Most of our knowledge in proteomics comes from comprehensive studies on model organisms, such as yeast, and in humans. Proteomics research in plants has not advanced at the same pace. The main reasons for this are: the lack of availability of full genome sequence of most plants; the complexity of protein samples which vary dramatically across different plant species and also across different tissues of the same plant; and the technical difficulties inherent in sample preparation from plant tissues and organelles. 

Nevertheless, in recent years the amount of published literature in plant proteomics has grown extremely rapidly, and it continues to accelerate. Plant proteomic studies have primarily been conducted in Arabidopsis thaliana and rice (Oryza sativa). Arabidopsis and rice are the long- and short-day flowering plants that serve as reference plants for dicot and monocot plant species, respectively. Arabidopsis is the only plant species with a genome that is fully decoded and almost completely annotated. In rice, the almost complete genome sequences of two widely cultivated rice cultivars, japonica (Nipponbare) and indica (93-11), are available. Importantly, rice proteomics is considered a cornerstone for cereal food crop proteomics because many physiological traits in other cereal crops can be mapped to syntenous genes in rice. Indeed, in 2002, Donald Kennedy, the editor of Science, wrote in a commentary on publication of a rice genome draft sequence that it "had the potential to be of greater significance to human health than the sequencing of the human genome". The genome sequences of several other important plant species, notably corn (Zea mays) and tomato (Lycopersicon esculentum) are expected to be completed in the near future, which will further facilitate proteomic studies in a diverse range of plants.

Proteomics is used within the plant and agricultural research fields in a wide range of contexts. Examples include the investigation of plant responses to abiotic stresses such as salt tolerance and drought resistance, or biotic stresses such as insect herbivory, investigation of crop growth and quality markers, and identification and functional analysis of unknown proteins expressed in plants.  Many of these studies are aimed at enabling selective breeding of crop species to increase yields and better cope with adverse environmental conditions.

Agricultural industries are continually seeking secondary value-added bioactive materials, be that in the livestock or crop fields. APAF, through TGR BioSciences has access to high throughput cell based screening assays which allow discovery of proteins and complexes with beneficial activity in the cosmaceutical, nutraceutical and even pharmaceutical industries. In addition to the Macquarie University high-throughput protein identification service, APAF can provide agricultural researchers with high value potential targets