色谱2024，Vol.42Issue(7)：658-668,11.DOI:10.3724/SP.J.1123.2024.02009
微生物宏蛋白质组——从样品处理、数据采集到数据分析
Microbial metaproteomics—From sample processing to data acquisition and analysis
摘要
Abstract
Microorganisms are closely associated with human diseases and health.Understand-ing the composition and function of microbial communities requires extensive research.Metap-roteomics has recently become an important method for throughout and in-depth study of mi-croorganisms.However,major challenges in terms of sample processing,mass spectrometric data acquisition,and data analysis limit the development of metaproteomics owing to the com-plexity and high heterogeneity of microbial community samples.In metaproteomic analysis,op-timizing the preprocessing method for different types of samples and adopting different microbi-al isolation,enrichment,extraction,and lysis schemes are often necessary.Similar to those for single-species proteomics,the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition(DDA)and data-independent acquisition(DIA).DIA can collect comprehensive peptide information from a sample and holds great potential for future development.However,data analysis for DIA is challenged by the complexity of metaproteome samples,which hinders the deeper coverage of metaproteomes.The most important step in da-ta analysis is the construction of a protein sequence database.The size and completeness of the database strongly influence not only the number of identifications,but also analyses at the spe-cies and functional levels.The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database.A public database-filtering meth-od based on an iterative database search has been proven to have strong practical value.The peptide-centric DIA data analysis method is a mainstream data analysis strategy.The develop-ment of deep learning and artificial intelligence will greatly promote the accuracy,coverage,and speed of metaproteomic analysis.In terms of downstream bioinformatics analysis,a series of annotation tools that can perform species annotation at the protein,peptide,and gene levels has been developed in recent years to determine the composition of microbial communities.The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches.Metaproteomics has become an important component of the multi-omics analysis of microbial communities,and has great development potential in terms of depth of coverage,sensitivity of detection,and completeness of data analysis.关键词
宏蛋白质组学/样品前处理/数据库/数据分析策略Key words
metaproteomics/sample pretreatment/database/data analysis strategy分类
化学化工引用本文复制引用
吴恩慧,乔亮..微生物宏蛋白质组——从样品处理、数据采集到数据分析[J].色谱,2024,42(7):658-668,11.基金项目
国家自然科学基金(22374031).National Natural Science Foundation of China(No.22374031). （22374031）
