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  • 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
  • Schedule: This course will be offered in Fall 2017 by Jose.


Course Information & Organization

  • Schedule:
    • Lectures: Tue & Thu 11:00-12:15, Ekeley W166
    • Office hours:
      • Mondays 1:15-2:15 pm
      • Wednesdays 9:30-10:30 am
      • Immediately after every class for up to 30 min (we could have a conflict on occasion so ask first if a specific day is important to you)
      • For Jose, pls warn him at least 1 hr in advance that you plan to come to a specific office hrs period

Introduction & Review of Fundamentals

Intro to Igor & MS Resolution

  • For you to do:

MS Analyzers: TOFMS

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

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

  • 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

Data Acquisition using Labview

Mass Analyzers

Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics

Time-of-Flight (TOFMS)

  • 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

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

  • Props: turbo pump, diaphragm pump

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.


MS of Peptides and Proteins

Aerosol Mass Spectrometry

Isotope Ratio MS

The Flowing Afterglow

Auto-resonant MS

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.



Lab 2: Electrospray MS

Lab 3: GC-MS of mixtures

Student Choice Projects

Award for the Best Performance in CHEM-5181

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

Other MS and Chrom. Resources

Mass Spectrometry Societies

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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