Proteomics technique applications have been rapidly increased for analyses of crop plants within the last 10 years. Although proteomic techniques are regularly used in plant research, bioinformatics is considered a relatively new field of biosciences yet is making progress in every field of biotechnology very rapidly. As it has its applications in the medical field by providing the genetic and proteomic information of various organisms, similarly the field of agriculture has also taken advantage of this field because microorganisms, plants, and their interaction play an important role in agriculture, and bioinformatics helps to provide and analyze the multi-“omics” information of these organisms. The genome sequencing, proteome database of the agriculturally related organism has also provided benefits to agriculture. The improvement of several cutting-edge tools for biology, statistics, and computer science are connecting protein-related research to other “omics,” and functional biology data are further initial new approaches for crop cultivation improvement studies via the plant signaling, regulatory hormones cross-talk essential in agricultural research. This chapter aims to highlight many applications of proteomic-related bioinformatic tools in agriculture in view of trait improvement, disease control and plant disease management, nutritional content, high-performance bioinformatic facilities in agriculture, and various bioinformatics software programs/database important for biotechnologists and pathologists as well as breeders. Moreover, the elaboration of the database, algorithms, and software development that have been implemented to overcome the difficulties of the protein analysis without the database containing molecular information is discussed.