Stanford Genome Technology Center, Biochemistry Department, Stanford University, Stanford, California, USA.
Adv Protein Chem Struct Biol. 2014;94:1-17. doi: 10.1016/B978-0-12-800168-4.00001-9.
Proteomics tries to understand biological function of an organism by studying its protein expressions. Mass spectrometry is used in the field of shotgun proteomics, and it generates mass spectra that are used to identify and quantify proteins in biological samples. In this chapter, we discuss the bioinformatics algorithms to analyze mass spectrometry data. After briefly describing how mass spectrometry generates data, we illustrate the bioinformatics algorithms and software for protein identification such as de novo approach and database-searching approach. We also discuss the bioinformatics algorithms and software to quantify proteins and detect the differential proteins using isotope-coded affinity tags and label-free mass spectrometry data.
蛋白质组学试图通过研究其蛋白质表达来了解生物体的生物学功能。质谱分析用于shotgun 蛋白质组学领域，它生成质谱，用于鉴定和定量生物样本中的蛋白质。在本章中，我们讨论了用于分析质谱数据的生物信息学算法。在简要描述了质谱如何生成数据之后，我们展示了用于蛋白质鉴定的生物信息学算法和软件，如从头测序和数据库搜索方法。我们还讨论了用于使用同位素编码亲和标签和无标记质谱数据定量蛋白质和检测差异蛋白质的生物信息学算法和软件。
