CB 399: An Overview of Mass-Spectrometry-based Proteomics Spring 2011

Intellectual Unit:

An Overview of Mass-Spectrometry-based Proteomics
Course Lecturers: Steve Gygi, Jarrod Marto, Hanno Steen

PLEASE NOTE THE CHANGE IN DATE AND LOCATION (MODIFIED 2-24-11)

Curriculum Fellow: Johanna Gutlerner, Johanna_Gutlerner@hms.harvard.edu

Mass spectrometry is the enabling tool in the field of proteomics. The field has advanced at such a pace that many papers now report the simultaneous identification of thousands of proteins directly from cells or tissues. We will discuss three areas where mass spectrometry can directly impact cell biology research. 1) Practical aspects of protein sequencing via mass spectrometry. 2) Determining sites of posttranslational modifications such as phosphorylation. 3) The use of stable isotopes to encode whole proteomes for protein profiling of different cell states.

 Schedule:

First Session: Tuesday, April 12, 2011 1 – 4:30 PM
Location: TMEC Building, Walter Amphitheater

Second Session: Thursday, April 21, 2011 1:30 – 4 PM
Location: TMEC Building, Room 309

DROP DEADLINE: Tuesday, April 5, 2011

Log in below to download the slides from session 1

Recommended background readings: (log on below to download)

Domon, B.  and Aebersold, R. (2006) Mass Spectrometry and Protein Analysis. Science, vol:312, pp. 213—217.

Mallick, P and Kuster, B (2010) Proteomics: a pragmatic perspective. Nature biotechnology, vol:28:7, pp. 695 – 709.

Bantscheff , M, et al (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem, vol:389, pp.1017–1031.

 

Required reading for second session: (log on below to download)

Kratchmarova, I, et al. (2005) Mechanism of Divergent Growth Factor Effects in Mesenchymal Stem Cell  Differentiation.  Science, vol: 308, pp. 1472 – 1477.

 

Required assignment for second session: (log on below to download)

Questions for Discussion
Thursday, April 21st, 2011, 1:30 – 4 pm
Room TMEC 309

 Instructions:  Please respond answer the questions with one paragraph for each and bring them to the second class session.

 1. What is the difference between “top-down” and “bottom-up” proteomics?

 2. How does a mass spectrometer “sequence” a protein? How does an algorithm like Sequest identify sequence from tandem mass spectra?  How does it identify phosphorylated peptides?

 3. How many proteins are expressed in a HeLa cell or a yeast cell?  How many proteins can large-scale proteomics experiments identify?  How big is this gap?

 4. What are the two most common ionization techniques?  What are four common mass analyzers?  What is the difference between mass resolution and mass accuracy?

 5. What are the iTRAQ and SILAC strategies for quantitative proteomics?  Compare and contrast them.

 6. Distinguish between absolute and relative quantification and how they are typically used in proteomics studies

 7. Discuss current limitations in interpretation of large-scale proteomics data sets.

 

AUDITORS (Post-Docs, Faculty, or Staff) DO NOT NEED TO SIGN UP TO ATTEND THE 1st SESSION.  PLEASE DO NOT ENROLL.