Current Protein and Peptide Science - Volume 15, Issue 1, 2014

Despite the increasing popularity of gel-free proteomic strategies, two-dimensional gel electrophoresis (2DE) is still the most widely used approach in top-down proteomic studies, for all sorts of biological models. In order to achieve meaningful biological insight using 2DE approaches, importance must be given not only to ensure proper experimental design, experimental practice and 2DE technical performance, but also a valid approach for data acquisition, processing and analysis. This paper reviews and illustrates several different aspects of data analysis within the context of gel-based proteomics, summarizing the current state of research within this field. Particular focus is given on discussing the usefulness of available multivariate analysis tools both for data visualization and feature selection purposes. Visual examples are given using a real gel-based proteomic dataset as basis.

Proteomics is a growing field that has the potential to be applied to many biology-related disciplines. However, the study of the proteome has proven to be very challenging due to its high level of complexity when compared to genome and transcriptome data. In order to analyse this level of complexity, high resolution separation of peptides/proteins are needed together with high resolution analysers. Currently, liquid chromatography and capillary electrophoresis (CE) are the two most widely used separation techniques that can be coupled on-line with a mass spectrometer (MS). In CE, proteins/ peptides are separated according to their size, charge and shape leading to high resolving power. Although further progress in the area of sensitivity, throughput and proteome coverage are expected, MS-based proteomics have developed to a level at which they are habitually applied to study a wide range of biological questions. The aim of this review is to present CE-MS as a proteomic analytical platform for biomarker research that could be used in farm animal and veterinary studies. This is a MS-analytical platform that has been widely used for biomarker research in the biomedical field but its application in animal proteomic studies is relatively novel. The review will focus on introducing the CE-MS platform and the primary considerations for its application to biomarker research. Furthermore, current applications but more importantly potential application in the field of farm animals and veterinary science will be presented and discussed.

The prevalence of cancer in companion animals has increased in the recent decade, making this disease one of the major causes of deaths. As in human medicine, veterinary medicine faces the problem of cancer prevention as well as early diagnosis and effective therapy. Early diagnosis of cancer is crucial for the successful treatment of the disease and there is a need for biomarkers that could be used as a diagnostic tool, and to guide a targeted therapy or monitor a therapeutic response. Proteomic technologies that were introduced to human cancer research over a decade ago provide the opportunity to identify distinct protein patterns for cancer diagnosis and therapy monitoring. These also have potential to be utilised in veterinary medicine. The present paper summarises the current knowledge about proteomic studies on animal cancer biomarker research published to date.

Our knowledge of the physiology and health of small ruminants, specifically sheep and goats, is frequently obtained by extrapolating information from other species, for example the cow. However, there are important genetic, physiological and anatomical differences between small and large ruminants that cannot be ignored. This review considers the advances that have been made in the investigation of sheep and goat physiology through the use of proteomic technologies. Proteomics is widely used to analyze clinically relevant body fluids for a number of animals to define productive traits and health status biomarkers as well as to monitor therapeutic interventions for infectious and metabolic diseases. Although the proteomes of body fluids have been described in detail for some animal species, there are few equivalent studies for sheep and goats. Nevertheless, the data now available for the proteomes of a range of body fluids in small ruminants have helped define new diagnostic and prognostic markers for these species. Moreover, these data are beneficial in studies where these small ruminants serve as models for human disease. However, despite the progress achieved to date, comprehensive data on the specific proteomes for many tissues and body fluids for sheep and goats remain scarce. The aim of this review is to describe the current status of small ruminant proteomic research and to demonstrate the potential benefits, as well as highlight the difficulties, of working with these animals.

This paper reviews recent progress in salivary animal proteomics, with special reference to the porcine proteome. Until fairly recently, most studies on saliva as a diagnostic fluid have focused on humans, primates and rodents, and the development of salivary analysis in monitoring health in farm animals including pigs has received only limited consideration. The porcine salivary proteome has been characterised by 2D-electrophoresis followed by mass spectrometry. Major and minor proteins have been identified. The use of saliva as a non-invasive biological fluid in monitoring health and disease in pigs will be reviewed, together with the potential use of proteomics for the development of biomarkers. In this review, methods of collection and the composition of porcine saliva will be considered, together with saliva handling and analysis. The overall findings indicate that there is considerable potential for the development of salivary analysis as a non-invasive diagnostic fluid in the pig, and that it offers advantages over other body fluids in this animal.

In this review authors address colostrum proteins implications in different domestic ruminant species. The colostrogenesis process and how different factors, such as litter size or nutrition during gestation can alter the different components concentrations in colostrum are also reviewed. The different colostrum fractions will be described, focusing on high and low abundant proteins. This review describes the major function of such proteins and their role on the passive immune transfer and nutrition in the newborn animal. It will be also performed a comprehensive review on different techniques and commercial kits available for high abundant protein depletion in colostrum. We will finally focus on how proteomics has been used to address this issue and how it can contribute to the major questions about colostrum associated immunology.

Lyme borreliosis (LB), caused by Borrelia burgdorferi (B.b.), is the most frequently diagnosed tick-borne zoonosis in temperate zones of the Northern hemisphere. Borrelia is unique among bacteria in its ability to express a wide variety of lipoproteins on its surface, which play an essential role in pathogenesis. Surface proteins of spirochetes are important virulence determinants, immune evasion molecules and adaptation factors in the transmission and interaction with host tissues. Vast diversity in the expressed surface proteome of Borrelia in different niches and multifunctionality of proteins are the major strategies of Borrelia to avoid the destructive effect of immune system. In this review we provide deep insight into the protein:protein interactions that take place between different stages of life of Borrelia. Precise knowledge of surface proteins may help in improvement of the vaccines as well as for therapeutic agents against borreliosis.