Proteomics Educational Resources

Tutorials

Scaffold software for complex sample analysis

• Introduction to Scaffold
• Self-Paced Scaffold Tutorial
• Sample Scaffold Data for tutorial (must have free Scaffold Viewer installed to view data)

How to interpret your Mascot search results

• Mascot tutorial for MALDI-TOF/TOF data
• Mascot tutorial for LC-MS/MS data

Workshops

Hands-on Proteomics Database Searching Workshop

• Sample MS data
• Sample MS/MS data (right click and save file to your computer)

Introduction to Proteomics Workshop

Posters

Two dimensional LC/MS-MS analysis of the Escherichia Coli Proteome: A Comparison of Protein and Peptide Fractionation in the First Dimension

Characterization of the Proteome of Tuberculin Using a Combination of LC-MALDIMS/
MS and LC-ESI-MS/MS

On-line Resources

Colorado Biological Mass Spectrometry Society

Scaffold http://www.proteomesoftware.com

Mascot http://www.matrixscience.com

SEQUEST http://fields.scripps.edu/sequest/index.html

X! Tandem http://www.thegpm.org/TANDEM/index.html

NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

Swiss-Prot http://us.expasy.org/sprot/

Various Mass Spec and Proteomics Tutorials http://www.ionsource.com/

Electrospray Ionization Tutorial http://www.newobjective.com/electrospray/index.html

Swiss Proteomics Society Digest (good resource to help keep up on the current literature) http://www.swissproteomicsociety.org/digest/

Gene Ontology Project (GO terms) http://www.geneontology.org/

Good Review Articles

Hoffert, J.D.; Knepper, M.A (2008) "Taking Aim at Shotgun Phosphoproteomics" Anal Biochem 375(1): 1–10.

Cravatt, B.; Simon, G.M.; Yates, J.R.(2007) "The biological impact of mass-spectrometry-based proteomics" Nature 450: 991-1000.

Marcus Bantscheff, M; Schirle, M; Sweetman, G; Rick, J; Kuster, B (2007) "Quantitative mass spectrometry in proteomics: a critical review" Anal Bioanal Chem 389:1017–1031.

Prenni, J.E.; Avery, A.C.; Olver, C.S. (2007) "Proteomics:  A review and an example using the reticulocyte membrane proteome."  Veterinary Clinical Pathology, 36(1) 13-24.

Domon, B. and R. Aebersold (2006). "Mass spectrometry and protein analysis." Science 312 (5771): 212-7.

Lambert, J. P., M. Ethier, et al. (2005). "Proteomics: from gel based to gel free." Analytical Chemistry 77 (12): 3771-3787.

Delahunty, C. and J. R. Yates (2005). "Protein identification using 2D-LC-MS/MS." Methods 35 (3): 248-255.

Steen, H. and M. Mann (2004). "The ABC's (and XYZ's) of peptide sequencing." Nature Reviews Molecular Cell Biology 5 (9): 699-711.

Tyers, M. and M. Mann (2003). "From genomics to proteomics." Nature 422 (6928): 193-197.

Aebersold, R. and M. Mann (2003). "Mass spectrometry-based proteomics." Nature 422 (6928): 198-207.