Top-Down Proteomics and Farm Animal and Aquatic Sciences

Abstract

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

A Proteomics and other Omics approach in the context of farmed fish welfare and biomarker discovery

“…; Almeida et al . ; Campos & de Almeida ). Recent research consortia were crucial in trying to overcome these difficulties as for the internationalisation and dissemination of proteomic advances in this area, like the FA1002 ‐ Farm Animal Proteomics COST action (http://www.cost-faproteomics.org/) and the PRIME‐XS initiative (http://www.primexs.eu/).…”

“…Bottom‐up strategies are also gaining popularity, mainly due to the availability of more complete databases and the advantage of high‐throughput analyses (Bassols et al . ; Campos & de Almeida ). Proteins' quantitation and identification are achieved by MS analysis, using label‐based or label‐free methods (Soares et al .…”

“…Besides the increasing interest in proteomics technologies, their use in the aquaculture field is still in its infancy, since it as only emerged in the 21st century, with a more accentuated increase in the number of related publications in the last decade (Eckersall et al 2012;Rodrigues et al 2012Rodrigues et al , 2018Almeida et al 2014). However, the establishment of available proteomes is expected to proceed at a slower pace than genome sequencing according to several proposed reasons: (i) the high dependency on sequenced genomes; (ii) the higher complexity of proteins structures, functions and interactions compared to nucleic acids; (iii) the greater number of protein species compared to the number of genes, in an organism, as a result of RNA splicing and post-translational modifications (PTMs); (iv) the lack of an amplification method for proteins; (v) the elevated cost of certain techniques, instruments and specialised staff for maintenance and; (vi) the lack of awareness and perception of the remarkable potential of these technologies (Zhou et al 2012;Almeida et al 2014;Campos & de Almeida 2016). Recent research consortia were crucial in trying to overcome these difficulties as for the internationalisation and dissemination of proteomic advances in this area, like the FA1002 -Farm Animal Proteomics COST action (http://www.cost-faproteomics.org/) and the PRIME-XS initiative (http://www.primexs.eu/).…”

Antibodies, Nanobodies, or Aptamers—Which Is Best for Deciphering the Proteomes of Non-Model Species?

“…This may be due to the low concentration of these immune-modulatory proteins in the biological samples when compared to other proteins, which increases the chances of them being undetected during analysis. When considering food security for the future, it is important that a different approach is considered to identify disease biomarkers and biomarkers relevant to health and immune function [38,39].…”

Proteomics in Veterinary Medicine and Animal Science: Neglected Scientific Opportunities with Immediate Impact

“…There are three MS‐based proteomics strategies that are employed in veterinary medicine: a top‐down approach (measurement of the intact proteins), a middle‐down approach (analysis of incomplete protein digests and protein fragments) on the protein level, and a bottom‐up approach (analysis of digested proteins) on the peptide level. Lack of expertise, knowledge, and limited availability of instrumentation has made top‐ and middle‐down approaches extremely rare in veterinary medicine . The bottom‐up approach has been the method of choice for protein identification and quantification used in both, gel‐based and LC‐based proteomic approaches.…”