QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal.
iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal.
Expert Rev Proteomics. 2020 Jul-Aug;17(7-8):595-607. doi: 10.1080/14789450.2020.1831387. Epub 2020 Oct 21.
Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed.
protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data.
As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.
蛋白质对于细胞的每一项活动都至关重要，而揭示其序列和结构是全面了解其生物学特性的关键步骤。早期的蛋白质测序方法主要基于酶解或化学降解肽链。随着人类基因组计划的完成，以及每个蛋白质的信息量不断扩大，形成了各种包含该序列信息的数据库。
蛋白质测序、鸟枪法蛋白质组学和其他质谱技术，以及目前可用于蛋白质基因组分析的各种软件。重点介绍测序方法，以及使用数据库解释蛋白质序列数据的潜力和局限性。
随着质谱测序性能的提高，通过更好的软件和硬件优化，结合用户友好的界面，在鸟枪法蛋白质组学研究中，蛋白质测序变得至关重要。需要解决未知或突变肽序列的问题，以及通过目标/诱饵策略的错误发现率搜索进行鉴定的意外翻译后修饰 (PTMs)。理想情况下，它应该作为常规数据库搜索引擎的附加组件集成到标准蛋白质组学工作流程中，从而能够提供改进的鉴定。
