The commercial value of the wheat crop is a function of the quality and amount of the storage protein and starch present in the grain, which in turn are influenced by environmental conditions during grain-fill. To understand how environment modifies the size and composition of wheat grains, we set out to identify the key metabolic and regulatory proteins in developing grain. We present results of initial studies aimed at establishing instrument conditions that will allow us to identify cytoplasmic proteins present in wheat endosperm. Proteins were isolated, separated by 2D gel electrophoresis and stained with Coomassie blue to visualize and quantify changes in protein expression. Mass spectrometry was used to identify protein spots in 2D gels by means of "peptide mass maps" of in-gel enzymatically digested protein spots. Because only about 30% of the proteins could be identified by "peptide mass mapping," we developed nano-flow LC-MS/MS techniques that allowed us to identify about 80% of the salt-soluble proteins in wheat endosperm.