Comparative Label-Free Liquid Chromatography–Mass Spectrometry Milk Proteomic Profiles Highlight Putative Differences between the Autochthon Teramana and Saanen Goat Breeds

SIMPLE SUMMARY: Milk is a valuable source of proteins and other nutrients. Changes in milk production toward systems that obtain increased milk yield have resulted in a change in milk composition in large and small ruminants, such as goats. A better characterisation of breeds that undergo a limited formal crossbreeding, such as the Teramana goat is pivotal in order to obtain useful data that could be applied for the management of the breed. Proteomic technologies have brought significant advances in the characteristion of new proteins. In this study, this technology was used to compare the proteome of the autochthon Teramana and Saanen breeds, which are commonly used by the industry to allow for the identification of a cohort of proteins that were able to discriminate the two goat breeds. Proteomics offered the potentiality for a deeper investigation of the biological differences of the breeds under study in a substrate easy to obtain. ABSTRACT: Goat’s milk is an excellent source of nutrients, with greater benefits compared to cow’s milk. Limited information is available on autochthon goat breeds, which are important for biodiversity preservation. In this study, the aim of using label-free quantification was to investigate the milk proteome of two goat breeds, the autochthon Teramana and Saanen breeds, which are commonly used by the industry. Utilising label-free proteomic analysis, 749 and 666 proteins, respectively were identified and quantified from the Teramana and Saanen goat milk. Moreover, utilising statistical analysis, 29 proteins were able to discriminate the two goat breeds, with many of the identified proteins involved in complement and coagulation cascades. This work enhances our understanding of the goat milk proteome and shows differences between the two breeds, leading to an important contribution toward a more detailed molecular-view of this unique substrate. Additionally, charactersation of the milk proteins can help in guiding genetic improvements in the goat herds, and thus increasing its use in human nutrition.