FAQs about CHEM-5181

• Can I audit the class?
  • Answer: Yes, but you need to register for it as "Audit / No Credit", either as a regular CU student or through the ACCESS Program. Auditors typically attend lectures but do not do the labs, homeworks, or exams, unless they want to.
  • Note that postdocs and researchers at CU can register for free using the Staff Tuition Benefit, see more details here and here. They need to apply for the tuition benefit at least 2 weeks before the start of classes, and then can register the day that classes start.

• But I don't want to register at all. Can you make an exception for me to still audit the class?
  • Answer: This is not possible for people in industry. For CU students we can sometimes make an exception, if there are at least 8 students registered for the class. Otherwise the Dean may cancel the class due to being too small, and in those cases we need all auditors to register as "Audit / No Credit".

• I work in industry and use MS and chromatography in my work, can I take the class?
  • Answer: Yes, registering through the ACCESS Program. You will have the option to take the class as "for grade", "Pass/Fail", and "Audit / No Credit." In making the choice, some things to think about are: (a) you need to have the relevant background or be willing to work to gain the background, especially if you want to take the class for credit. (b) This is a class for 1st year graduate students in Anaytical & Environmental Chemistry, and it takes quite a bit of work to take the class for credit. If you don't have much time for the class due to your work responsibilities, you should register as "Audit / No Credit".

• I am an undergraduate at CU, can I take the class?
  • Answer: Yes, if you have the prerequisites. Contact Jose in case of doubt. However you need to take into account that this class takes substantially more work than a typical undergraduate course.

• Do I need a laptop for this class?
  • Yes, as we will do a lot of work using Igor, Labview, and other computer programs. A PC is much preferable as Labview does not work well on Macs, and many other programs, including the NIST MS database only run on PCs. If you already have a Mac laptop, we strongly recommend that you install a Windows partition using e.g. Bootcamp. You will find it useful well beyond the class, as much research-related software does not run on Macs. Otherwise it is your responsibility to identify a PC where you can do the assigned homework and readings that only work on PCs.

• Do I need a background in computer programming or on Igor to take the class?
  • Answer: We cover those topics but we assume that people have no strong background when they start the class. However we progress quickly, and any prior work that you can do in this area will be very useful in the course. If you do NOT have a background on computer programming (i.e. you don't know how to use FOR loops, DO-WHILE loops, IF-ELSE statements etc.), we strongly recommend downloading a demo version of Igor and going through the Getting Started section of the manual and the Video tutorials before the class starts, as well as doing some of the first homeworks from previous years.

• Could I use a programming language different than Igor for this class?
  • Answer: No. It is important to be able to project the screen and discuss code from all students in class, during office hours and HW help sessions, in Piazza etc. That is facilitated by using a single programming language, and would be very confusing if we were to use multiple languages, especially since typically 2/3 of the students in the class have very limited to no previous programming experience. The choice of Igor instead of other equally capable languages such as IDL or Matlab is due to the fact that most groups in our Analytical Chemistry program, as well as many collaborators and future employers, use Igor heavily and they do not use the alternatives. Thus research is made more efficient because one can ask Igor questions from dozens of people in our program. Our groups also use large data analysis packages that are available only in Igor.

Labs

• Home Page of CU Mass Spec. Facility

Lab 1: MALDI-TOFMS

• Background: Instrument Description I & Instrument Description II
• Pre-Lab
• Lab: Procedure & Instrument Instructions

Lab 2: Electrospray MS

• Background
  • Synapt G2 Instrument Info (used in 2011)
  • Pulsar Instrument Description & Instructions (used in 2010)* Pre-Lab
• Lab: Procedure & LS/MS Test Mixture.pdf

Lab 3: GC-MS of mixtures

• Background:
  • Intro to Gas Chromatography
  • GC Column Selection, & column used in lab
  • BSTFA derivatization
• Pre-Lab
• Lab: Procedure & GC-MS Operation Instructions

Student Choice Projects

• Final Project Organization

Award for the Best Performance in CHEM-5181

• Fall 2014: Samantha Miller (PhD Chemical Engineering, Musgrave/Weimer groups)
• Fall 2013: Demetrios Pagonis (PhD Chemistry, Ziemann group)
• Fall 2011: Rui Li (PhD Atmospheric Sciences, de Gouw group)
• Fall 2010: Brett Palm (PhD Chemistry, Jimenez group)
• Fall 2009: Eleanor Waxman (PhD Chemistry, Volkamer group)
• Fall 2007: Sean Coburn (PhD Chemistry, Volkamer group)
• Fall 2006: Jesse Marcum (PhD Chemistry, Weber group)
• Fall 2004: Steve Dutton (PhD Mechanical Engineering, Hannigan group)
• Fall 2003: Melinda Beaver (PhD Chemistry, Tolbert group)
• Fall 2002: Aaron Appel (PhD Chemistry, Rakowski-Dubois group)

Other MS and Chrom. Resources

Mass Spectrometry Societies

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

MS & Chrom. Courses at other Universities

• 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.

Journals with Substantial Mass Spectrometry and Analytical Separations Content

Analytical Chemistry Journals

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

Mass Spectrometry Journals

• 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

Chromatography and Analytical Separations Journals

• 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