CHEM-5181

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.

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 [http://conted.colorado.edu/programs/access/ 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;

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

Mass Spectrometers

• TOFMS
  • Mass Spec. Oscilloscope Simulator (PC Download)

• Sector, FTICR, Orbitrap
  • Simulator of Magnetic Sector MS (PC Download)
  • Introd. animation of FTICR

• Quadrupoles
  • 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

Ionization Sources

• Introduction and Electron Ionization
  • Ion Optics Simulator
  • Prop: EI ionizer, filaments, magnets

• Electrospray and its Ion Chemistry (from Invited Lecturer Dr. Shuji Kato)
  • Prop: ESI Source

• Chemical Ionization
  • PTRMS Commercial Instrument
  • SYFT Commercial Instrument

• Invited Lecture: the Flowing Afterglow by Prof. Chuck dePuy

• Ionization IV: Bombardment, MALDI and Elemental
  • ICP-MS Facility at CU-Boulder
  • Prop: MALDI plate

Detectors and Data Acquisition

• MS Detectors, A/D, Signal-to-Noise
  • Props: EMs, MCP
  • Simulation of an Electron Multiplier
  • Simulation of an Analog-to-Digital Converter
  • Manual and specifications of a typical analog-to-digital converter

MS Interpretation

• Introduction to MS Interpretation
  • NIST Chemistry WebBook
  • Example of ions in high-resolution MS of Ambient Aerosols (Fig. S-18)
  • MS Tools from NIST

• Using Elemental Composition in Interpretation
  • IsoPro Isotopic Distribution (PC Download)
  • ChemCalc Isotopic Distribution (Online)
  • Periodic Table of the Isotopes

• Interpretation of Mass Spectra III (The Molecular Ion)
• Interpretation of Mass Spectra IV (Fragmentation Mechanisms)

Chromatography and Chemical Separations

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

Homeworks

Reference material for homeworks

• • Template for Journal Skims (.doc)
  • Igor Programming Conventions (v2)
  • Tips for Student Presentations
  • Checklist for interpretation HW

HW on Intro and Review of Fundamentals

• HW1: Igor & 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

• Home Page of CU Mass Spec. Facility
• Lab Schedule for 2010

• Lab 1: MALDI-TOFMS:
  • catalog.pdf Instrument Description I
  • Instrument Description II
  • Pre-Lab
  • Lab Procedure
  • Instrument Instructions

• Lab 2: Electrospray MS:
  • Pre-Lab
  • Lab
  • Pulsar Instrument instructions

• Lab 3: GC-MS of mixtures

• Final Project Organization