Proteomic Advances in Cereal and Vegetable Crops

Using long columns to quantify over 9200 unique protein groups from brain tissue in a single injection on an Orbitrap Exploris 480 mass spectrometer

The most exciting advancement in LC-MS/MS-based bottom-up proteomics has centered around enhancing mass spectrometers. Among these, the latest and most advanced mass spectrometer for bottom-up proteomics is the Orbitrap Astral that has the highest scan rate to accelerate throughput and the highest sensitivity to handle a very small amount of peptide samples and to achieve deeper proteomics. However, its affordability remains a challenge for most laboratories. While significant strides have been made in improving mass spectrometry, advancing liquid chromatography (LC) to achieve deeper proteomics has not achieved significant successes since the innovation of Multidimensional Protein Identification Technology (MudPIT) in 2001. To achieve deeper proteomics in a less labor-intensive and more reproducible approach while using a more cost-effective mass spectrometer, such as the Orbitrap Exploris 480, we evaluated trap columns as long as 40 cm and analytical column as long as 600 cm besides sample loading amount, gradient time, and analytical column particle size to enable a fractionation-free method for a single injection to obtain deeper proteomics. The length of trap and analytic columns is the key factor. Using a 30 cm trap column and 250 cm analytical column with other optimized LC conditions, we quantified over 9200 unique protein groups from brain tissue in a single injection using a 24-h gradient on an Orbitrap Exploris 480 mass spectrometer.

The potential of proteomics in the study of processed meat products

Proteomics is a field that has grown rapidly since its emergence in the mid-1990s, reaching many disciplines such as food technology. The application of proteomic techniques in the study of complex biological samples such as foods, specifically meat products, allows scientists to decipher the underlying cellular mechanisms behind different quality traits. Lately, much emphasis has been placed on the discovery of biomarkers that facilitate the prediction of biochemical transformations of the product and provide key information on parameters associated with traceability and food safety. This review study focuses on the contribution of proteomics in the improvement of processed meat products. Different techniques and strategies have recently been successfully carried out in the study of the proteome of these products that can help the development of foods with a higher sensory quality, while ensuring consumer safety through early detection of microbiological contamination and fraud. SIGNIFICANCE: The food industry and the academic world work together with the aim of responding to market demands, always seeking excellence. In particular, the meat industry has to face a series of challenges such as, achieving sensory attributes in accordance with the standards required by the consumer and maintaining a high level of safety and transparency, avoiding deliver adulterated and/or contaminated products. This review work exposes how the aforementioned challenges are attempted to be solved through proteomic technology, discussing the latest and most outstanding research in this regard, which undoubtedly contribute to improving the quality, in all the extension of the word, of meat products, providing relevant knowledge in the field of proteomic research.

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects

Wheat is an important staple cereal for global food security. However, climate change is hampering wheat production due to abiotic stresses, such as heat, salinity, and drought. Besides shoot architectural traits, improving root system architecture (RSA) traits have the potential to improve yields under normal and stressed environments. RSA growth and development and other stress responses involve the expression of proteins encoded by the trait controlling gene/genes. Hence, mining the key proteins associated with abiotic stress responses and RSA is important for improving sustainable yields in wheat. Proteomic studies in wheat started in the early 21st century using the two-dimensional (2-DE) gel technique and have extensively improved over time with advancements in mass spectrometry. The availability of the wheat reference genome has allowed the exploration of proteomics to identify differentially expressed or abundant proteins (DEPs or DAPs) for abiotic stress tolerance and RSA improvement. Proteomics contributed significantly to identifying key proteins imparting abiotic stress tolerance, primarily related to photosynthesis, protein synthesis, carbon metabolism, redox homeostasis, defense response, energy metabolism and signal transduction. However, the use of proteomics to improve RSA traits in wheat is in its infancy. Proteins related to cell wall biogenesis, carbohydrate metabolism, brassinosteroid biosynthesis, and transportation are involved in the growth and development of several RSA traits. This review covers advances in quantification techniques of proteomics, progress in identifying DEPs and/or DAPs for heat, salinity, and drought stresses, and RSA traits, and the limitations and future directions for harnessing proteomics in wheat improvement.

Foodomic-Based Approach for the Control and Quality Improvement of Dairy Products

The food quality assurance before selling is a needed requirement intended for protecting consumer interests. In the same way, it is also indispensable to promote continuous improvement of sensory and nutritional properties. In this regard, food research has recently contributed with studies focused on the use of 'foodomics'. This review focuses on the use of this technology, represented by transcriptomics, proteomics, and metabolomics, for the control and quality improvement of dairy products. The complex matrix of these foods requires sophisticated technology able to extract large amounts of information with which to influence their aptitude for consumption. Thus, throughout the article, different applications of the aforementioned technologies are described and discussed in essential matters related to food quality, such as the detection of fraud and/or adulterations, microbiological safety, and the assessment and improvement of transformation industrial processes (e.g., fermentation and ripening). The magnitude of the reported results may open the door to an in-depth transformation of the most conventional analytical processes, with the introduction of new techniques that allow a greater understanding of the biochemical phenomena occurred in this type of food.