The NIH ProtIG has some on-line lectures from the 2003 Exploring the Proteome II symposium.
Richard Caprioli
Profiling and Imaging of Proteins in Tissue Sections using Mass Spectrometry as a Discovery Tool in Biological and Clinical Research
Steven Carr
Biomarker Discovery by Proteomics
Donald Hunt
Analysis of Differential Protein Expression, the Phosphoproteome, Protein-Protein Interactions, and the Histone Code by Fourier Transform and Ion Trap MS
Steven Gygi
A proteomics approach to understanding protein ubiquitination
Peter Roepstorff
Assignment of post translational modifications is essential in proteomics
Rolf Apweiler
Integration and Standardization: Driving forces in protein informatics
Carol Robinson
Exploring dynamic protein interactions using mass spectrometry
The above lectures are in Shockwave format: lecture audio over Powerpoint slides. The NIH video archives also have Realplayer format video lectures, for example, New Mass Spectral Strategies for Proteomics and Glycomics, a lecture by Cathy Costello on May 14, 2004 and Towards Comprehensive Proteomics of Cells by John Yates, April 04, 2003.