Analytical challenges and strategies for the characterization of gp96-associated peptides.

This paper describes the methods that were used for the preparation of gp96-associated peptides and the analysis of these peptides using mass spectrometry. A general approach for stripping, enriching, and separating peptides associated with gp96 is presented. Protocols for the demonstration of the diversity of gp96-associated peptides using mass spectrometry and the identification of these peptides using a combination of tandem mass spectrometry and protein database searching are described. Important parameters and factors that affect the outcome of the experiments are discussed.