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Proteomics Syllabus


Please find below the syllabus for the proteomics module.  A pdf version can be found here.



 Term:  Spring 2011                                                                

Course dates/times:  T, R 2:45-4:00 p.m.                               

Course location: ED2 South 1308                                         

Instructor:  Assoc. Professor Karen Jonscher

Office:  R2 10112

Phone:  303-724-7244

Office Hours:  By arrangement                                             

email:  karen.jonscher@


For course information:


Course Description

 The discipline of mass spectrometry first became broadly applicable in 1956 when J.H. Beynon described the utility of mass spectrometry for the identification of organic compounds.  This transformed a highly specialized technique primarily utilized by physicists for inorganic isotope determination into an approach suitable for routine analysis of relatively nonpolar organic molecules, especially when used as a detector for gas chromatography. Over the last decade, mass spectrometric technologies have been developed that have revolutionized the field.  New “soft” ionization methods have facilitated the application of mass spectrometry, particularly when coupled to liquid chromatography, to the analysis of larger biomolecules such as proteins, peptides, lipids, DNA, RNA, and carbohydrates.  These innovations have enabled entirely new approaches to fundamental biology and drug discovery. The tremendous impact of these developments was recognized when the 2002 Nobel Prize in chemistry was awarded to Fenn and Tanaka, two pioneers of these techniques.


This module seeks to provide a technical overview of analytical mass spectrometry as it is currently practiced for proteomics applications. Students will review the predominant types of instrument platforms in current use and as well as concepts in sample preparation and bioinformatics.  Reading material will be predominantly comprised of primary source literature, review papers and web content.  A virtual laboratory will provide a practical application of concepts learned in lectures.  The course will conclude with students learning to interpret and validate bioinformatic output from proteomic studies.


Module Objectives

 After taking this module, students should:

      •  Be familiar with different types of sample preparation workflows.
  • Be able to identify advantages and limitations of the major types of mass spectrometers and ion sources, and appropriately select instrumentation that will provide useful information for a given proteomics application.  
  • Use a general protocol for interpretation of data from peptides and be able to validate data based on chemical “rules.”   


Module Requirements

 Students should have a bachelor’s degree in chemistry, biology or a related area.  Knowledge of undergraduate physics (electric and magnetic fields and forces) will be helpful, but not required.

 Required Texts:  None.  The reading assignments will be based on review papers and primary research papers.

 Some Texts Referred to in Lectures:

 J. Gross

Mass Spectrometry - A Textbook, 1st Ed., Springer-Verlag:  Berlin, Heidelberg, 2004.  ISBN-10 3-540-40739-1; ISBN-13 978-3-540-40739-3.

 E. de Hoffmann and V. Stroobant

Mass Spectrometry: Principles and Applications, 2nd Ed. (English), Wiley: New York, 2002.  ISBN 0-471-48565-9. (On reserve at Auraria Library)

 G. Suizdak

The Expanding Role of Mass Spectrometry in Biotechnology, 2nd Ed., MCC Press:  San Diego, CA, 2006.  ISBN 0-9742451-0-0.

 Additional, Materials, Equipment or Skills:  Students should bring a basic calculator to each class.  Much of the reading material and homework assignments will be web-based.  Students will need access to a computer, printer and the Internet. Module information may be distributed via e-mail and will be located under the Education tab on the Systems Biology Core Facility website.  Students will need to provide me with an e-mail address.  We will participate in a virtual laboratory on 4/12/11.  If at all possible, students should bring a wireless-enabled laptop to that class session.


Module Assignments


One homework assignment involving data validation will be assigned on 4/14/11 and will be due on 4/19/11.  Although the homework will not be graded, I encourage you to attempt it.  This will solidify your learning!  If you turn in the homework I will be happy to review it and go over it with you at a convenient time.

 Reading Assignments

There will not be required reading from a textbook.  Journal papers and web content will be assigned for daily reading.  These recommended reading assignments are important for understanding the lecture material more effectively. 

 Virtual Laboratory

Students will participate in 1 virtual laboratory.  Students will take a pretest.  Following the laboratory, the students will take a post-test to assess the change in understanding of the material.  I encourage you to generate a lab report, although it will not be graded for this class.  A lab guideline and a rubric for the report is available on the Systems Biology Core Facility website.


The best way to learn is by asking questions and providing input.  I encourage your questions, either during lecture time, or outside of the classroom.


Course Schedule






Review of syllabus, introductory topics, sample preparation, ionization.

Review “What is Mass Spectrometry” on the ASMS website (  An additional site is  Read Spectroscopy Mass Spec Tutorial.


Instrumentation and applications


Review MALDI-TOF tutorials at:  .  Other good things to look at include a presentation on time of flight mass analyzers by Carty and the 2001 review on MALDI imaging by Caprioli.  Review interpretation of ESI spectra at Read Anal Biochem Ion Trap Review Jonscher.



Virtual laboratory

Review introductory material for virtual lab at VMSL website  Read Shevchenko papers for the Protein Identification Case Study  and the MALDI matrix guide, look up common MALDI matrices.  Take the Case Study pre-test, print and turn in on 4/12/11.  Read Cottrell Database Searching Tutorial.


Data interpretation and validation

Lab report due.  Read Steen and Mann, ABCs and XYZs of protein sequencing.  Turn in data validation homework by 4/19/11.


Student Success

Your presence and participation will be key for you to learn the material and benefit from taking this module.  Read the assignments before class, ask questions during lectures, contact me to discuss anything you don’t understand – contribute to your learning process!  Everyone has something to offer – some knowledge or experience.  Your involvement in class discussions will help make the module a richer educational experience for everyone.

 Module Communication

In addition to announcements made and written handouts distributed in class, I may need to contact you between classes, which I'll do through individual and group email messages. One of the requirements for this course is that you maintain an email address, check it regularly for messages, be sure it is working, and let me know if you change your email address. You are responsible for any messages, including assignments and schedule changes, I send you via email. Please contact me by e-mail for office hours if you are having problems with the work.


Please turn off beepers and cell phones during class.  We will all learn more effectively if we treat classmates and their contributions respectfully.  You are expected to adhere to the Student Code of Conduct.  No texting during class!

 Military Duty

Please let me, the Advising Office and your school Associate Dean know immediately if you might be called to military service/training during the semester.