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SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics. SEMQuant：利用匹配运行（Match-Between-Runs）扩展 Sipros-Ensemble，实现全面的定量元蛋白质组学。

Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference) Pub Date : 2024-07-01 Epub Date: 2024-07-12 DOI: 10.1007/978-981-97-5087-0_9

Bailu Zhang, Shichao Feng, Manushi Parajuli, Yi Xiong, Chongle Pan, Xuan Guo

{"title":"SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics.","authors":"Bailu Zhang, Shichao Feng, Manushi Parajuli, Yi Xiong, Chongle Pan, Xuan Guo","doi":"10.1007/978-981-97-5087-0_9","DOIUrl":"10.1007/978-981-97-5087-0_9","url":null,"abstract":"Metaproteomics, utilizing high-throughput LC-MS, offers a profound understanding of microbial communities. Quantitative metaproteomics further enriches this understanding by measuring relative protein abundance and revealing dynamic changes under different conditions. However, the challenge of missing peptide quantification persists in metaproteomics analysis, particularly in data-dependent acquisition mode, where high-intensity precursors for MS2 scans are selected. To tackle this issue, the match-between-runs (MBR) technique is used to transfer peptides between LC-MS runs. Inspired by the benefits of MBR and the need for streamlined metaproteomics data analysis, we developed SEMQuant, an end-to-end software integrating Sipros-Ensemble's robust peptide identifications with IonQuant's MBR function. The experiments show that SEMQuant consistently obtains the highest or second highest number of quantified proteins with notable precision and accuracy. This demonstrates SEMQuant's effectiveness in conducting comprehensive and accurate quantitative metaproteomics analyses across diverse datasets and highlights its potential to propel advancements in microbial community studies. SEMQuant is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/SEMQuant.","PeriodicalId":93167,"journal":{"name":"Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference)","volume":"14956 ","pages":"102-115"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dilated-DenseNet For Macromolecule Classification In Cryo-electron Tomography. 低温电子断层扫描中用于大分子分类的膨胀致密网。

Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference) Pub Date : 2020-12-01 Epub Date: 2020-08-18 DOI: 10.1007/978-3-030-57821-3_8

Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhiyong Liu, Min Xu, Fa Zhang

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引用次数: 4