(P06-040-23) The Proteomes That Feed the World

Objectives: Plants represent the nutritional basis of all life on earth. While the genomes of the crop plants are increasingly elucidated, little is known about the crop proteomes. To close this knowledge gap, we have launched the international doctoral program "The Proteomes that Feed the World". One of the program´s aims is to map the proteomes of all major tissues and organs of the 100 crop plants most important for human nutrition.

Methods: The international doctoral program brings together an interdisciplinary team of 16 PhD students and 12 principal investigators with leading expertise in plant science, proteomics, and bioinformatics. This so-called Proteome Engine is supported by an international network of more than 30 partners.

To manage a plant proteomics project of this scale, it requires optimized and balanced sample preparation, liquid chromatography tandem mass-spectrometry (LC-MS/MS) measurements, and bioinformatics workflows. Comparison of different protein extraction methods showed that a serial three-step process with trichloracetic acid/acetone extraction, sodium dodecyl sulfate (SDS) solubilization, and phenol extraction provided the highest protein yields. We developed an automated one-pot sample preparation protocol (SP3) on a liquid-handling robot, and we utilize an automated off-line peptide separation protocol using an AssayMap Bravo liquid handling platform and optimized micro-LC-MS/MS conditions. This method enables the identification and quantification of more than 10,000 proteins within 6 hours of instrument time. The raw mass spectrometric data as well as protein identification and quantification results will be made publicly available on PRIDE and in ProteomicsDB on regular basis throughout the project.

Results: A robust and reproducible protocol for the proteomic analysis of plant tissues by LC-MS/MS was developed. To date, we elucidated the first comprehensive proteome of Quinoa bicolor, which covers more than 20,000 proteins, and the identification of more than 10,000 proteins in the fruit of Solanum lycopersicum.

Conclusions: With this project, we are creating a Crop Proteome Atlas of extremwly high value to academia as well as the agricultural, food, beverage, and pharmaceutical industries.

Funding Sources: The program was launched at the Technical University of Munich, and is funded by the Elite Network of Bavaria.