在过去的十年里，我们见证了蛋白质组学的巨大进步,主要是由于质谱领域的重大技术改进,允许高通量产生用于大量蛋白质鉴定和定量的高质量数据.从实践的角度来看，这些进展主要被用于涉及模式生物的研究项目，这些模式生物在公共数据库中具有丰富的基因组和蛋白质组信息。然而,越来越多的生物体对不同的学科有很高的兴趣，比如生态，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该技术对许多研究实验室的容易接近性,如今已经使得产生任何生物体的定制基因组和蛋白质组数据库成为可能。沿着这条线,通过在相同的分析中结合从不同组学水平获得的数据，使用蛋白质组学方法已经成为一种非常有用和强大的策略，可以进行专门针对非模型生物的shot弹枪蛋白质组学实验。在这一章中,我们提供了详细的程序来进行鸟枪定量蛋白质组学实验，在非模型生物中采用无标记或等量异位标记方法，还强调了与实验设计和数据分析相关的几个关键方面。
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.
