Prof. David Henderson Spring 1999


Class will begin in the assigned classroom and will move to the Instrument Room Cl 122 for the lab. Students should expect to spend some additional time in lab on another afternoon to finish assigned experiments and process data.

TEXTS: Introduction to Mass Spectrometry, J.T. Watson (JTW) 3rd Ed.

Supplemental Materials on Reserve in Library

Interpretation of Mass Spectra, 4th Ed., F. McLafferty and F. Turecek (FmcL)

Mass Spectrometry - Principles and Applications, E. De Hoffman, J. Charette and V. Stroobant (MS-P&A)

A programmed learning text, Mass Spectrometry, R. Davis and M. Frearson, will be available in the Library for your use to supplement the text. Also in the library is Practical Organic Mass Spectrometry, J.R. Chapman. (JRC)

The Mass Spectrometer is arguable the single most important tool of chemical analysis and chemical identification. In order to full master this technique there are four distinct areas of knowledge which you must acquire

1. How to use the software

2. How to use the hardware

3. How to interpret the data

4. How to design experiments to get results.

These areas all interact with each other, so it is not possible to separate them completely for instructional purposes. The lab activities during the first half of the semester will be designed to impart a working knowledge of the first three areas, beginning with software.

During the second half of the course, the course will focus on giving you both a reading knowledge of the literature in the field and also an in depth experience with at least two major aspects of the use of mass spectrometry. This will be accomplished through group projects.

Detailed Syllabus

Class and Topic Reading Assignment Exercises and Homework. Materials to hand in are due the next class after the assignment. Lab Activity
I. Introduction to Mass Spectrometry


J.T.W. Ch. 1 and 14   Overview of instrument and LabBase, Excaliber and HP data systems.
II. Identification of compounds by MS


J.T.W. CH. 2 & Ch 7 pp 139-161 Problem set II Tuning and Calibration of MS
III. Instrumentation


J.T.W Ch. 4, 13, & 19 Problem set IV GC-MS analysis of unknown mixture
IV. Ionization Modes EI/CI


J.T.W Ch. 6 & 8

Solid Probe EI/CI
V. Quantitative MS


J.T.W. Ch. 3, 15 & 20 Problem set III Quantitative Analysis
VI. Environmental MS Analysis and Ancillary Techniques


JTW Ch 12 & 16

EPA Methods 3550 B and 8270C

  Quantitative Analysis part 2


  Detailed plan for project 1 due You will go to the site and obtain samples for analysis. This may also be a good time to do sample workup
VII. Fragmentation mechanisms structural elucidation


JTW Ch 7 Problem set V Project 1 Environmental analysis using EPA Method
VIII. MS-MS and Electrospray Ionization


JTW Ch 5 & 11

J. Chem Ed.

1996, Vol 73, pp A82-88, A118-123, and A162-168

Each Student will find an application article using ES/MS and present a 5 minute summary of the article to the class. Project 1 cont
IX. Biochemical MS


MS-P&A Ch 7

PTW Ch 10

Problem set VI

Detailed plan for Project 2 due

Project 1 concludes
X. LC/MS interfaces


JTW Ch 17 Find, read, and summarize one article on LC/MS. You will each be assigned a specific topic. Project 2 Protein Sequencing using enzymes and MS-MS
XI. Fast Atom Bombardment


J.T.W. Ch 9 Find, read, and summarize one article on FAB-MS. Project 2 cont


Literature Papers 1 .Each student will present a 10 minute presentation on a paper Project 2 concludes


Literature Papers 2 Each student will present a 10 minute presentation on a paper Presentation of Project Results

The lecture portion of the course will deal with the general instrumentation, theory, practice and data interpretation for mass spectrometry. The reading assignments are heavily loaded toward the beginning of the course. It is recommended that you read through the readings quickly to prepare for class. Then plan to go through them in more detail after the class discussion. The rather lengthy chapters on spectral interpretation will make the most sense in context of trying to solve unknowns. You should not go to the answers until you have worked through them on your own.

The laboratory will introduce the specific details of the VG Trio-2 GC/LC/MS/Computer system. All of the capabilities of this instrument will be employed. Most of the techniques used for this instrument are generally applicable to all similar instruments.

Each student will select a short project to conduct using the instrument. The results of the projects will be presented in poster format and in a final written report.

One exam will be given during the Final Exam time. Part of this exam will be in class and part will be take home.


Projects 30

Homework 15

Labs 20

Quizzes and Class Participation 15

Final Exam 20

Project Experiments

The final six weeks of labs will be devoted to project experiments. You will work in groups of at least 2 or 3. One project will involve environmental analysis, both qualitative and quantitative using GC-MS. The default project will be analysis of soils from a contaminated site in Hartford identified by the DEP for semivolatile organic pollutants. However, students who wish to devise their own project along similar lines are welcome to propose an alternative. The other project must involve sequencing a protein (or nucleotide though these are harder) using ESI-MS-MS. Students may select a protein of interest to them or the professor will select something commercially available.

One student in the group will be appointed as group leader and will be responsible for coordinating the groups activities and serve as liason to the professor..

The process of preparing for this experiment is divided into several parts.

1. Identifying literature relevant to the project

2. Researching the required methods.

3. Devising a detailed plan of approach with lists of required chemicals and equipment and an outline of the operations to be performed and any safety precautions required.

4. Conducting the research.

5. Interpreting the results.

6. Presenting the Results.

Detailed Plan for Project One per group.

1. Bibliography and a 1-2 paragraph summary of each article and its relation to the project. Summaries must be written in your own words. Do not just submit the abstract of the paper!! It should be clear that you have read and understood the articles. Only published, peer reviewed articles are acceptable.

2. Detailed plan of approach. The specific steps in the protocol should be explained in detail and rationalized with reference to the literature. Details of sample collection, storage, preparation, and interpretation of results must be addressed in addition to the analysis method. Also, look up the MSDS (Internet OK) for each chemical and identify any hazardous materials and the precautions needed to work with them.

3. Appendix - Formal Protocol for the analysis. This will include a list of required chemicals, equipment, instrumentation, etc., outline of procedure, and safety precautions required for the equipment and chemicals to be used.

4. Writing folder containing all photocopies used in preparing the proposal, research notes, and anything else accumulated relevant to the project.

5. Detailed time log (up to this point) for each member of the group with a summary table.

6. Photocopy of proposal which will not be returned.

No proposals will be accepted for evaluation which do not include all six of the items above.

Written Project Report - Each individual will prepare a journal style report on the project. Each report will include, Introduction and Literature Background, Experimental, Data and Results, Conclusions, and Bibliography. A single Experimental and Data section may be prepared by the group. Each individual will complete all of the other portions of the report individually and independently.

Evaluation - The group will be evaluated based on the total time spent on the project and the quality of the proposal and final presentation. Individual grades will be assigned for the written reports.

It is not necessary to get an answer to the analytical question, but only to apply yourselves effectively to that goal.

Detailed project log. Each individual must keep a detailed log of their activities including the time, duration (day, hour, and minute), identity of group member doing the work, and the specific tasks accomplished. Each student should obtain a small notebook (or I can supply a blue book) for this log. All work will be recorded, library time, group discussion time, individual work time, etc. The notebooks are a complete journal of all individual activities. At the end of the project, a detailed time sheet for the project must be submitted showing the total time the group spent on the project and the individual contributions. (In industry, this information would be needed to provide accounting for the project. It will be used as a part of the evaluation of the project.) The time summary for each student, logs which support it and a copy of the summary table below will be submitted with the written proposal and again at the end of the project.

Student Individual hours Pair hours Group Hours Total Hours

Individual hours are time spent working alone, Pair hours refers to time when two people are working together, and Group hours represent time when three people are working together.

Evaluation- The overall evaluation of the Project Lab will be based on these factors.

1. Summary of Intended Project (Group)

2. Accuracy and completeness of experimental protocol (Group).

4. Total hours spent on project. 7 hours/student - C, 10 hours/student B, 13 hours/student A. (Group grade if all equal contributors)

Total hours will be the sum of individual hours + Group (of 3) hours x 0.66 + Pairs hours x 0.75.

5. Final report. (Individual)

All members of the group will share evenly in the group grades as long as the time contributions of the members are within 10% of the average for the group. Students who do less or more than their share will be rewarded according to their efforts.

Please note, you do not have to be completely successful in your analysis to obtain an excellent grade for the project. What is required is for you to spend your time efficiently and effectively. Reports which include no results and those with partial results should provide a detailed explanation of what would be required to complete the project in their final report. A critical evaluation of any deficiencies in a seemingly successful result is also expected.

When you have been checked out on the necessary instrumentation, you may work on your project at any time during normal working hours. No lab work may be conducted alone without written approval. You may not work during evenings without specific written approval of Prof. Henderson. Sign up sheets for the Mass Spec will be posted to facilitate scheduling. Note that research students are also using the MS, so it is important for everyone to sign up for times they want and use the times they sign up for. If you consistently sign up for time and then fail to appear, you will be penalized by limiting your access to the machine to the least popular times.