metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis

文献类型： 外文期刊

第一作者： Sun, Yingying

作者： Sun, Yingying;Xing, Ziyuan;Liang, Shuang;Miao, Zelei;Jiang, Wenhao;Zhao, Hui;Gao, Huanhuan;Xie, Yuting;Zhou, Yan;Yue, Liang;Cai, Xue;Zheng, Ju-Sheng;Guo, Tiannan;Sun, Yingying;Xing, Ziyuan;Liang, Shuang;Jiang, Wenhao;Gao, Huanhuan;Xie, Yuting;Zhou, Yan;Yue, Liang;Cai, Xue;Guo, Tiannan;Sun, Yingying;Xing, Ziyuan;Liang, Shuang;Miao, Zelei;Jiang, Wenhao;Zhao, Hui;Gao, Huanhuan;Xie, Yuting;Zhou, Yan;Yue, Liang;Cai, Xue;Zheng, Ju-Sheng;Guo, Tiannan;Liang, Shuang;Miao, Zelei;Zhao, Hui;Zheng, Ju-Sheng;Zhuo, Lai-bao;Chen, Yu-ming

作者机构：

期刊名称：MOLECULAR & CELLULAR PROTEOMICS （ 影响因子：5.5； 五年影响因子：6.2 ）

ISSN：

年卷期： 2024 年 23 卷 10 期

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收录情况： SCI

摘要： Analysis of large-scale data-independent acquisition mass spectrometry metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS, protein identification and quantification using data-independent acquisition mass spectrometry, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-min diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67-0.90) in genus diversity and showed a high correlation (r Spearman = 0.73-0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the micro- biota and the host.

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