The specific state of the proteome in a given cell, tissue, or organism is known as the proteotype. The proteotype integrates constraints imposed by the genotype, the environment, and by developmental history (e.g., a leaf cell has a different proteotype than a root cell with the same genotype in the same environment). The proteotype directly determines phenotype since all molecules are made by and regulated by proteins. Thus, a complete description of the proteotype should define a phenotype at the molecular level. We have constructed an Atlas of Proteotypes that currently includes 162,777 peptides from 41,553 proteins in 65 different tissues and stages of development. In addition, we have identified and measured more than 30,000 phosphopeptides from these same samples. The 65 resultant proteotypes are revealing thousands of unanticipated regulatory relationships. The relationships between mRNA levels and protein levels are fascinating; they indicate that protein levels from some genes are regulated by transcription but that most protein levels are under post-transcriptional control. The proteotypes explain and expand upon known tissue-specific phenotypes including oil accumulation in the embryo and starch accumulation in the endosperm. Protein networks such as enzyme-substrate relationships between protein kinases and phosphoproteins are emerging from analyses of the proteotypes. The data are also being used for proteogenomics in which the peptide sequences are mapped back to the genomic DNA sequence to identify new protein coding genes and to correct existing gene models.

Protein networks from an atlas of proteotypes

245th National Meeting (2013)

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