2021 syllabus at: http://tinyurl.com/CHEM-5181-Syll-2021
Syllabus – Fall 2019
CHEM 5181 – Mass Spectrometry, Chromatography, and Computer Programming
University of Colorado at Boulder – Department of Chemistry
Tue & Thu 11:00-12:25 - Ekeley W165
This Syllabus: http://tinyurl.com/CHEM-5181-Syll (online version is always the most up-to-date)
Taught by:
Prof. Paul J. Ziemann
Prof. Jose-Luis Jimenez
1. Course Overview
1.1. Course Objectives
After taking this course you should have developed an understanding of:
- Physico-chemical principles underlying MS and chromatography
- Main types of MS & Chrom. techniques and instruments in use
- “Applied” focus: fundamentals, applicability, extractable information, advantages and limitations
- Fundamentals of data interpretation
- Intermediate ability for computer programming & graphing for data analysis and simulations (together with CHEM-5131)
You are likely to encounter in your graduate and professional careers many problems for which MS or separation or programming techniques that we do not cover in the course (or that don’t even exist today) are very useful. Another way to state our objective is that after taking this course you should be able to ask intelligent questions, look for the information you need, and 1) decide whether the technique is useful for your problem; and 2) quickly learn to use the technique and interpret its data.
This is a core course for PhD students in Analytical, Environmental, and Atmospheric Chemistry at CU. Most students taking the course will also join a research lab in one of the Atmospheric Chemistry groups at the end of the semester. Experience has shown that if we focus too strictly on the technical content of the class, students are slow in getting started in research because they are missing critical skills. Thus a key goal of this course is to give you an introduction to critical computer programming skills. This course is part of the “Grad School Boot Camp” and can be pretty intense at times.
This class is partially “tilted”, meaning that you may be required to read some of the material before class in the books or other resources, and we will spend more of the class time answering questions or working together on examples that apply the concepts. Research shows that students learn more with this type of “active learning” approach (even though they sometimes complain because they are more used to being passive during lecturing, and active learning requires more energy).
Finally, Paul and Jose have quite different teaching styles. They will alternate in 4 segments (2 each) during the semester, to provide continuity of material and style. ½ of the final grade is determined by each professor.
1.2. Structure of the course
The course will address 4 topics:
- Computer Programming for data analysis and simulation (Igor)
- Mass spectrometry instrumentation
- Mass spectrometry interpretation
- Chromatography
1.3. Course prerequisites
The course prerequisites are undergraduate physics (Newton’s laws of motion, electric and magnetic fields and forces, heat and mass transfer, basic fluid mechanics), calculus, probability and statistics, and basic physical chemistry. Also basic computer programming, or a willingness to work very hard on it. You are responsible for supplemental work that you may need to catch up in any of the prerequisite areas.
2. Practical Items
2.1. Web page & Schedule for the course
- We will use extensively the Piazza system for this course
- Jose will bring printed notes before every class and post the lecture notes on the homework web page after each lecture. There are several old web pages still online with past versions of the notes. Do not print old versions of the notes that before class, as those are from previous course offerings and are updated each year.
- The course schedule will be kept at this link
2.2. Textbooks:
- We will provide PDFs of chapters that need to be read, but these books will be useful to have if you plan to use MS a lot in your research. They are also available from the library.
- Gross: Mass Spectrometry, A Textbook, 3rd Ed
- Hoffmann & Stroobant. Mass Spectrometry: Principles and Applications, 3rd Ed.
- McLafferty & Turecek. Interpretation of Mass Spectra, 4th Ed.
- Suggested: Printed manuals for Igor Pro software, which can be ordered from Lulu. These manuals are also available electronically once you install Igor, and also online at http://www.wavemetrics.com/products/igorpro/manual.htm. However we will use them a lot and many of you will continue to use them in research for years, so working with a printed version can be very useful. For this course you will not need the XOP, Filter, or NIDAQ Igor manuals.
mat
2.3. Other Useful Books
- Taylor, An Introduction to Error Analysis, 2nd Ed., 1996.
- Press et al., Numerical Recipes, 3rd Ed., 2007. Also available online at http://numerical.recipes/, but I have found it very useful to have a printed copy.
- Moore et al., Building Scientific Apparatus, 3rd Ed., 2009.
- There is no textbook for the chromatography part, as we have not found a good one. Past students may have the Braithwaite book that is a reasonable reference. We will provide reading materials for some of the topics. See below for other reference books.
- Reading will be assigned for some class periods. You will have to answer a few standard questions by email before each lecture, per the Just-in-Time Teaching technique (see http://webphysics.iupui.edu/jitt/what.html). Graded clicker questions may be given at the start of class to test the level of understanding and encourage people to do the reading.
Useful reference books at a more introductory level:
Some other good books on mass spectrometry:
Some other good books on separations:
Also note that lots of information on these topics is available online. But also do note that there is much more crap than good information online, so you have to use your judgment!
2.4. Office Hours
- 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).
- We will try to find another time that works for everyone (or most people), so please complete the form at http://tinyurl.com/j-class-sched with the times when you are NOT available (TA conflicts, other classes, group meetings etc.). The times will be announced in class
- We can also do office hours by appointment. But do not show up to our offices without warning, as chances are we may be meeting with someone else and not able to answer your questions right then.
- Paul & Jose will monitor Piazza (below) and reply that way, so people are encouraged to ask questions using that method.
- Questions will be addressed in the order of prior contact / showing up for office hours, up to the time allocated.
- Late evening requests before a homework is due will typically not be answered, though you can try to discuss with your fellow students on Piazza (see next item).
2.5. Piazza Bulletin Board
- We will use the Piazza system for communication, both as an email list and as a bulletin board.
- It is essential that you are subscribed and that you receive the emails. Note that you can set up a “digest mode” on the upper right corner under “Account / Email Settings.”
- All class-related questions need to be posted in Piazza. Note that you can post anonymously if you prefer. Questions asked via email will be replied to with “please post this in Piazza and I’ll reply there.” This allows others to benefit from the exchange of information. The only exception are personal questions (e.g. you’ve been sick etc.).
- We strongly encourage students to discuss / answer other students questions in Piazza.
- Note the difference from the Wiki Student Answer vs the Individual Comment (we’ll come back to this)
- Some items will require a response from you in a certain timeframe. Lack of response by the deadline will be penalized on the class participation grade.
2.6. Clickers
- We will use iClickers during the lectures for interactive questions and quizzes.
- Unless you already have an iClicker, you will be issued one at the start of class. You are responsible for returning it at the end of the course, otherwise you will be given a grade of “Incomplete” until a working iClicker is returned..
- Unless otherwise stated, clicker questions will be part of the class participation grade (just the fact that you answered, not whether the answer was correct).
- You will be excused forgetting your clicker or having low batteries 2 times during the course, after that your class participation grade will the reduced proportionally, no exceptions. Again, you are responsible for replacing the batteries when needed.
2.7. Laptop and General Programming
- A working Windows or Mac laptop is required for the Igor part of the course.
- We will use the scientific programming software package Igor Pro as an integral tool during the course, including homeworks, and you will have to turn in your code as part of the assignment.
- Exams may include a programming question(s) to be programmed in class and emailed at the end of the exam.
2.8. Igor Software and Programming
- This year CHEM-5181 is offered in coordination with CHEM-5131 (Prof. Browne), as the two courses constitute the core requirements for the Graduate Analytical Chemistry program this Fall. We will delay the start of the programming tasks to give time for that course to get started. We will assume that you are also taking that course, or that you already have the main skills that you would learn in that course.
- You will need to install the Igor Pro 8 software in your laptop, and bring your laptop for use in class for some lectures, per announcements on the previous lecture or via Piazza.
- Info on IGOR is at: http://www.wavemetrics.com/.
- Igor is a very powerful data analysis, programming, and graphing software. This software is a main research tool in several CU groups, including the Tolbert, Ziemann, de Gouw, Browne, and Jimenez groups, but it will be useful if you join other groups as well. Igor is comparable to other packages such as Matlab or IDL. Each has its strengths and weaknesses, but as a friend of mine said "many Science and Nature papers have been written with each one of those", so they all do the job.
- If you don't have experience with this software, you should install it in your computer and go thru the "Getting Started" booklet ASAP. Other resources will also be distributed via Piazza.
- If you are not interested in learning the necessary basic computer programming, you should drop the course, as it is a very integral part of it.
- If learning IGOR is not acceptable to you, and you already know very well an alternative software package such as Matlab or IDL, please discuss with Jose.
- We have purchased an academic license for use by students on coursework. You should install IGOR 8 in your laptops by downloading it from:
https://www.wavemetrics.com/order/order_downloads.htm
and then entering the Serial Number and Activation Key that will be distributed via email or Piazza.
- Once you have installed, you should open the online manual (PDF) and go through the "Getting Started in IGOR" section. There are also video tutorials and various other materials online, that you are encouraged to review as needed.
- The IGOR license is for coursework only for any course in the CHEM Dept., so after the end of the semester, those of you joining one of the IGOR-equipped groups should install their licenses. For the rest of you, you can try to convince your advisors to get a license (pretty cheap at $450 or so, as research costs go) or get a personal license ($85 for student personal purchases).
2.10. Helping Get the Classroom Ready
- Whoever gets to class first should erase all boards, turn on the projector, and lower the screen. This helps with a smooth start.
- Also please silence your cell phones and laptops.
3. Grading, Homeworks, etc.
3.1. Course Grading Policy
The grade will be determined as the weighted average of the following parts, with typical percentages given below.
- Class participation (including clicker response rate and feedback on class) - 10%
- Homework, including reading questions - 40%
- Midterms - 20%
- Final exam - 30%
3.2. Homework Details for Jose’s Part
- Since this is a graduate course, we often treat the homeworks as pieces research problems that we may give to students in my own group. I assign an interesting question for which I don’t know the exact answer. At times the problem may not be solvable or be more complex than I anticipated. This is good training for research in your groups. However it can prove disorienting at the start for people coming just from undergrad, who are used to “perfectly posed homework problems” that have been tested many times.
- HW will be turned in electronically via email to chem5181@gmail.com. Attachments larger than 25 MB will not go through.
- I will grade some HWs each time, selected with a random number generator. This will typically be ~2-4 HWs per person per semester. It would be great to be able to grade more HWs, but it would just take too much time.
- I can always discuss your specific homework solution during office hours, whether I graded it or not.
3.3. Policy about Homework Collaboration
- It is OK to discuss the problems in small groups or in Piazza, and in fact this will help you learn (teach each other, bounce ideas, etc.) and is more relevant for preparing you for research.
- However everyone is still responsible for working out, understanding, and writing their own solution separately. If you don't go through the effort of understanding and solving every problem yourself (after discussing it with others if you want) you will find yourself at a large disadvantage in the exams where you have to solve new problems very quickly. To reiterate, it is OK to discuss the problems but not to write solutions together or to compare them or the results. If you do any of the later, it often becomes obvious when grading because multiple people have the same wrong solutions to several problems.
3.4. Homework and Exam Legibility & Units
It is often a significant problem to “decode” homeworks and exam if the writing is too small or messy, or if they are poorly organized. We will take points out for poor legibility. For homeworks, we prefer if you type them in a computer, although this is not required. A scan of a neat handwritten homework works too, but if your handwriting is small or otherwise hard to read, either make an effort to write in a more readable form, or type it up. The current homework will be posted on the course page and announced in class and/or via Piazza.
Please list the units of all results. SI units are required, with some exceptions that will be discussed in class.
All graphs need to be properly annotated, with axis labels, legends, and units. All code needs to be clear, following the Course Igor conventions, with clear variable and function names, and with enough comments for one of your colleagues to be able to understand what you are doing.
3.5. Attendance Policy
You are required to attend all the lectures. If you need to miss a lecture, let us know ahead of time. You are still responsible for completing reading quizzes and turning in HWs on time even if you will be absent for that class period.
3.6. Policy on Course Auditing
- Every CU student attending the course needs to register, either as (a) for grade; (b) for pass/fail; or (c) for "Audit/No Credit".
- Postdocs can register for free (CU employees get one free class per semester).
- 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".
- The rules for people registered as “Audit/No Credit” are as follows:
- We hope that you attend all the lectures and do the reading and HW. However there are no consequences if you don't do any of those things for whatever reason.
- If you are going to miss multiple classes, we would appreciate if you let us know so that we can adjust the number of printouts we bring to class.
- We will assume that you will do the reading and the HW, and we will call on you during the discussions and ask you to present the HWs similarly to the registered students. If you don't have time to do this for some sections of the course, just let us know in advance to save time and confusion during class. Also if you are not doing the reading and HW for part of the class, please refrain from asking basic questions in class that would have been answered by doing the reading or HW, so that we save time during class. We can still discuss those items with you at the end of class or during office hours.
3.7. Best Grade in the Course
The student with the highest grade at the end of the course will be immortalized in the CHEM-5181 web page.
3.8. Some Information about Grades
Please don’t obsess in grad school about grades! They are much less important tool than they were in undergrad. They should not become an end in themselves (the “professional student syndrome”), rather they should be a feedback tool to help you identify your strengths and weaknesses and to learn.
Grading is absolute, we don’t grade on a curve. Not everyone has gotten an A in past offerings of this course (although we would be very happy if that was the case), and from experience a good grade requires hard work. You need to get at least a B- for the course to count towards graduate credit and a B (average of all courses) to avoid being placed on probation (for CHEM graduate students). Everyone who takes the class seriously and works hard has been able to meet those criteria in past years.
Note that we determine the grading policy, and always make an effort to grade all students with the same criteria. For this reason we cannot change your grades unless we made a mistake. So please don’t tell us thigns like “yes, it is true I made that mistake in that question, but I think you should only discount 2 points instead of the 4 you took for it.”
3.9. Changes to the Course During the Semester
As with life, this syllabus is subject to change. We may make some changes to the course during the semester if we think is appropriate, including to lectures, assignments, presentations, and exams.
3.10. Feedback on the Course
- We are always experimenting with some new ideas to try to improve the course, many of which were suggested from previous years’ students. The purpose of having a course is that it will be useful to you, the students!
- Do not hesitate to give us feedback early on about what’s working or not working – chances are that we can fine-tune the course as we go along, as we have done in previous years.
- At the end of the course we will send an online questionnaire with specific questions about the course, so that we can use your experience to improve the next offering. This is complementary to the FCQs, and allows us to get more specific feedback. We ask that you take this seriously as it really helps us improve. You will get some class credit for doing this as part of the class participation grade (proportional to the total number of respondents since the responses are anonymous).
3.11. Pets
No pets are allowed in class, office hours, or labs (and in fact in any CU building) at any time for any reason, per the CU policy specified at http://www.colorado.edu/policies/CUUF. The only exception are service dogs.
4. Other Matters as Required by CU
Accommodation for Disabilities
If you qualify for accommodations because of a disability, please submit your accommodation letter from Disability Services to your faculty member in a timely manner so that your needs can be addressed. Disability Services determines accommodations based on documented disabilities in the academic environment. Information on requesting accommodations is located on the Disability Services website. Contact Disability Services at 303-492-8671 or dsinfo@colorado.edu for further assistance. If you have a temporary medical condition or injury, see Temporary Medical Conditions under the Students tab on the Disability Services website.
Classroom Behavior
Students and faculty each have responsibility for maintaining an appropriate learning environment. Those who fail to adhere to such behavioral standards may be subject to discipline. Professional courtesy and sensitivity are especially important with respect to individuals and topics dealing with race, color, national origin, sex, pregnancy, age, disability, creed, religion, sexual orientation, gender identity, gender expression, veteran status, political affiliation or political philosophy. Class rosters are provided to the instructor with the student's legal name.
Faculty will honor your request to address you by an alternate name or gender pronoun. Please advise faculty of this preference early in the semester so that they may make appropriate changes to their records. For more information, see the policies on classroom behavior and the Student Code of Conduct.
Honor Code
All students enrolled in a University of Colorado Boulder course are responsible for knowing and adhering to the Honor Code. Violations of the policy may include: plagiarism, cheating, fabrication, lying, bribery, threat, unauthorized access to academic materials, clicker fraud, submitting the same or similar work in more than one course without permission from all course instructors involved, and aiding academic dishonesty. All incidents of academic misconduct will be reported to the Honor Code (honor@colorado.edu); 303-492-5550). Students who are found responsible for violating the academic integrity policy will be subject to nonacademic sanctions from the Honor Code as well as academic sanctions from the faculty member. Additional information regarding the Honor Code academic integrity policy can be found at the Honor Code Office website.
Sexual Misconduct, Discrimination, Harassment and/or Related Retaliation
The University of Colorado Boulder (CU Boulder) is committed to fostering a positive and welcoming learning, working, and living environment. CU Boulder will not tolerate acts of sexual misconduct intimate partner abuse (including dating or domestic violence), stalking, protected-class discrimination or harassment by members of our community. Individuals who believe they have been subject to misconduct or retaliatory actions for reporting a concern should contact the Office of Institutional Equity and Compliance (OIEC) at 303-492-2127 or cureport@colorado.edu. Information about the OIEC, university policies, anonymous reporting, and the campus resources can be found on the OIEC website.
Please know that faculty and instructors have a responsibility to inform OIEC when made aware of incidents of sexual misconduct, discrimination, harassment and/or related retaliation, to ensure that individuals impacted receive information about options for reporting and support resources.
Religious Holidays
Campus policy regarding religious observances requires that faculty make every effort to deal reasonably and fairly with all students who, because of religious obligations, have conflicts with scheduled exams, assignments or required attendance. For each class, check with your faculty member in advance so that you are aware of their specific requirements for accommodating religious observances.
See the campus policy regarding religious observances for full details.
MATERIAL AFTER THIS POINT IS FROM PREVIOUS COURSES (FOR OUR REFERENCE) AND IS NOT PART OF THIS YEAR’S SYLLABUS
3.4. Journal Skims and Paper presentations.
Students will be required to summarize ~2 journal papers on each of the areas of the class, posting a summary to the Google+ CHEM-5181 Community in the specified format. Due dates will be announced in class. The purpose is to gain familiarity with current topics in the field and with the G+ method of using a group to stay on top of the scientific literature.. The appropriate journals are linked at the bottom of the course page (you can also select papers from other journals or possibly web pages, if appropriate). Please +1 the papers that you find interesting, as that will be a criterion to select papers for presentation, AND add a comment on why you find that paper interesting or useful (or not interesting or useful) (+ class participation points for +1 some papers, not all!).
Students will also present a summary of ~1-2 papers each during some lectures. Check with the instructor for the suitability of a paper for presentation no later than 2 weeks prior to presentation (so that there is time to find a new one, should the chosen one not work).
2.11. Screen Projection in Class
For both homeworks and paper presentations, students will be required to project from their computer at different times during the semester. Projecting your screen is something you will do MANY times in your professional career, and fumbling around and wasting people’s time is unprofessional. Each student is responsible for having the right adapter to project from their computer to the VGA connector in the classroom, and for carrying it at all times, and for setting the resolution to 1028 x 764 (or as close as possible to that, in order for the projection to be viewable from all locations in the classroom). A penalty of 15% of the grade of the activity being projected will be applied otherwise.