Latest revision as of 17:07, 23 December 2017

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.

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THIS WEB PAGE HAS MOVED to http://tinyurl.com/Main5181. PLEASE FOLLOW THAT LINK FOR THE UPDATED MATERIAL
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1 Course Information & Organization
2 Introduction & Review of Fundamentals
3 Intro to Igor & MS Resolution
4 MS Analyzers: TOFMS
5 MS Analyzers: Quadrupole
6 MS Analyzers: Ion Traps, FTICR, Orbitrap
7 Chemical Ionization (CI)
8 Electrospray Ionization (ESI) & Ambient Ionization Sources
9 Old Materials from Here Down, for Reference

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: readings and class slides
- Piazza bulletin board: for Q&A & email list
- Homeworks

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

Introduction & Review of Fundamentals

Lecture Notes: Organization, Introduction & Review of Fundamentals

Readings:
- Electric and Magnetic Fields & Forces:
  - Electric & Magnetic Fields / Magnetic Fields & Forces
  - Suggested: Electrostatics (W)
- Probability and Statistics:
  - Basic Statistics: Statistics Demo / Central Limit Theorem
  - Suggested: Probability & Statistics (KhA)

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

- For all the readings that include a simulation, you are required to use the simulation for a range of parameters.

- Kinetic Theory and Gas Properties: Kinetic Theory of Gases / Mean Free Path / Ideal Gas Law, Diffusion / (Suggested: MFP (W))

- Complete this Reading Quiz by 9am on Thu.

HW for Thu 28-Aug-2014

Intro to Igor & MS Resolution

Lecture Notes: Intro to Igor

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

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.

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:
Pre-Lab
Lab: Procedure & GC-MS Operation Instructions

Student Choice Projects

Final Project Organization

Other MS and Chrom. Resources

Mass Spectrometry Societies

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.

@@ Line 1: / Line 1: @@
-This is the new home for the CU-Boulder Graduate Course CHEM-5181: Mass Spectrometry and Chromatography
-== Lectures ==
-* [http://www.colorado.edu/chemistry/chem5181/Lectures/2010/L1_Intro_Review_Fundamentals.pdf Lecture 1: Introduction and Review of Fundamentals]
-	** [http://www.vias.org/simulations/simusoft_linregr.html Regression Demo Program] (PC Download)
-	** [http://www.chem.uoa.gr/applets/AppletTheil/Appl_Theil2.html Non-Parametric Regression Demo] (Web)
-	** [http://www.chem.uoa.gr/applets/AppletPoly/Appl_Poly2.html Least Squares Polynomial Approximation Demo] (Web)
-	** [http://www.chem.uoa.gr/applets/AppletCentralLimit/Appl_CentralLimit2.html Central Limit Theorem Demo] (Web)
-	** [http://www.chem.uoa.gr/applets/AppletFourier/Appl_Fourier2.html Fourier Synthesis Demo] (Web)
-	** [http://www.chem.uoa.gr/applets/AppletFourAnal/Appl_FourAnal2.html Fourier Analysis Demo] (Web)
-* [http://www.colorado.edu/chemistry/chem5181/Lectures/2010/L2_Intro_Igor.pdf Introduction to Igor Pro]
-* [http://www.colorado.edu/chemistry/chem5181/Lectures/2010/MS1_Analyzers_TOFMS_2010.pdf Mass Analyzers I: TOFMS]
+* This is the new home for the CU-Boulder Graduate Course <b>CHEM-5181: Mass Spectrometry, Chromatography, and Research Methods</b> (note new name in Fall 2013). ''A shortcut to this page is [http://tinyurl.com/CHEM-5181 http://tinyurl.com/CHEM-5181].''
-	** [http://www.vias.org/simulations/simusoft_msscope.html Mass Spec. Oscilloscope Simulator]  (PC Download)
+* Schedule: <font color="blue">'''This course will be offered in Fall 2017 by Jose.'''</font>
-<li><a href="Lectures/2010/MS2_Analyzers_Sector_HR_2010.pdf">Lecture 4: Mass Analyzers II: Sector, FTICR, Orbitrap</a>
+<span style="color:#FFFF00; background:#00C000">================================================<br>THIS WEB PAGE HAS MOVED to [http://tinyurl.com/Main5181 http://tinyurl.com/Main5181]. PLEASE FOLLOW THAT LINK FOR THE UPDATED MATERIAL<br>================================================</span>
-	** [http://www.vias.org/simulations/simusoft_ms_sectorfield.html Simulator of Magnetic Sector MS]  (PC Download)
-* Ionization 3: Chemical Ionization
-	** [http://www.ptrms.com PTRMS Commercial Instrument]
-	** [http://www.syft.com SYFT Commercial Instrument]
-* [http://www.colorado.edu/chemistry/chem5181/Lectures/L_dePuy_Flowing_Afterglow.pdf Invited Lecture: the Flowing Afterglow] by Prof. Chuck dePuy
+== Course Information & Organization ==
-* [http://www.colorado.edu/chemistry/chem5181/Lectures/MS_Detectors_AD_SNR MS Detectors, A/D, Signal-to-Noise]
+* [http://tinyurl.com/CHEM-5181-Syll Syllabus: http://tinyurl.com/CHEM-5181-Syll]
-        ** [http://www.vias.org/simulations/simusoft_emultiplier.html Simulation of an Electron Multiplier]
-	** [http://www.vias.org/simulations/simusoft_adconversion.html Simulation of an Analog-to-Digital Converter]
-== Homeworks ==
+* 3 Key Electronic Resources for the Course
+** This Wiki page [http://tinyurl.com/CHEM-5181 http://tinyurl.com/CHEM-5181]: readings and class slides
+** [https://piazza.com/class/j6wrqna1p7w13s Piazza bulletin board]: for Q&A & email list
+** [http://tinyurl.com/hw-5181 Homeworks]
+* Other Resources:
+** [https://docs.google.com/spreadsheets/d/1ZiYkjswI7UD1D1V5JiS7EQeg_-yACUp6vRnuDd_erlI/edit#gid=0 Spreadsheet for time conflicts]
+** [https://docs.google.com/spreadsheets/d/1QlPkrmRnmxyQjDAZmcsf4YdyhUsxXMW3xX3kBJ5ak6Q/edit#gid=895878608 Course schedule] (to be updated)
+== Introduction & Review of Fundamentals ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_1_Review_Fundamentals.pdf Organization, Introduction & Review of Fundamentals]
+* Readings:
+** Electric and Magnetic Fields & Forces:
+*** [http://srikant.org/core/node8.html Electric & Magnetic Fields] / [http://hyperphysics.phy-astr.gsu.edu/hbase/magnetic/magfie.html#c1 Magnetic Fields & Forces]
+*** Suggested: [http://en.wikipedia.org/wiki/Electrostatics Electrostatics (W)]
+** Probability and Statistics:
+*** Basic Statistics: [http://onlinestatbook.com/stat_sim/sampling_dist/ Statistics Demo] / [http://www.chem.uoa.gr/applets/AppletCentralLimit/Appl_CentralLimit2.html Central Limit Theorem]
+*** Suggested: [https://www.khanacademy.org/math/probability Probability & Statistics (KhA)]
+* Textbooks (reading will be assigned from these):
+** Required: de Hoffmann & Stroobant [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC ''Mass Spectrometry, Principles and Applications''], 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
+** Required: McLafferty & Turecek [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC ''Interpretation of Mass Spectra''], 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993
+** Required: Wavemetrics [http://www.lulu.com/spotlight/wavemetrics ''Igor Pro Manuals''] (available as PDFs inside Igor, but printed version recommended)
+** Suggested: Travis & Kring, [http://www.amazon.com/LabVIEW-Everyone-Graphical-Programming-Edition/dp/0131856723 Labview for Everyone] /  Suggested: Press et al. [http://www.nr.com/ ''Numerical Recipes''] / Suggested: Taylor, [http://www.amazon.com/Introduction-Error-Analysis-Uncertainties-Measurements/dp/093570275X ''An Introduction to Error Analysis''], 2nd Ed., 1996. / Suggested: Moore et al. [http://app.knovel.com/web/toc.v/cid:kpBSAE0006/viewerType:toc/root_slug:building-scientific-apparatus/url_slug:building-scientific-apparatus/? ''Building Scientific Apparatus''], 4th Ed., 2009. [http://0-library.books24x7.com.libraries.colorado.edu/toc.aspx?bookid=42919 Alt. Link]
+** ''For all the readings that include a simulation, you are required to use the simulation for a range of parameters.''
+** Kinetic Theory and Gas Properties: [http://celiah.usc.edu/collide/1/ Kinetic Theory of Gases] / [http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/menfre.html Mean Free Path] / [http://phet.colorado.edu/en/simulation/gas-properties Ideal Gas Law, Diffusion] / (Suggested: [http://en.wikipedia.org/wiki/Mean_free_path MFP (W)])
+** Complete this [https://docs.google.com/forms/d/1oL2N908rzAnkYC3-bvGX7MEeWS6OghNH0DZUZwjCZFs/viewform Reading Quiz] by 9am on Thu.
+* [http://tinyurl.com/hw-5181 HW for Thu 28-Aug-2014]
+== Intro to Igor & MS Resolution ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_Igor.pdf Intro to Igor]
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_Igor.pdf Intro to Igor] & [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol.pdf MS Resolution]
+* Basic info:
+** [http://www.wavemetrics.com/products/igorpro/igorpro.htm Igor Pro graphing and programming software]
+** [https://www.wavemetrics.com/order/order_coursework.htm 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
+*** [http://cires.colorado.edu/jimenez/CHEM-5181/Read/2004_Resol_Acc_MS_v2.pdf Debating Resolution and Mass Accuracy in Mass Spectrometry] (for 19-Sep)
+*** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac022010j Scaling MS Plateaus with High-Resolution FT-ICRMS]. A. G. Marshall, C. L. Henderickson, and S. D.-H. Shi <i>A. Chem</i>, 74(9), 252A (2002)
+** On Igor
+*** Igor: [http://www.wavemetrics.com/products/igorpro/manual.htm "Getting Started" section of the manual]
+*** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/IgorProgConv_v3.ipf Igor Programming Conventions] (v3, 24-Sep-2013)
+*** [http://payam.minoofar.com/igor/ Unofficial Igor Programming Manual]
+*** [http://cires.colorado.edu/jimenez-group/wiki/index.php/Igor_Quick_Reference Igor Quick Reference Page] / [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video Tutorials]
+*** [http://www.wavemetrics.net/doc/igorman/IV-01%20Commands.pdf Working with Commands]
+*** [http://www.wavemetrics.net/doc/igorman/IV-02%20Prog%20Overview.pdf Programming Overview]
+*** [http://www.wavemetrics.net/doc/igorman/IV-03%20User%20Functions.pdf User-Defined Functions]
+*** [http://www.wavemetrics.net/doc/igorman/IV-08%20Debugging.pdf Debugging]
+* For you to do:
+** Complete this [https://docs.google.com/forms/d/1oL2N908rzAnkYC3-bvGX7MEeWS6OghNH0DZUZwjCZFs/viewform Reading Quiz] by 9am on class day.
+** [http://tinyurl.com/hw-5181 HW2] due Tue 2-Sep-2014
+== MS Analyzers: TOFMS ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOF.pdf Time-of-Flight]
+* Reading for next class:
+** Required: [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.4 (start) and 2.4.1 of de Hoffman & Stroobant on linear TOFMS]
+** Required: Agilent videos: [https://www.youtube.com/watch?v=iF21xzaY07w ESI TOFMS] & [https://www.youtube.com/watch?v=BFuZaIi-zDk ESI Q-TOFMS w/ MW/MS]
+** Suggested, Intro: [http://www.rmjordan.com/Resources/Tutorial.pdf Tutorial on TOFMS] (from RM Jordan, manufacturer of custom MS)
+** Suggested, Intro: [http://en.wikipedia.org/wiki/Time-of-flight_mass_spectrometry TOFMS in Wikipedia]
+** Suggested, Historical: [http://www.asms.org/docs/history-posters/bendix-tof.pdf?sfvrsn=2 ASMS poster on the Bendix TOFMS] (first commercial TOFMS)
+** Suggested, Intro: [http://www.chem.agilent.com/temp/radF998C/00045384.pdf Agilent's Tutorial on Time-of-Flight Mass Spectrometry]
+** Suggested, Intro: [http://www3.interscience.wiley.com/cgi-bin/abstract/110464657/ABSTRACT Tutorial. Principles and instrumentation in time-of-flight mass spectrometry. Physical and instrumental concepts]. M. Guilhaus, <i>J. Mass. Spec.</i>, Volume 30: 1519-1532, 1995. [http://www.colorado.edu/chemistry/chem5181/Restricted/Guilhaus_ToFRev_JMS1995.PDF (pdf)]
+* For you to do
+** [http://tinyurl.com/hw-5181 HW3]
+** [https://docs.google.com/forms/d/17zQGXhIKpJot_-RZbhu3TLqBdPOTxMrLW8hbwIVEPcQ/viewform Reading Quiz] (needs to be completed at least 2 hrs before the start of class)
+* Reading for 2nd Lecture
+** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC All of Sect. 2.4 of de Hoffman & Stroobant on TOFMS]
+** Suggested: also the suggested readings for the previous lecture
+** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/13069/ABSTRACT Perfect Timing: Time-of-flight Mass Spectrometry] M. Guilaus, RCMS, 1997, 951-962
+** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009442/ABSTRACT  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: [http://jchemed.chem.wisc.edu/Journal/issues/1997/nov/abs1288.html Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Instrumentation and Applications] D. C. Muddiman, R. Bakhtiar, S. A. Hofstadler, and R. D. Smith <i>J. Chem. Ed.</i> 74, 1288, 1997.
+** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/71004180/ABSTRACT Orthogonal acceleration time-of-flight mass spectrometry]. Guilhaus et al., <i>Mass Spec. Rev.</i>, 19: 65-107, 2000.
+** Suggested, Advanced: [http://link.aip.org/link/%3FRSINAK/26/1150/1 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: [http://www.ingentaconnect.com/content/els/13873806/2001/00000206/00000003/art00392 Time-of-flight mass spectrometry (concepts, achievements, and prospects)] B. A. Mamyrin, Int J Mass Spec, 2001, 251-266
+* For you to do
+** [http://tinyurl.com/hw-5181 HW4]
+** Reading Quiz (needs to be completed at least 2 hrs before the start of class)
+* Reading for 25-Sep-2014
+** [http://en.wikipedia.org/wiki/Euler_method Euler Method]
+** [https://www.youtube.com/watch?v=4CqaepeaJHA Euler Method Video]
+== MS Analyzers: Quadrupole ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]
+** ''Prop: Quadrupole''
+* Reading for Tue 30-Sep
+** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.1 of de Hoffmann & Stroobant]
+** Suggested, will use in HW: [http://cires.colorado.edu/jimenez/CHEM-5181/Read/1998_JCE_Steel_Quad_Simul.pdf Understanding the Quadrupole Mass Filter through Computer Simulation], Steel and Henchman, <i>J. Chem. Ed.</i> 75:1049-1054, 1998.
+** (Will use in HW) [http://cires.colorado.edu/jimenez/CHEM-5181/HW/2013-10-15_Quad_Simulation.pxp 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.
+*** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/2013-10-15_Quad_Simulation.ipf IPF of quad simulation] (only needed if PXP is giving you problems)
+** [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 Agilent GC/MS Triple Quad Video]
+** Suggested: [http://jchemed.chem.wisc.edu/Journal/Issues/1996/Dec/abs1142.html Quadrupole Mass Spectrometers: An Intuitive Look at the Math]. Leary and Schmidt, <i>J. Chem. Ed.</i> 73: 1142-1144, 1996.
+** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/mas.20249/abstract Linear Quadrupoles in Mass Spectrometry], D.J. Douglas, <i>Mass Spec. Rev.</i>, 28: 937-960, 2009.
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/85010411/ABSTRACT An introduction to quadrupole–time-of-flight mass spectrometry] I. V. Chernushevich, A. V. Loboda, and B. A. Thomson, JMS, 2001, 849-865
+** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-8-Tandems-and-Hybrids.pdf Lecture on MS/MS from Prof. Bob Cotter]
+== MS Analyzers: Ion Traps, FTICR, Orbitrap ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf 3d & 2d Quadrupole Ion Traps, FTICR, Orbitrap]
+* Reading: (all required unless marked otherwise):
+** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC: Sect. 2.2, 2.3, 2.6 & 2.7 of de Hoffmann and Stroobant 2007]
+** Ion trap movies: [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/1_dampinggas.exe geometry + buffer gas], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/2_trappingmsms.exe trapping], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/3_scanning_ms.exe scanning], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/5_esilcq.exe ESI-IT overview], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_1_elimination.exe MS/MS elimination], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_2_capture.exe capture], and [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_3_collision.exe collision-induced dissociation]
+*** Note: IT movies only work on PCs, find a PC to watch them if you have a Mac
+** [https://www.youtube.com/watch?v=PYpbKSmOnNc Homemade ion trap with two spons and a wire!]
+** [http://www.youtube.com/watch?v=KjUQYuy3msA Orbitrap animation]
+** Suggested if you are curious: [https://www.youtube.com/watch?v=8NAFdjfM-ds Short interview of Alexander Makarov] (Orbitrap inventor, very commercial)
+** [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introductory animation of FTICR]
+** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-9888(199704)32:4%3C351::AID-JMS512%3E3.0.CO;2-Y/abstract An Introduction to Quadrupole Ion Trap Mass Spectrometry], R. Mach, <i>J. Mass Spec.</i>, 32: 351-369, 1997.
+** Suggested: [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2001/73/i03/abs/ac000973h.html Baseline mass resolution of peptide isobars: A record for molecular mass resolution], He F, Hendrickson CL, Marshall AG, <i>Anal. Chem.</i> 73 (3): 647-650, 2001.
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/24610/ABSTRACT Fourier Transform Mass Spectrometry (Tutorial)] I. J. Amster, JMS, 1996, 1325-1337.
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009487/ABSTRACT Fourier transform ion cyclotron resonance mass spectrometry: A primer]. A.G. Marshall et al., <i>Mass Spec. Rev.</i> 17: 1-35, 1998.
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/110471441/ABSTRACT The Orbitrap: a new mass spectrometer (Perspective)]. R.G. Cooks et al., <i>J Mass Spec.</i> 40: 430-443, 2005.
+** [https://docs.google.com/forms/d/1l5AH8QkKPtAaBprvTBOJzEZ-FndScaFShvnCyxyhrUg/viewform Reading Quiz]
+== Chemical Ionization (CI) ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz2_CI.pdf Chemical Ionization]
+* Reading
+** de Hoffmann and Stroobant 2007, Sections 1.2, 1.12, 1.13, 1.16
+** [http://www.ptrms.com PTRMS Commercial Instrument] (read at least 10 pages on the site, focusing on the most relevant to the fundamentals and the course)
+** [http://www.syft.com/about-sift-ms SYFT Commercial Instrument] (same)
+** [https://sites.google.com/site/citofms/ ToF-CIMS Commercial Instrument] (same)
+** Suggested: [http://www.atmos-meas-tech.net/4/1471/2011/ Bertram. et al. 2011] on Aerodyne ToF-CIMS
+** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ja00964a001 Chemical Ionization Mass Spectrometry. I.  General Introduction]. M.S.B. Munson and F.H. Field, <i>J. Am. Chem. Soc.</i>, 2621, 1966. (First paper on CI)
+== Electrospray Ionization (ESI) & Ambient Ionization Sources ==
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz3_ESI.pdf Electrospray and its Ion Chemistry]
+** ''Prop: ESI Source''
+* Reading on ESI (suggested unless marked otherwise)
+** Required: de Hoffmann and Stroobant 2007, Section 1.11
+** [http://www3.interscience.wiley.com/journal/122463140/abstract Electrospray: From ions in solution to ions in the gas phase, what we know now]. P. Kebarle and U.H. Verkerk, <i>Mass Spec. Rev.</i> doi: 10.1002/mas.20247, 2009.
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/72512664/ABSTRACT  A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry] P. Kebarle, <i>J.Mass Spec.</i>,804-817, 2000.
+** [http://www.pnas.org/cgi/content/abstract/91/24/11290 The Emergence of Mass Spectrometry in Biochemical Research] G. Siuzdak, <i>Proc. Natl. Acad. Sci. USA</i>, 91(24), 11290, 1994.
+** [http://nobelprize.org/nobel_prizes/chemistry/laureates/2002/chemadv02.pdf Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules.] Advanced Information on the Nobel Prize in Chemistry 2002.
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/93518527/ABSTRACT Practical implications of some recent studies in electrospray ionization fundamentals]. Cech and Enke, <i>Mass Spec. Rev.</i>, 20: 362-387, 2002.
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/72512616/ABSTRACT Some tenets pertaining to ESI-MS] R. B. Cole, <i>J. Mass Spec.</i>,763-772,2000.
+** [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/1996/68/i01/abs/ac9509519.html Analytical Properties of the Nanoelectrospray Ion Source] M. Wilm and M. Mann, <i>A. Chem.</i>, 1-8, 1996.
+* Reading on Ambient Sources
+** Required: [http://www3.interscience.wiley.com/journal/122518620/abstract Atmospheric Pressure Ion Sources]. <i>Mass Spec. Rev.</i>, doi: 10.1002/mas.20246, 2009.
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/112126895/ABSTRACT 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, <i>J. Mass Spec.</i>,1261-1275, 2005.
+** [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i08/abs/ac050162j.html Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions] R. B. Cody, J. A. Laramee, H. D. Durst, <i>A. Chem.</i>, 2297-2303, 2005.
+= Old Materials from Here Down, for Reference =
+== Introduction & Review of Fundamentals ==
+* Reading on math & statistics (required unless marked otherwise):
+** Linear Regression: [http://www.vias.org/simulations/simusoft_linregr.html Regression] / [http://www.chem.uoa.gr/applets/AppletTheil/Appl_Theil2.html Non-Parametric Regression] /  [http://www.chem.uoa.gr/applets/AppletPoly/Appl_Poly2.html Least Squares Polynomial Approximation] / [http://apps.nrbook.com/c/index.html Numerical Recipes] (pages 656-662 of chapter 15) / [http://www.nlreg.com/orthogonal.htm Intro to Orthogonal Distance Regression] (for 10-Sep) / [http://www.wavemetrics.net/doc/igorman/III-08%20Curve%20Fitting.pdf Orthogonal Distance Regression in Igor Manual] (pages III-208 to III-212) (for 10-Sep)
+** Fourier Analysis: [http://www.chem.uoa.gr/applets/AppletFourAnal/Appl_FourAnal2.html Fourier Analysis] /  [http://www.chem.uoa.gr/applets/AppletFourier/Appl_Fourier2.html Fourier Synthesis] /
+** Differential Equations:
+*** [http://en.wikipedia.org/wiki/Differential_equation DEs (W)]
+*** Suggested: [https://www.khanacademy.org/math/differential-equations DE Videos (KhA)]
+*** Suggested: [http://dspace.mit.edu/handle/1721.1/70961 DE Videos (MIT OCW)]
+* Reading on basic physical chemistry, physics, fluids (required unless marked otherwise):
+** Reynolds Number & laminar turbulent / flow (for 5-Sep): [https://www.youtube.com/watch?v=XOLl2KeDiOg video demo of the transition] / [http://udel.edu/~inamdar/EGTE215/Laminar_turbulent.pdf Laminar & Turbulent flows] (up to page 6) / [http://en.wikipedia.org/wiki/Reynolds_number Reynolds number (W)] (until "Flow in a wide duct")
+* Info for Student Presentations
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_presentations.pdf Tips for Student Presentations]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/JournalSkim_Template.doc Template for Journal Skims (.doc)]
+** Required reading: [http://cires.colorado.edu/jimenez/CHEM-5181/Read/Advice_Beginning_Speakers.pdf 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: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2_Intro_Igor.pdf Intro to Igor Pro] (2011 lecture slides)
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Read/2013-10_Igor_Reading_Map.pdf 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): [https://www.khanacademy.org/cs/programming Computer Programming (KhA)]
+** Suggested: [http://lists.info-igor.org/listinfo.cgi/info-igor-info-igor.org 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: [http://payam.minoofar.com/wp-content/uploads/2007/07/introduction_to_igor_programming.pdf Intro to Igor Programming]
+* Reading from Igor Users' Guide I & II (when releant for a corresponding HWs) (required unless marked otherwise):
+** [http://www.wavemetrics.net/doc/igorman/II-01%20Getting%20Help.pdf Getting Help]
+** [http://www.wavemetrics.net/doc/igorman/II-02%20Command%20Window.pdf The Command Window]
+** Suggested: [http://www.wavemetrics.net/doc/igorman/II-03%20Expts%20Files%20Folders.pdf Experiments, Files, and Folders]
+** [http://www.wavemetrics.net/doc/igorman/II-05%20Waves.pdf Waves]
+** Suggested: [http://www.wavemetrics.net/doc/igorman/II-08%20Data%20Folders.pdf Data Folders]
+** [http://www.wavemetrics.net/doc/igorman/II-11%20Tables.pdf Tables]
+** [http://www.wavemetrics.net/doc/igorman/II-12%20Graphs.pdf Graphs]
+** [http://www.wavemetrics.net/doc/igorman/II-14%20Contour%20Plots.pdf Contour Plots]
+** [http://www.wavemetrics.net/doc/igorman/II-15%20Image%20Plots.pdf Image Plots]
+** Suggested: [http://www.wavemetrics.net/doc/igorman/III-01%20Notebooks.pdf Notebooks]
+** Suggested: [http://www.wavemetrics.net/doc/igorman/III-02%20Annotations.pdf Annotations]
+=== Data Acquisition using Labview ===
+* Lecture Materials:
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/LV_Class_2_PID.pdf Intro to PID control]
+* Reading:
+** [http://www.ni.com/labview/skills-guide/en/ Labview Skills Guide]
+** [http://www.ni.com/gettingstarted/labviewbasics/ Labview Basics]
+** [http://www.ni.com/academic/students/learn-labview/ Learn Labview]
+** [http://sine.ni.com/myni/self-paced-training/app/main.xhtml Self-Paced Training]
+** Specific reading items required for each day are listed [https://docs.google.com/document/d/1NZAvXmL43BZHpOleswY6bITdOpdKpzgZt9OzipDvYu8/pub here]
+** [http://en.wikipedia.org/wiki/PID_controller Reading on PID]
+* Practice Programs:
+** [http://cires.colorado.edu/science/groups/volkamer/wiki/index.php/CHEM5161#Lecture_Schedule Example VIs in the CHEM-5161 page]
+**  Example:[http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example.vi Error Example 1] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example_2.vi Error Example 2] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example_3.vi Error Example 3] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Global_1.vi Global Example] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Simulated_AI_Data.vi Simulated AI Example] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Simulated_AO_Data.vi Simulated AO Example]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/USB6008_P_controller_w_simulated_data_homework.vi 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: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol_Sector.pdf Intro to MS, Sector MS, Resolution/Accuracy, Ion Optics]
+** Resources we may use in class: [http://www.vias.org/simulations/simusoft_msscope.html MS Oscilloscope Simulator] /  [http://www.vias.org/simulations/simusoft_ms_sectorfield.html Magnetic Sector MS Simulator] / [http://www.vias.org/simulations/simusoft_ionoptics.html Ion Optics Simulator]
+* Required Reading:
+** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Introduction Chapter & Sect. 2.5.1 & 2.5.2 of de Hoffman & Stroobant] (for 12-Sep)
+** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC 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)
+** [http://apps.nrbook.com/c/index.html NR Ch 9: 9.0 Intro and 9.1 Bracketing & Bisection] (p.347-354) (for 24-Sep)
+** [https://www.youtube.com/watch?v=DGmNbs5Cywo&list=TLzb5ziJ1Ft_E Bisection method (Video)] & [https://www.youtube.com/watch?v=ErmB2v80tnA Its advantages & disadvantages (Video)] (for 24-Sep)
+** [http://www.asms.org/docs/history-posters/evolution-of-ms-1910-to-1940-2010.pdf The Early History of MS]
+** [http://www.asms.org/docs/history-posters/thomson's-vision-commercialization-2009.pdf The Commercialization of MS]
+* Suggested Reading:
+** [http://www.nature.com/nmeth/journal/v8/n8/abs/nmeth.1659.html A century of mass spectrometry: from atoms to proteomes], Yates, Nature Methods 2011.
+** [http://www.chemheritage.org/research/policy-center/oral-history-program/projects/critical-mass/index.aspx Critical Mass: a History of MS]
+** [http://www.asms.org/publications/historical/history-posters ASMS Posters on the History of MS]'' (for 19-Sep)
+** [http://mass-spec.lsu.edu/msterms/index.php/Resolution_(mass_spectrometry) 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)
+** [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-5-Instrumentation.pdf Instrumentation lecture from Prof. Cotter]
+** Suggested: [http://pubs.acs.org/toc/chreay/101/2 Chemical Reviews Issue on "Frontiers in Mass Spectrometry"]
+** Suggested: [http://pubs.acs.org/doi/abs/10.1021/cr990087a Mass Analysis at the Advent of the 21st Century] S. A. McLuckey and J. M. Wells, <i>Chem. Rev.</i> 101(2), 571, 2001.
+** Suggested: (for all of MS): [http://libraries.colorado.edu/record=b3604631 Encyclopedia of Mass Spectrometry] (Hard Copy at the Library]
+** Suggested: (for all of MS): [http://www.spectroscopynow.com/ms The Base Peak Mass Spec Site]
+** Suggested: [http://www.asms.org/whatisms/index.html ASMS Tutorial: What is Mass Spectrometry?]
+** Suggested: [http://www.msterms.com/wiki/index.php?title=Main_Page MS Terms and Definitions Project]
+** Suggested: [http://www.colorado.edu/chemistry/chem5181/Restricted/Cooks_Thompson.pdf The 'Thomson'. A Suggested Unit for Mass Spectroscopists]. R. G. Cooks RG and A. L. Rockwood, <i>Rap. Comm. Mass Spec.</i> 5, 93, 1991.
+** Suggested: [http://www.asms.org/Default.aspx?tabid=190 Selected Award/Plenary/Tutorial Lectures from the Annual Conferences of the American Society of Mass Spectrometry]
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/66001221/ABSTRACT Ion Optics in Mass Spectrometry]. H. Wollnik, <i>J. Mass. Spec.</i>, 34: 991-1006, 1999.
+=== Time-of-Flight (TOFMS) ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOFMS.pdf Time-of-Flight MS]
+* Reading for Thu 3-Oct.
+** Required: [http://www.wavemetrics.net/doc/igorman/III-10%20Function%20Analysis.pdf Igor Manual on Solving Ordinary-Differential Equations (ODEs)] (p. III-270 to III-283)
+** Required: Runge-Kutta Method: [https://www.youtube.com/watch?v=AT7Olelic8U Part I] & [https://www.youtube.com/watch?v=gzgghqto1Ws Part II]
+** Suggested: [http://apps.nrbook.com/c/index.html Numerical Recipes Chapter 16]
+** Suggested: [http://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods Wikipedia on Runge-Kutta]
+** [https://docs.google.com/forms/d/1PHZToo88a9IA4i4eAny4YCtyqiLUTQx5oxMbclAJcrU/viewform Reading Quiz] (needs to be completed at least 90 min before the start of class)
+* Reading for Thu 10-Oct. (Required unless marked otherwise)
+** [http://www.wavemetrics.net/doc/igorman/III-07%20Analysis.pdf Histograms in Igor] (p. III-128 to III-136)
+** [https://piazza.com/class/hiy250ehses10l?cid=93 Piazza post on responses to the last reading]
+** [https://plus.google.com/u/0/communities/100585967223170475855 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!)
+** [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Ch. 6 of McLafferty] (p. 103-114)
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Voyager_Biospectrometry_user_guide.pdf Appendix E of Voyager MALDI-TOFMS User's Guide]
+*** Chapter 1 of the same guide is suggested if you have time
+** [https://docs.google.com/forms/d/1hjnnT3YQvY7UYBge1SZwgHbYvq-j1QPl51YG06fSj2A/viewform Reading Quiz]
+* Reading for Thu 17-Oct. (Required)
+** Required (for HW): [http://www.wavemetrics.net/doc/igorman/III-08%20Curve%20Fitting.pdf 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: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp1_Intro_Elem.pdf Introduction to MS Interpretation & Elemental Composition 1]
+** ''Prop: Offline NIST database''
+* Reading for Tue 8-Oct
+** Required: [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Ch. 1 and Sect. 2.1-2.4 of McLafferty & Turecek]
+** Required: [http://webbook.nist.gov NIST Chemistry WebBook]
+** Suggested: [http://www.atmos-chem-phys.net/9/6633/2009/acp-9-6633-2009-supplement.pdf 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.
+** [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Sect. 2.5-2.8 McLafferty & Turecek]
+** [http://las.perkinelmer.com/Content/TechnicalInfo/TCH_ICPMSThirtyMinuteGuide.pdf Periodic Table of the Isotopes (only)] (the rest of this document is only suggested)
+** [http://mathworld.wolfram.com/Multichoose.html Multichoose combinations] (this is what applies for isotopes. Note that k is # of atoms and n is # of isotopes to choose from)
+** Software Tools:
+*** [http://www.chemcalc.org/ ChemCalc Isotopic Distribution] (Online) (play with the different functions)
+*** [http://www.sisweb.com/mstools/isotope.htm Isotopic Calculator (SIS)] (same)
+*** [http://sites.google.com/site/isoproms/ IsoPro Isotopic Distribution] (PC Download, install, play with)
+*** [http://chemdata.nist.gov/ MS Tools from NIST]
+*** [http://www.webelements.com Webelements Online Periodic Table] (with isotope info)
+*** [http://www.sisweb.com/referenc/source/exactmas.htm Exact Masses and Isotopic Abundances] (SIS)
+*** Suggested: [http://www.mmass.org/ NMass] (very powerful, but note that it has a lot of proteomics functions that are not relevant to us)
+*** Suggested: [http://www.cem.msu.edu/~reusch/OrgPage/mass.htm Exact Mass and Isotope Calculator]
+** Suggested: [https://www.khanacademy.org/math/probability/probability-and-combinatorics-topic/permutations_and_combinations/v/combinations Combinations videos (KA)]
+** Suggested: [http://www.science.uottawa.ca/eih/ch1/ch1.htm Use of isotopes for environmental studies] (the "small" isotopic fractionations that we discussed in class)
+** Suggested: [http://en.wikipedia.org/wiki/Isotope_fractionation Isotopic Fractionation (W)]. See the links these, those are the processes that cause the deviations studied by stable isotope research.
+** Suggested: [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1922/aston-lecture.pdf Aston Nobel Prize Lecture on the Discovery of Isotopes]
+** [https://docs.google.com/forms/d/13OZ1kkzLXyvTPU_jGFTFbMfJmJI7y9VwuFMrrqqxMHI/viewform Reading Quiz]
+** Suggested: [http://www.jce.divched.org/Journal/Issues/2006/Feb/PlusSub/V83N02/p228.pdf Using Punnett Squares To Facilitate Students' Understanding of Isotopic Distributions in Mass Spectrometry], L.T. Sein, <i>J. Chem. Ed.</i>, 83: 228, 2006.
+=== The Molecular Ion ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp3_Molec_Ion.pdf Interpretation III: The Molecular Ion]
+* Reading for Tue 29-Oct (Required unless noted otherwise)
+** McLafferty and Turecek 1993, Chapter 3
+** [http://www.chem.ucla.edu/harding/ec_tutorials/tutorial28.pdf 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)
+** [http://webbook.nist.gov/chemistry/ NIST Chemistry Webbook] (Explore for a few molecules, look at the MS data and its format, can it be donwloaded etc.)
+** [https://secure.sisweb.com/download/nist08demo.exe 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)
+** [http://www.sisweb.com/software/ms/nist.htm NIST MS Database (SIS)] [http://www.nist.gov/srd/nist1a.cfm (NIST)]
+** Suggested: NIST Database 2011: What's New and What Value Does it Offer (D. Sparkman) [http://www.sepscience.com/Techniques/MS/Articles/647-/MS-Solutions-11-NIST-11-Whats-New-and-What-Value-Does-it-Offer-Part-1 Part 1] + [http://www.sepscience.com/Techniques/MS/Articles/648-/MS-Solutions-12-NIST-11-Whats-New-and-What-Value-Does-it-Offer-Part-2 Part 2] + [http://www.sepscience.com/Techniques/MS/Articles/649-/MS-Solutions-13-NIST-11-Whats-New-and-What-Value-Does-it-Offer-Part-3 Part 3] + [http://www.sepscience.com/Techniques/MS/Articles/650-/MS-Solutions-14-NIST-11-Whats-New-and-What-Value-Does-it-Offer-Part-4 Part 4] + [http://www.sepscience.com/Techniques/MS/Articles/652-/MS-Solutions-15-NIST-11-Whats-New-and-What-Value-Does-it-Offer-Part-5 Part 5]
+** Suggested: [http://www.sisweb.com/software/ms/nist.htm#msms NIST MS/MS Database] (esp. for Demetrios and anyone who may do MS/MS)
+** Suggested: [http://www.sisweb.com/software/ms/nist.htm#gc NIST GC Database]; [http://www.sisweb.com/software/ms/nist.htm#amdis AMDIS Program Description] and [http://chemdata.nist.gov/mass-spc/amdis/downloads/AMDIS32_V2.71_setup.zip AMDIS Software Demo] (PC-only) (esp. for Abby and anyone who may do GC)
+** Suggested: [http://www.chem.arizona.edu/massspec/ Intro to interpretation with Quizzes] (Univ. of Arizona)
+** Suggested: [http://jchemed.chem.wisc.edu/Journal/issues/1983/Aug/jceSubscriber/JCE1983p0626.pdf Molecular formulas of organic compounds: the nitrogen rule and degree of unsaturation]. V. Pellegrin, <i>J. Chem. Ed.</i>, 60(8): 626, 1983.
+** Suggested: [http://littlemsandsailing.wordpress.com/ Little MS and Sailing Blog]
+** [https://docs.google.com/forms/d/1-jlKCkGpRcoqKca1di4AH4gxWC-syV6yVOC08KGCUM4/viewform Reading Quiz]
+=== Fragmentation Mechanisms ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp4_Frag_Mech.pdf Interpretation IV: Fragmentation Mechanisms]
+** ''Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 7 & 8''
+=== Postulation of Molecular Structures ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp5_Molec_Struct.pdf Interpretation V: Postulation of Molecular Structures]
+** ''Required Reading: McLafferty and Turecek 1993, Chapter 5''
+* Old Homeworks & Additional Practice on interpretation
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/Unknowns_Lee.pdf Additional Practice Problems] & [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/Solutions_Lee.pdf  Their Solutions]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp1_Elemental_Comp.doc HW Int1 (elemental composition)]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp2_2011.pdf HW Int2]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp3_2011.pdf HW Int3]
+== Ionization Sources ==
+=== Fundamentals & Electron Ionization (EI) ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz1_EI.pdf Fundamentals & Electron Ionization]
+** ''Prop: EI ionizer, filaments, magnets''
+* Reading for Tue 5-Nov
+** de Hoffmann and Stroobant 2007, Section 1.1, 1.17
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/OSS_1stEd_IonChemistry.pdf Ion Chemistry] (p. 421-427 including 'Rates of Ion-Molecule Reactions. Rest of the reading is suggested)
+** Suggested: [http://pubs.acs.org/doi/abs/10.1021%2Fcr990104w Methods of Ion Generation] M. L. Vestal, <i>Chem. Rev.</i>, 101(2), 361, 2001.
+** Reference: [http://books.google.com/books?id=TA5N2svGCK4C&lpg=PA1&ots=VkoweozDrO&dq=Fundamental%20Electron%20Interactions%20with%20Plasma%20Processing%20Gases Fundamentals of Electron Interactions with Plasma Processing Gases], by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
+** [https://docs.google.com/forms/d/1zoYhXLCokDL7H_BadoT5CCXXArJps6RuTvcTblgTGA4/viewform Reading Quiz]
+=== Other Types of Ionization: SIMS, MALDI, ICP etc. ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz4_Others.pdf 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
+** [http://www.spectroscopyonline.com/spectroscopy/data/articlestandard//spectroscopy/052002/8458/article.pdf A beginner's guide to ICPMS]
+** [http://las.perkinelmer.com/content/TechnicalInfo/tch_icpmsthirtyminuteguide.pdf The 30-minute guide to ICPMS]
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/114201969/ABSTRACT Tutorial. Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool.] A. Ammann, <i>J. Mass. Spec.</i>, 42: 419-427, 2007.
+** [http://pprco.tripod.com/SIMS/Theory.htm SIMS Tutorial]
+** Suggested: [http://instaar.colorado.edu/~marchitt//lab.html ICP-MS Facility at CU-Boulder]
+** Suggested: [http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=RSINAK000024000007000518000001&idtype=cvips&gifs=yes Surface Ionization Source Using Multiple Elements] M. G. Inghram and W. A. Chupka <i>Rev. Sci. Inst.</i>,24(7), 518, 1953.
+** Suggested: [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i08/abs/ac050162j.html Recent Developments in Thermal Ionization Mass Spectrometric Techniques for Isotope Analyis] K.G. Heumann et al, <i>Analyst</i>, 1291, 1995.
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/110464831/ABSTRACT Tutorial. Glow discharge mass spectrometry: Trace element determinations in solid samples.] King et al., <i>J. Mass. Spec.</i>, 30: 1061-1075 [http://www.colorado.edu/chemistry/chem5181/Restricted/GlowDischarge_King_JMS1995.PDF (pdf)]
+** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-2-Basic-MALDI-ESI.pdf MALDI & ESI lecture from Prof. Cotter]
+** Suggested: [http://www.mc.vanderbilt.edu/msrc/tutorials/MALDI_MS_Tutorial.pdf MALDI Tutorial from Vanderbilt]
+** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/61005725/ABSTRACT Ion formation in MALDI mass spectrometry]. Zenobi and Knochenmuss, <i>Mass. Spec. Rev.</i>, 17: 337-366, 1999.
+** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ac990998k Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry] V. V. Laiko, M. A. Baldwin, and A. L. Burlingame, <i>A. Chem.</i>,652-657, 2000.
+* Homeworks on Ionization:
+** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_ESI_Charge_States.docx HW5.1: ESI charge states]
+== MS Detectors, Data Acquisition, Vacuum ==
+=== MS Detectors, A/D Conversion, Signal-to-Noise ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS_Detectors_AD_SNR.pdf MS Detectors, A/D, Signal-to-Noise]
+** ''Props: EMs, MCP, EM in vacuum mount''
+* Reading:
+** de Hoffmann and Stroobant 2007, Chapter 3
+** [http://www.vias.org/simulations/simusoft_emultiplier.html Simulation of an Electron Multiplier]
+** [http://www.vias.org/simulations/simusoft_adconversion.html Simulation of an Analog-to-Digital Converter]
+** [http://cires.colorado.edu/jimenez-group/QAMSResources/Docs/PCI-6110E.pdf Manual and specifications of a typical analog-to-digital converter]
+** [http://www.wavemetrics.net/doc/igorman/III-09%20Signal%20Processing.pdf Igor Manual on FFT] (p. III-237 to III-241) (Rest of the chapter is 'suggested')
+** [http://www.burle.com/cgi-bin/byteserver.pl/pdf/tp214.pdf Microchannel Plate Detectors] J. L. Wiza, Nuc Inst Meth, 1979, 587-601.
+** Suggested: [http://apps.nrbook.com/c/index.html Numerical Recipes Chapter 12.0-12.2 on FFT]
+=== Vacuum Technology ===
+* ''Props: turbo pump, diaphragm pump''
+* Reading:
+** [http://isnap.nd.edu/Lectures/urls/LEYBOLD_FUNDAMENTALS.pdf Fundamentals of Vacuum Technology] (Leybold)
+** [http://www.colorado.edu/chemistry/chem5181/Restricted/MooreDavisCoplan_Chap3.pdf Vacuum Technology], Davis, Moore, and Coplan
+** Suggested: [http://www.pfeiffer-vacuum.com/cnt/technology.action?chapter=tec1 Introduction to Vacuum Technology] (Pfeiffer)
+** Suggested: [http://www.pfeiffer-vacuum.com/products/vacuum-technology-book/container.action Vacuum Technology Book] (Pfeiffer)
+== Chromatography and Analytical Separations ==
+=== Ion Mobility Spectrometry ===
+* Lecture Notes: [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C3_IMS_CE.pdf Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis]
+* Reading for Tue 12-Nov
+** [http://www.sepscience.com/Techniques/MS/Articles/1473-/MS-Solutions-25-Ion-Mobility-Spectrometry-A-Primer Ion Mobility Spectrometry: A Primer]
+** [http://www.sepscience.com/Information/Archive/MS-Solutions/1797-/MS-Solutions-26-FAIMSDMS-Applications-Overview FAIMS & DMS Applications Overview]
+** [http://onlinelibrary.wiley.com/doi/10.1002/jms.1383/pdf Ion Mobility - Mass Spectrometry]
+** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac071226o 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: [http://pubs.acs.org/doi/abs/10.1021/ac00222a001 Ion Mobility Spectrometry], Hill et al., Anal. Chem., 1990.
+** Suggested: [http://en.wikipedia.org/wiki/Ion-mobility_spectrometry IMS (W)]
+** Suggested: [http://www.tofwerk.com/cms/?Products:IMS-TOF Tofwerk IMS-TOF]
+** Suggested (for all of chromatography): [http://www.lcgcmag.com/lcgc/ LC-GC]. The best industry publication on general chromatographic techniques.
+** Suggested: [http://www.faims.com/ FAIMS website]
+** Suggested: [http://www.nature.com/nchem/journal/v6/n4/full/nchem.1889.html?WT.ec_id=NCHEM-201404 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: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C1_Intro_Theory.pdf  Introduction and Theory of Chromatography]
+* Reading for Thu 14-Nov:
+** [http://www.chem.uoa.gr/applets/AppletChrom/Appl_Chrom2.html Chromatographic Separation Demo]
+** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap1.PDF Introduction to Chromatography], Braithwaite and Smith
+** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap2.PDF Theory of Chromatography], Braithwaite and Smith
+** Suggested: [http://sciencecases.lib.buffalo.edu/cs/collection/detail.asp?case_id=386&id=386 A Play about the Van Deemter equation]
+** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac00255a033 Equations for Calculation of Chromatographic Figures of Merit for Ideal and Skewed Peaks], J.P. Foley and J.G. Dorsey, <i>Anal. Chem.</i>, 55: 730-737, 1983.
+** Suggested: [http://www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf Nomenclature for Chromatography (IUPAC Recommendations)], L.S. Etre, <i>Pure & Appl. Chem.</i>, 65(4): 819-872, 1993.
+** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/462001/2090/article.pdf The Birth of Partition Chromatography], L.S. Ettre, <i>LC-GC North America</i>, 19(5), 2001.
+** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/202003/56954/article.pdf M.S. Tswett and the Birth of Chromatography], L.S. Ettre, <i>LC-GC North America</i>, 2003.
+** Suggested: [http://www.lcgcmag.com/lcgc/article/articleDetail.jsp?id=358293 The Centenary of "Chromatography"], L.S. Ettre, <i>LC-GC North America</i>, 2006.
+=== Gas Chromatography ===
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/GC_Jessica.pdf Gas Chromatography]
+** ''Prop: GC column''
+* Reading:
+** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/252004/99406/article.pdf More Speed, Better Precision, Higher Sensitivity: Why Buy a New Gas Chromatograph?], Engewald and Ettre, <i>LC-GC North America</i>, 2004.
+** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ac060638e 2006 Analytical Chemistry Review on Gas Chromatography], Gary A. Eiceman, Jorge Gardea-Torresdey, Frank Dorman, Ed Overton, A. Bhushan, and H. P. Dharmasena, <i>Anal. Chem.</i>, 78(12) pp 3985 - 3996, 2006.
+** Suggested: [http://www.lcgcmag.com/lcgc/article/articleDetail.jsp?id=147842 Fifty Years of GC Instrumentation], L.S. Ettre, <i>LC-GC North America</i>, 2005.
+** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/492001/3156/article.pdf Evolution of Capillary Columns for Gas Chromatography], L.S. Ettre, <i>LC-GC North America</i>, 10(1), 2001.
+** [http://dx.doi.org/10.1016/S0021-9673(03)00242-5 Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool], J. Dalluge, J. Beens, and U.A.T. Brinkman, <i>Journal of Chromatography A</i>, 1000, 69-108, 2003.
+** Suggested [http://dx.doi.org/10.1021/ac041549+ GC x GC], J.M.D. Dimandja, <i>Anal. Chem.</i>, 76, 167A - 174A, 2004.
+** Suggested: [http://dx.doi.org/10.1080/10826070600574762 Recent advances in comprehensive two-dimensional gas chromatography (GC x GC)], T. Gorecki, O. Panic, and N. Oldridge, <i>Journal of Liquid Chromatography & Related Technologies</i>, 29(7-8), 1077-1104, 2006.
+** Suggested: [http://www.j-chrom-sci.com/index.php?option=com_virtuemart&page=shop.product_details&flypage=flypage.tpl&product_id=2127 Using Comprehensive Two-Dimensional Gas Chromatography to Study the Atmosphere], J.F. Hamilton, <i>Journal of Chromatographic Science</i>, 48, 274-282, 2010.
+=== Liquid Chromatographies ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C4_HPLC.pdf LC, HPLC, and IC], [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C5_Ion_Chrom.pdf Ion Chromatography], and [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C6_TL_Chrom.pdf Thin Layer Chromatography]
+* Reading
+** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-4-Chromatography.pdf Lecture on HPLC and CE from Prof. Bob Cotter]
+** Suggested: [http://www.lcgcmag.com/lcgc/article/articleDetail.jsp?id=159255 Csaba Horvath and the Development of the First Modern High Performance Liquid Chromatograph], L.S. Ettre, <i>LC-GC North America</i>, 2005.
+** Suggested: [http://www.lcgcmag.com/lcgc/article/articleDetail.jsp?id=172945 Jim Waters: The Development of GPC and the First HPLC Instruments], L.S. Ettre, <i>LC-GC North America</i>, 2005.
+** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ac060098l 2006 Analytical Chemistry Review on Planar Chromatography], Joseph Sherma, <i>Anal. Chem.</i>, 78(12) pp 3841 - 3852, 2006.
+=== Chromatographic Detectors ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C7_Detectors.pdf Chromatographic Detectors]
+* Reading
+** [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/062002/9029/article.pdf The Invention, Development, and Triumph of the Flame Ionization Detector], L.S. Ettre, <i>LC-GC North America</i>, 30(1), 2002.
+=== Capillary Electrophoresis ===
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C8_Electrophoresis Capillary Electrophoresis]
+* Reading:
+** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-4-Chromatography.pdf Lecture on HPLC and CE from Prof. Bob Cotter]
+** Suggested: [http://www.annualreviews.org/doi/abs/10.1146/annurev.fluid.38.050304.092053 Electrokinetic Flow and Dispersion in Capillary Electrophoresis], S. Ghosal, <i>Ann. Rev. Fluid Mech.</i>, 38: 309-338, 2006.
+== Invited Lectures on Applications of MS & Chrom. ==
+=== GCxGC-MS ===
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2013_GCxGC_Handouts.pdf Lecture Notes] by Dr. Lucas Smith, LECO Corp. (2013)
+* Reading:
+** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20158/abstract Comprehensive two-dimensional gas chromatography-mass spectrometry: A review]. Mondello et al., Mass. Spec. Rev. 2008.
+** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/jssc.200301643/abstract 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: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Protein_Peptides_W_Old.pdf Mass Spectrometry of Peptides and Proteins] by Prof. W. Old (2011)
+* Reading:
+** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20024/abstract Paizs and Suhai: Fragmentation Pathways of Protonated Peptides], Mass Spec. Rev., 24:508-548, 2005.
+** Suggested: [http://dx.doi.org/10.1016/j.ymeth.2004.08.013 Wysocki, Resing et al., 2005: Mass spectrometry of peptides and proteins]
+** Suggested: [http://www.colorado.edu/chemistry/chem5181/Restricted/CID_Peptides.pdf The Interpretation of Collision Induced Dissociation Tandem Mass Spectra of Peptides], I.A. Papayannopoulos, <i>Mass Spec. Reviews</i> 14: 49-73, 1995.
+** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr990076h Mass Spectrometry in Proteomics] R. Aerbersold and D.R. Goodlett, <i>Chem. Rev.</i> 101(2), 269, 2001.
+** Suggested: [http://www.matrixscience.com/ MASCOT Protein MS Database]
+=== Aerosol Mass Spectrometry ===
+* Lecture Notes: [http://cires.colorado.edu/jimenez/Papers/2010-09_IAC_Aerosol_MS_Tutorial.pdf Aerosol Mass Spectrometry] by J.L. Jimenez (2010)
+* Reading:
+** [http://www3.interscience.wiley.com/cgi-bin/abstract/72001802/ABSTRACT?CRETRY=1&SRETRY=0 Tutorial: Sampling and analysis of individual particles by aerosol mass spectrometry.], M.V. Johnston, <i>J. Mass Spectrom.</i> 35, 585–595 (2000).
+** [http://cires.colorado.edu/jimenez/Papers/Canagaratna_Review_Published.pdf Chemical and Microphysical Characterization of Ambient Aerosols with the Aerodyne Aerosol Mass Spectrometer]. Canagaratna et al., <i>Mass Spectrometry Reviews</i>, 2007.
+** [https://www.youtube.com/watch?v=kmZHwCBJHO8 Video tutorial on AMS]
+** Suggested: [http://www.aaar.org/ast_abst/v33n12pref.htm Special Issue of AS&T on Aerosol Mass Spectrometry]
+** Suggested: [http://cires.colorado.edu/jimenez/ams.html Aerosol Mass Spectrometry Web Page]
+** Reference: [http://cires.colorado.edu/jimenez/ams-papers.html Publications using the Aerodyne Aerosol Mass Spectrometer (AMS)]
+** Reference: [http://mae.ucdavis.edu/wexler/spa_refs.html A List of Publications in Single Particle Mass Spectrometry], maintained by Prof. Tony Wexler.
+** Reference: [http://www.udel.edu/chem/johnston/SPMSdbase.html Another List of Publications in Single Particle Mass Spectrometry], this one maintained by Prof. Murray Johnston.
+=== Isotope Ratio MS ===
+* Reading: [http://rsi.aip.org/resource/1/rsinak/v84/i1/p011101_s1?TRACK=RSIJAN13 Isotope Ratio MS]
+=== The Flowing Afterglow ===
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/L_dePuy_Flowing_Afterglow.pdf The Flowing Afterglow and its application to Astrochemistry] by Prof. Chuck dePuy (2010)
+=== Auto-resonant MS ===
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/ART_MS_Invited.pdf Autoresonant MS (ART-MS)] (Invited Lecture by Jeff Rathbone, Brooks Inc., Fall 2012)
+** [http://www.brooks.com/documents.cfm?documentID=5413 IJMS paper on ART-MS]
+** [http://www.brooks.com/pages/4209_simplicity_solutions_830_vqm_mass_spectrometer.cfm 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 [http://conted.colorado.edu/programs/access/ 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 [http://www.alumniconnections.com/links/link.cgi?l=5070036&h=10104&e=UCBI-20131029125211 here] and [http://www.cu.edu/employee-services/tuition-waiver-benefit-boulder-campus 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 [http://conted.colorado.edu/programs/access/ 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. [http://www.apple.com/support/bootcamp/ 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 [http://www.wavemetrics.com/support/demos.htm demo version of Igor] and going through the [http://www.wavemetrics.com/products/igorpro/manual.htm Getting Started section of the manual] and the [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video tutorials] before the class starts, as well as doing some of the [http://tinyurl.com/hw-5181 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 ==
+* [http://www.colorado.edu/chemistry/masspec/ Home Page of CU Mass Spec. Facility]
+=== Lab 1: MALDI-TOFMS ===
+* Background: [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Voyager_DE_STR_catalog.pdf Instrument Description I] &  [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/MALDI_description.pdf Instrument Description II]
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_MALDI_Prelab.pdf Pre-Lab]
+* Lab: [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_MALDI_Lab_Procedure.pdf Procedure] &  [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/MALDI_Instructions_simplified.pdf Instrument Instructions]
+=== Lab 2: Electrospray MS ===
+* Background
+** [http://www.waters.com/waters/nav.htm?cid=10110048&locale=en_US Synapt G2 Instrument Info] (used in 2011)
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Pulsar_description.pdf Pulsar Instrument Description] & [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Pulsar_Instructions_101410.pdf Instructions] (used in 2010)* [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_ESI_Prelab.pdf Pre-Lab]
+* Lab: [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_ESI_lab.pdf Procedure] & [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/LCMS_test_mixture LS/MS Test Mixture.pdf]
+=== Lab 3: GC-MS of mixtures ===
+* Background:
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Gas_Chromatography.pdf Intro to Gas Chromatography]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/GCMS_column_info.pdf GC Column Selection, & column used in lab]
+** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/BSTFA_derivatization.pdf BSTFA derivatization]
+* [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_GCMS_prelab.pdf Pre-Lab]
+* Lab: [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/2011_GCMS_lab.pdf Procedure] & [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/GCMS_operation.pdf GC-MS Operation Instructions]
+=== Student Choice Projects ===
+* [http://www.colorado.edu/chemistry/chem5181/Labs/2007_Final_Project.pdf Final Project Organization]
+== Other MS and Chrom. Resources ==
+=== Mass Spectrometry Societies ===
+*[http://www.asms.org American Society for Mass Spectrometry (ASMS)]
+*[http://www.bmb.leeds.ac.uk/esms/ European Society for Mass Spectrometry (ESMS)]
+*[http://www.imss.nl/ International Mass Spectrometry Society (IMSS)]
+*[http://wwwsoc.nacsis.ac.jp/mass/index.html Mass Spectrometry Society of Japan (MSSJ)]
+=== MS & Chrom. Courses at other Universities ===
+*[http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/msbiomed.htm MS and Chromatography in Biomedical Research] by Prof. Bob Cotter, John Hopkins Univ.
+*[http://www.uvm.edu/~dmatthew/chem223/?Page=chem223.html&MM=chem223_menu.html Mass Spectrometry] by Prof. Dwight Matthews, Univ. of Vermont
+*[http://www.rpi.edu/dept/chem-eng/WWW/faculty/cramer/csp/lectures.html Chromatography and Separations Course] by Prof. Cramer, RPI
+*[http://www.mc.vanderbilt.edu/msrc/tutorials/ms/ms.htm MS Tutorial] by by Richard Caprioli and Marc Sutter, Vanderbilt Univ.
+== Journals with Substantial Mass Spectrometry and Analytical Separations Content ==
+=== Analytical Chemistry Journals ===
+*[http://pubs.acs.org/journals/ancham/index.html Analytical Chemistry]
+**[http://pubs.acs.org/journals/ancham/reviews/index.html Analytical Chemistry Reviews] (highly recommended)
+*[http://link.springer-ny.com/link/service/journals/00216/ Analytical and Bioanalytical Chemistry]
+*[http://www.elsevier.com/inca/publications/store/5/0/2/6/9/5/ Trends in Analytical Chemistry]
+*[http://www.rsc.org/Publishing/Journals/an/ The Analyst]
+=== Mass Spectrometry Journals ===
+*[http://www3.interscience.wiley.com/cgi-bin/jtoc?ID=49879 Mass Spectrometry Reviews]
+*[http://www.sciencedirect.com/science?_ob=JournalURL&_issn=13873806&_auth=y&_acct=C000047944&_version=1&_urlVersion=0&_userid=918210&md5=a040de59a240c21a86c8e27e7ca55b39 International Journal of Mass Spectrometry] (Norlin Basement, QC451.I54)
+*[http://www.interscience.wiley.com/jpages/0951-4198/ Rapid Communications in Mass Spectrometry]
+*[http://link.springer.com/journal/volumesAndIssues/13361 Journal of the American Society for Mass Spectrometry]
+*[http://www.impub.co.uk/abstract.html European Mass Spectrometry Journal]
+*[http://www.interscience.wiley.com/jpages/1076-5174/ Journal of Mass Spectrometry]
+=== Chromatography and Analytical Separations Journals ===
+*[http://www.sciencedirect.com/web-editions?_ob=JournalURL&_issn=00219673&_auth=y&_acct=C000019778&_version=1&_urlVersion=0&_userid=417887&md5=fcc3f6a7f4b4896b16c00bd4d9b928fc Journal of Chromatography A]
+*[http://www.sciencedirect.com/web-editions?_ob=JournalURL&_issn=15700232&_auth=y&_acct=C000019778&_version=1&_urlVersion=0&_userid=417887&md5=ad8ab019c3b6255b0443e6a7e41c665f Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences]
+*[http://www.interscience.wiley.com/jpages/0269-3879/ Biomedical Chromatography]
+*[http://www3.interscience.wiley.com/cgi-bin/jtoc?ID=76510662 Journal of Separation Science]
+*[http://www3.interscience.wiley.com/cgi-bin/jtoc?ID=5008460 Journal of High Resolution Chromatography]

Difference between revisions of "CHEM-5181"

Latest revision as of 17:07, 23 December 2017

Contents

Course Information & Organization

Introduction & Review of Fundamentals

Intro to Igor & MS Resolution

MS Analyzers: TOFMS

MS Analyzers: Quadrupole

MS Analyzers: Ion Traps, FTICR, Orbitrap

Chemical Ionization (CI)

Electrospray Ionization (ESI) & Ambient Ionization Sources

Old Materials from Here Down, for Reference

Introduction & Review of Fundamentals

Computer Programming, Igor Pro, and Labview

Igor Pro

Data Acquisition using Labview

Mass Analyzers

Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics

Time-of-Flight (TOFMS)

MS Interpretation

Intro & Elemental Composition

The Molecular Ion

Fragmentation Mechanisms

Postulation of Molecular Structures

Ionization Sources

Fundamentals & Electron Ionization (EI)

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

MS Detectors, Data Acquisition, Vacuum

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

Vacuum Technology

Chromatography and Analytical Separations

Ion Mobility Spectrometry

Introduction and Theory of Chromatography

Gas Chromatography

Liquid Chromatographies

Chromatographic Detectors

Capillary Electrophoresis

Invited Lectures on Applications of MS & Chrom.

GCxGC-MS

MS of Peptides and Proteins

Aerosol Mass Spectrometry

Isotope Ratio MS

The Flowing Afterglow

Auto-resonant MS

FAQs about CHEM-5181

Labs

Lab 1: MALDI-TOFMS

Lab 2: Electrospray MS

Lab 3: GC-MS of mixtures

Student Choice Projects

Other MS and Chrom. Resources

Mass Spectrometry Societies

MS & Chrom. Courses at other Universities

Journals with Substantial Mass Spectrometry and Analytical Separations Content

Analytical Chemistry Journals

Mass Spectrometry Journals

Chromatography and Analytical Separations Journals

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