Proteomics omics applications

Foodomics involves the use of multiple tools to deal with its different applications. Thus, the use of omics tools (as e.g., transcriptomics, proteomics, or metabolomics) is a must in this new discipline. Although a detailed description on these tools is out of the scope of this chapter, some fundamental concepts on different omics techniques are provided below. 

The MAGE has built within it a controlled vocabulary that is used to standardize communication between data providers. However, MAGE can also be extended to encode other types of omic data beyond genomics, such as proteomic data, so long as a reference to the ontology or controlled vocabulary is provided. Although a description of the extension mechanism is beyond scope of this book, practitioners must become familiar with it in order to ensure their software products and applications will be able to accept any and all annotation data that may be submitted with the genomic data. 

Many existing chemicals have not been thoroughly evaluated for potential developmental/adult neurotoxicity. Currently there is a need for cost-effective predictive tools and testing methods to generate human safety information to make regulatory decisions. The application of innovative methods such as high content OMICS techniques (transcriptomics, proteomics, and metabolomics) (described in Chap. 18) in combination with stable human in vitro... 

The use of human-derived stable differentiated cultures of target organs will be extremely useful for the discovery and development of new translational biomarkers. Omic technologies such as transcriptomics, proteomics, and metabolomics have proven to be excellent tools for understanding drug-induced perturbations, especially when used in combination with appropriate cell culture models [13, 122], The further understanding of how cells differentiate and maintain tissue-specific functions will also be crucial for the discovery of new biomarkers [123]. Importantly, the development of new mechanistically informative biomarkers is not just useful for clinical applications, but these markers will also be useful to drive the development of better, more predictive, human-based in vitro test systems to improve on the predictive power of whole-animal experiments in preclinical testing scenarios. 

Flow-based analytical procedures are already used in many fields, e.g., environment, food and health. In tandem with the developments described above, flow analysers will also be used in new and emerging fields of application such as the "omics" (metallomics, genomics and proteomics), biotechnology (enzymatic assays, platforms for bio-sensors and flow immunoassays) and quality-control applications in general. Economic resources will also be a driver for more multi-parametric flow-based methods, particularly with spectrophotometric detection. 

Immunomics offers an excellent example for application of the systems biology and modern genomics/proteomics technology. Immunomics comprises a fruitful combination of modern molecular immunology, animal modeling, omics technologies, and application of ever-increasing immune databases. 

Fig. 3 Omics methods and their areas of application. Alterations can be detected at several biological levels in the organism. Transcriptomics, proteomics and metabolomics have all been employed to detect unintended effects but most published examples relate to metabolomics...

Therefore, some applications restricted until now to FT-ICR (TOF analyzers have not been used, due to lack of resolving power) can be transferred to orbitrap analyzers, such as proteomics metabolomics, and other omics approaches. The main advantage is that orbitrap does not need such an expensive and delicate maintenance as FT-ICR does. 

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