The proteome of maize leaves: Use of gene sequences and expressed sequencetag data for identification of proteins with peptide mass fingerprints

As a first step in establishing a proteome database for maize, we have emba rked on the identification of the leaf proteins resolved on two-dimensional (2-D) gels. We detected nearly 900 spots on the gels with a pH 4-7 gradien t and over 200 spots on the gels with a pH 6-11 gradient when the proteins were visualized with colloidal Coomassie blue. Peptide mass fingerprints fo r 300 protein spots were obtained with matrix assisted laser desorption/ion ization-time of flight (MALDI-TOF) mass spectrometer and 149 protein spots were identified using the protein databases. We also searched the pdbEST da tabases to identify the leaf proteins and verified 66% of the protein spots that had been identified using the protein databases. Sixty-seven addition al protein spots were identified from expressed sequence tags (ESTs). Many abundant leaf proteins are present in multiple spots. Functions of over 50% of the abundant leaf proteins are either unknown or hypothetical. Our resu lts show that EST databases in conjunction with peptide mass fingerprints c an be used for identifying proteins from organisms with incomplete genome s equence information.