Downard Kevin M
Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW 2031, Australia.
Anal Methods. 2021 Mar 28;13(12):1442-1454. doi: 10.1039/d1ay00153a. Epub 2021 Mar 16.
Advances in protein mass spectrometry have provided the ability to identify and sequence proteins with unprecedented speed, sensitivity and accuracy. These benefits now offer advantages for studies of protein evolution and phylogeny avoiding the need to generate and align DNA sequences which can prove time consuming, costly and difficult in the case of large genomes and for highly diverse organisms. The methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by multiple sequence alignment for classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using expressed protein mass profiles exploited in microbial biotyping applications, and (3) the construction of trees using proteolytic peptide mass map or fingerprint data. This review describes the three approaches together with the relevant tools and algorithms required to implement them. It also compares each of these alternative protein based methods alongside conventional gene sequence based phylogenetics.
蛋白质质谱技术的进步使人们能够以前所未有的速度、灵敏度和准确性对蛋白质进行鉴定和测序。这些优势为蛋白质进化和系统发育研究带来了便利，无需再生成和比对DNA序列，而在大型基因组和高度多样化生物的情况下，生成和比对DNA序列可能既耗时、成本又高且困难重重。利用蛋白质质谱技术进行系统发育分析的方法可分为三类：（1）从头蛋白质测序，随后进行多序列比对以进行经典的系统发育重建；（2）利用微生物生物分型应用中所采用的表达蛋白质质量图谱进行直接系统发育重建；（3）使用蛋白水解肽质量图谱或指纹数据构建树状图。本综述介绍了这三种方法以及实施它们所需的相关工具和算法。它还将这些基于蛋白质的替代方法与传统的基于基因序列的系统发育学方法进行了比较。
