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Chem204: Introduction to Proteomics

Winter Quarter 2013

Starting with a review of protein chemistry, emphasizing chemical modification and separation technologies, the course will review current approaches to the study of proteomics, how proteomics interacts with other fields and discuss what is likely to be realized in the next several years.

This course is not restricted to only graduate students. If you are not a student and are interested in attending, please contact Robert Chalkley.

Lecture Series

All lectures will take place from 9:00am - 10:30am in room GH-S261.

Date Topic Lecturer Student Materials
1. Tue. 1/8 Overview / Protein Chemistry RAB lecture notes
2. Thu. 1/10 Protein Purification and Separation/Gels RJC lecture notes
3. Tue. 1/15 Peptide Purification and Separation RAB lecture notes
4. Thu. 1/17 Introduction to Mass Spectrometry RJC lecture notes
5. Tue. 1/22 Protein ID 1 – Non-MS RAB lecture notes
6. Thu. 1/24 Protein ID 2 – MS RJC lecture notes
7. Tue. 1/29 Quantification KFM lecture notes
8. Thu. 1/31 Bioinformatics PCB lecture notes
9. Tue. 2/5 Biophysical Methods (Fluorescence / Hydrodynamics) KFM lecture notes
10. Thu. 2/7 Protein – Protein Interactions: AP-MS; Xlinking RJC lecture notes
11. Tue. 2/12 Protein – Protein Interactions: Intact Complex Analysis KFM lecture notes
12. Thu. 2/14 PTMs – Overview KFM lecture notes
13. Tue. 2/19 PTMs – Complex / Crosstalk KFM lecture notes
14. Thu. 2/21 Signaling RAB lecture notes
15. Tue. 2/26 Network Analysis and Clustering RJC lecture notes
16. Thu. 2/28 Arrays RAB lecture notes
17. Tue. 3/5 Micro-fluidics / Robotics / Nanotech RAB lecture notes
18. Thu. 3/7 Translational / Biomarkers RAB lecture notes
19. Tue. 3/12 Protein Machines / Sociology AS
20. Thu. 3/14 Interaction with other OMICS RJC, KFM, RAB

Lecturers

RAB - Ralph Bradshaw
RJC - Robert Chalkley
KFM - Katalin Medzihradszky
PCB - Patricia Babbitt
AS - Andrej Sali

Course Assessment

In addition to attending the lectures, students taking this course for credit will be required to select and present a review of a published paper (from a pool of papers selected by the instructors). These will be presented during the last half hour of several of the later lectures in the series. Students will also be expected to write a paper on a topic of current interest to the field (from a list provided, or select their own topic after instructor approval).

Possible Papers for Presentation

  1. Deeb SJ, D'Souza RC, Cox J, Schmidt-Supprian M, Mann M. Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Mol Cell Proteomics 2012 11 (5) 77-89i.
  2. Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics 2012 11 (8) 215-29.
  3. Mommen GP, van de Waterbeemd B, Meiring HD, Kersten G, Heck AJ, de Jong AP. Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion. Mol Cell Proteomics 2012 11 (9) 832-42.
  4. Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011 7 548.
  5. Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bähler J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell. 2012 151 (3) 671-83.
  6. Frei AP, Jeon OY, Kilcher S, Moest H, Henning LM, Jost C, Plückthun A, Mercer J, Aebersold R, Carreira EM, Wollscheid B. Direct identification of ligand-receptor interactions on living cells and tissues. Nat Biotechnol. 2012 30 (10) 997-1001.
  7. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2012 31 (1) 38-45.
  8. Kwong GA, von Maltzahn G, Murugappan G, Abudayyeh O, Mo S, Papayannopoulos IA, Sverdlov DY, Liu SB, Warren AD, Popov Y, Schuppan D, Bhatia SN. Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease. Nat Biotechnol. 2012 31 (1) 63-70.
  9. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 150 (2) 413-25.
  10. Jaros JA, Martins-de-Souza D, Rahmoune H, Rothermundt M, Leweke FM, Guest PC, Bahn S. J Protein phosphorylation patterns in serum from schizophrenia patients and healthy controls. Proteomics. 2012 76 43-55.
  11. Piroddi M, Palmese A, Pilolli F, Amoresano A, Pucci P, Ronco C, Galli F. Plasma nitroproteome of kidney disease patients. Amino Acids. 2011 40 (2) 653-67.
  12. Xu G, Paige JS, Jaffrey SR. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol. 2010 28 (8) 868-73.
  13. Masri S, Patel VR, Eckel-Mahan KL, Peleg S, Forne I, Ladurner AG, Baldi P, Imhof A, Sassone-Corsi P. Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A. 2013.
  14. Dastidar EG, Dzeyk K, Krijgsveld J, Malmquist NA, Doerig C, Scherf A, Lopez-Rubio JJ. Comprehensive histone phosphorylation analysis and identification of pf14-3-3 protein as a histone h3 phosphorylation reader in malaria parasites. PLoS One. 2013 8 (1) e53179.
  15. Li X, Foley EA, Kawashima SA, Molloy KR, Li Y, Chait BT, Kapoor TM. Examining posttranslational modification-mediated protein-protein interactions using a chemical proteomics approach. Protein Sci. 2012 Dec 27.
For more details contact course organizer: Robert Chalkley.

 

Course Organizer

Robert Chalkley.