CHEM-5181
From Jimenez Group Wiki
This is the new home for the CU-Boulder Graduate Course CHEM-5181: Mass Spectrometry and Chromatography
- The old web page is located here, and I'll be gradually move things over to this Wiki page, which is much easier to update.
Contents
Course Information
- This course WILL be offered in Fall 2011, and WILL NOT be offered in Fall 2012
- Fall 2010 Syllabus
- Registering for the course:
- Every CU student attending the course needs to register, either as (a) for grade; (b) for pass/fail; or (c) for "Audit/No Credit".
- For non-CU students, you can register for the course through the CU Continuing Education Program ("ACCESS"), again as either (a) for grade; (b) for pass/fail; or (c) for "Audit/No Credit".
- Lectures: Tue & Thu 11:00-12:15, Ekeley W166
- Labs: to be determined, based on the student and MS facility schedules (typically three Tue afternoons 1-3 pm)
- Office hours: immediately after class on Tue & Thu
- Textbooks:
- de Hoffmann & Stroobant. Mass Spectrometry, Principles and Applications, 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
- McLafferty & Turecek Interpretation of Mass Spectra, 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993;
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.
- But I don't want to register at all. Can I still audit the class?
- Answer: No.
- I work in industry and use MS and chromatography in my work, can I take the class?
- Answer: Yes, registering through the ACCESS Program. Some things to think about: (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".
- Do I need a background in computer programming or on Igor to take the class?
- Answer: No. We cover those topics but we assume that people have no background when they start the class. We strongly recommend donwloading a demo version of Igor and going through the Getting Started section of the manual and the Video tutorials before the class starts.
Lectures
Introduction, Review, Igor
- Introduction and Review of Fundamentals
- Regression Demo Program (PC Download)
- Non-Parametric Regression Demo (Web)
- Least Squares Polynomial Approximation Demo (Web)
- Central Limit Theorem Demo (Web)
- Fourier Synthesis Demo (Web)
- Fourier Analysis Demo (Web)
- Introduction to Igor Pro
- Required Reading: "Getting Started" section of the manual and the Video tutorials
Mass Spectrometers
- TOFMS
- Required Reading: de Hoffmann and Stroobant 2007, Section 2.4
- Mass Spec. Oscilloscope Simulator (PC Download)
- Sector, FTICR, Orbitrap
- Required Reading: de Hoffmann and Stroobant 2007, Sections 2.3, 2.5, 2.6
- Simulator of Magnetic Sector MS (PC Download)
- Introd. animation of FTICR
- Quadrupoles
- Required Reading: de Hoffmann and Stroobant 2007, Section 2.1
- Video of Agilent GC/MS Triple Quad
- Video of Agilent LC/MS Quad
- Video of Agilent LC/MS Triple Quad
- Prop: Quadrupole
- 3D Ion Traps
- Required Reading: de Hoffmann and Stroobant 2007, Section 2.2
Ionization Sources
- Introduction and Electron Ionization
- Required Reading: de Hoffmann and Stroobant 2007, Section 1.1, 1.17 (need more)
- Ion Optics Simulator
- Prop: EI ionizer, filaments, magnets
- Electrospray and its Ion Chemistry (from Invited Lecturer Dr. Shuji Kato)
- Required Reading: de Hoffmann and Stroobant 2007, Section 1.11
- Prop: ESI Source
- Chemical Ionization
- Required Reading: de Hoffmann and Stroobant 2007, Section 1.2, 1.10, 1.12, 1.16, 1.17
- PTRMS Commercial Instrument
- SYFT Commercial Instrument
- Invited Lecture: the Flowing Afterglow by Prof. Chuck dePuy
- Ionization IV: Bombardment, MALDI and Elemental
- Required Reading: de Hoffmann and Stroobant 2007, Section 1.4, 1.7, 1.8, 1.9, 1.14, 1.15
- ICP-MS Facility at CU-Boulder
- Prop: MALDI plate
MS Detectors, Data Acquisition, Vacuum
- MS Detectors, A/D, Signal-to-Noise
- Required 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
- Props: EMs, MCP, EM in vacuum mount
- Vacuum Technology
- Props: turbo pump, diaphragm pump
MS Interpretation
- Introduction to MS Interpretation
- Required Reading: McLafferty and Turecek 1993, Chapters 1 and 6
- NIST Chemistry WebBook
- Example of ions in high-resolution MS of Ambient Aerosols (Fig. S-18)
- MS Tools from NIST
- Prop: Offline NIST database
- Using Elemental Composition in Interpretation
- Required Reading: McLafferty and Turecek 1993, Chapter 2
- IsoPro Isotopic Distribution (PC Download)
- ChemCalc Isotopic Distribution (Online)
- Periodic Table of the Isotopes
- Interpretation of Mass Spectra III (The Molecular Ion)
- Required Reading: McLafferty and Turecek 1993, Chapters 3 and 5
- Interpretation of Mass Spectra IV (Fragmentation Mechanisms)
- Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 9
Chromatography and Chemical Separations
- Gas Chromatography
- Prop: GC column
- LC and HPLC
- Ion Chromatography & Thin Layer Chromatography
- Chromatographic Detectors
Homeworks
Reference material for homeworks
HW on Intro and Review of Fundamentals
HW on TOFMS
- HW2: TOFMS
- TOFMS spectrum for Problem #1 (Igor Text File, save and double-click to open in Igor)
HW on Resolution & Accuracy
- HW 3.1: mass spec resolution and accuracy
- Quadrupole MS for donwload (Igor PXP format)
- Orbitrap MS for download (Excel format)
HW on Quadrupoles
- HW3.2: Quadrupole MS simulation
- Understanding the Quadrupole Mass Filter through Computer Simulation, Steel and Henchman, J. Chem. Ed. 75:1049-1054, 1998.
- 4th order Runge-Kutta Integration Method
HW on Ion Optics
- HW4.1: Ion Options Simulation Part 1
- HW4.2: Ion Options Simulation Part 2
- HW4.3: EI Source
- HW4.4: ESI charge states
Labs
Lab 1: MALDI-TOFMS
- catalog.pdf Instrument Description I
- Instrument Description II
- Pre-Lab
- Lab Procedure
- Instrument Instructions
Lab 2: Electrospray MS
Lab 3: GC-MS of mixtures
- Pre-Lab
- Lab
- GC-MS Operation Instructions
- GC Column Chart
- GC Column Info
- column1.pdf Info on Column used in the lab
Reference Materials
Suggestions Encouraged. Please send links to jose.jimenez at colorado.edu (All .pdf's are password restricted)
Introduction to Mass Spectrometry
- (General, Suggested ASMS Tutorial: What is Mass Spectrometry?
- (General, Reference) MS Terms and Definitions Project
- (General, Reference) "Frontiers in Mass Spectrometry" ,Special issue Chem. Rev. 101(2), 2001.
- (General, Reference) The 'Thompson'. A Suggested Unit for Mass Spectroscopists. R. G. Cooks RG and A. L. Rockwood, Rap. Comm. Mass Spec. 5, 93, 1991. [Restricted/Cooks_Thompson.pdf (pdf)]
- (Ion Optics, Advanced) Ion Optics in Mass Spectrometry. H. Wollnik, J. Mass. Spec., 34: 991-1006, 1999.
- (Vacuum, Reference) [Restricted/MooreDavisCoplan_Chap3.pdf Vacuum Technology], Davis, Moore, and Coplan
- (Kinetics, Animation) Simple gas kinetic theory simulator
- (Various Topics, Advanced) Selected Award/Plenary/Tutorial Lectures from the Annual Conferences of the American Society of Mass Spectrometry
- (General, Reference, Hard Copy at Libraries): Encyclopedia of Mass Spectrometry
Ionization Methods
- (General, Reference) Methods of Ion Generation M. L. Vestal, Chem. Rev., 101(2), 361, 2001.
- (General, Reference) The Emergence of Mass Spectrometry in Biochemical Research G. Siuzdak, Proc. Natl. Acad. Sci. USA, 91(24), 11290, 1994.
- (EI, Advanced) Fundamentals of Electron Interactions with Plasma Processing Gases, by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
- (CI, Advanced) Chemical Ionization Mass Spectrometry. I. General Introduction. M.S.B. Munson and F.H. Field, J. Am. Chem. Soc., 2621, 1966.
- (ESI, Advanced) Practical implications of some recent studies in electrospray ionization fundamentals. Cech and Enke, Mass Spec. Rev., 20: 362-387, 2002.
- (ESI, Advanced) A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry P. Kebarle, J.Mass Spec.,804-817, 2000.
- (ESI, Advanced) Electrospray: From ions in solution to ions in the gas phase, what we know now. P. Kebarle and U.H. Verkerk, Mass Spec. Rev. doi: 10.1002/mas.20247, 2009.
- (ESI, Advanced) Some tenets pertaining to ESI-MS R. B. Cole, J. Mass Spec.,763-772,2000.
- (ESI, Advanced) Analytical Properties of the Nanoelectrospray Ion Source M. Wilm and M. Mann, A. Chem., 1-8, 1996.
- (MALDI & ESI, Reference) Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules. Advanced Information on the Nobel Prize in Chemistry 2002.
- (MALDI, ESI, Suggested) MALDI & ESI lecture from Prof. Cotter
- (MADLI, Suggested) MALDI Tutorial from Vanderbilt
- (MALDI, Advanced) Ion formation in MALDI mass spectrometry. Zenobi and Knochenmuss, Mass. Spec. Rev., 17: 337-366, 1999.
- (MALDI, Advanced) Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry V. V. Laiko, M. A. Baldwin, and A. L. Burlingame, A. Chem.,652-657, 2000.
- (SIMS, Advanced) SIMS Tutorial On Evans Analytical Group Website
- (DESI, Advanced) Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology Z. Takats, J. M. Wiseman, and R. G. Cooks, J. Mass Spec.,1261-1275, 2005.
- (DART, Advanced) Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions R. B. Cody, J. A. Laramee, H. D. Durst, A. Chem., 2297-2303, 2005.
