Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
Marine Research Center, University of Vigo (CIM-UVIGO), Vigo, Spain.
Methods Mol Biol. 2021;2259:77-102. doi: 10.1007/978-1-0716-1178-4_6.
During the last decade, we have witnessed outstanding advances in proteomics led mostly by great technological improvements in mass spectrometry field allowing high-throughput production of high-quality data used for massive protein identification and quantification. From a practical viewpoint, these advances have been mainly exploited in research projects involving model organisms with abundant genomic and proteomic information available in public databases. However, there is a growing number of organisms of high interest in different disciplines, such as ecological, biotechnological, and evolutionary research, yet poorly represented in these databases. Important advances in massive parallel sequencing technology and easy accessibility of this technology to many research laboratories have made nowadays possible to produce customized genomic and proteomic databases of any organism. Along this line, the use of proteogenomic approaches by combining in the same analysis the data obtained from different omic levels has emerged as a very useful and powerful strategy to run shotgun proteomic experiments specially focused on non-model organisms. In this chapter, we provide detailed procedures to undertake shotgun quantitative proteomic experiments following either a label-free or an isobaric labeling approach in non-model organisms, emphasizing also a few key aspects related to experimental design and data analysis.
在过去的十年中，我们见证了蛋白质组学的杰出进展，这主要得益于质谱领域的重大技术改进，这些改进允许高通量生成高质量数据，用于大规模蛋白质鉴定和定量。从实际的角度来看，这些进展主要在涉及具有丰富基因组和蛋白质组信息的模式生物的研究项目中得到了利用，这些信息可在公共数据库中获得。然而，越来越多的生物在不同的学科中具有重要的研究意义，例如生态、生物技术和进化研究，但在这些数据库中的代表性不足。大规模平行测序技术的重要进展以及许多研究实验室对这项技术的便捷获取，使得现在可以为任何生物体制作定制的基因组和蛋白质组数据库。沿着这条线，通过将不同组学水平获得的数据结合到同一分析中，利用蛋白质基因组学方法已经成为针对非模式生物体进行鸟枪法蛋白质组学实验的非常有用和强大的策略。在本章中，我们提供了在非模式生物体中进行无标记或同位标记定量蛋白质组学实验的详细步骤，还强调了与实验设计和数据分析相关的几个关键方面。
