悟空云平台交流第42期---《pseudoQC工具-模拟质控数据》
本期视频给大家介绍如何在悟空云平台使用pseudoQC工具模拟出QC样本数据。该模块目前主要利用四种常用的回归模型，从蛋白质组或者代谢组的样本数据中对质控数据（Quality Control）进行模拟（即‘拟质控数据’或‘伪质控数据’，pseudoQC）。可能应用的场景有：1. 数据中没有QC样本的；2. QC数据质量不是很好的。尤其是当数据出现较为严重的批次效应时，该工具可能可以提供一种尝试。本系列视频会收录在我们公众号菜单：技术动态->悟空云系列讲座
1) 比如在正文Methods部分：We use 'Wu Kong' platform (https://www.omicsolution.com/wkomics/main/) for relative xxx analysis.
2) 比如在致谢(Acknowledgements)部分：Thank Dr. Shisheng Wang (West China Hospital, Sichuan University) and Dr. Chengpin Shen (Omicsolution Co., Ltd) for giving some advices about data analysis and 'Wu Kong' platform (https://www.omicsolution.com/wkomics/main/) for relative xxx analysis.
目前基于悟空平台开发的分析工具已发表以下文章：
1. (2020) Shisheng Wang , Wenxue Li, Liqiang Hu, Jingqiu Cheng, Hao Yang, Yansheng Liu, NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses, Nucleic Acids Research, gkaa498. (2021 IF: 19.16). Link to article.
2. (2022) Huilin Yu, Haiyu Luo, Luping Chang, Shisheng Wang （共一作） , ..., Hao Yang, Wenying Fan & Bing-Qiao Zhao, The NEDD8-activating enzyme inhibitor MLN4924 reduces ischemic brain injury in mice. Proceedings of the National Academy of Sciences, 119(6). (2021 IF: 12.779). Link to article.
3. (2022) Yi Zhong Shisheng Wang (共通讯) , et al. Proteome and phosphoproteome profiling of non-small cell lung cancer cell line A549 treated with TRAIL, Proteomics, 10.1002/pmic.202200248. (2021 IF: 5.393). Link to article.
4. (2021) Shisheng Wang , et al. StatsPro: Systematic integration and evaluation of statistical approaches for detecting differential expression in label-free quantitative proteomics, Journal of Proteomics, 10.1016/j.jprot.2021.104386. (2020 IF: 4.04). Link to article.
5. (2021) Shisheng Wang , Yi Zhong, Jingqiu Cheng, Hao Yang, EnrichVisBox: A Versatile and Powerful Web Toolbox for Visualizing Complex Functional Enrichment Results of Omics Data, Journal of computational biology, 10.1089/cmb.2020.0564. (2020 IF: 1.479). Link to article.
6. (2020) Shisheng Wang , Hongwen Zhu, Hu Zhou, Jingqiu Cheng and Hao Yang. MSpectraAI: a powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks. BMC Bioinformatics 21, 439 (2020). (2019 IF: 3.242). Link to article.
7. (2019) Shisheng Wang , Yue Cai, Jingqiu Cheng, Wenxue Li, Yansheng Liu and Hao Yang. motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs. Proteomics: 201900245. (2018 IF: 3.106). Link to article.
8. (2019) Shisheng Wang and Hao Yang. pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets. Proteomics: 1900264. (2018 IF: 3.106). Link to article.
9. (2018) Shisheng Wang , ..., and Meng Gong. MetaboGroupS: A Group Entropy-Based Web Platform for Evaluating Normalization Methods in Blood Metabolomics Data from Maintenance Hemodialysis Patients. Anal Chem 90, 11124-11130. (2017 IF: 6.042). Link to article.
10. (2018) Shisheng Wang , ..., and Hao Yang. MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data. Journal of computational biology : a journal of computational molecular cell biology 25, 1123-1127. (2017 IF: 1.191). Link to article.
11. (2018) Qing-Run Li, Shi-Sheng Wang(共一作) , Hong-Wen Zhu, Fang-Ying Xia, Peter Roepstorff, Jia-Rui Wu, and Rong Zeng. Data-Independent Acquisition Mass Spectrometry to Localize Phosphosites. bioRxiv: 464545. Link to article.
同时悟空平台整合上百个分析模块，包括且远不止以下功能
DeepFLR facilitates false localization rate control in phosphoproteomics
Y.Zong, Y.Wang, Y.Yang, D.Zhao, Xiaoqing Wang, Chengpin Shen, and Liang Qiao* Nature Communications IF18,2023
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota
J. Zhao, Y.Yang, H.Xu,..., Chengpin Shen,.. Xia Li* and Liang Qiao* npj Biofilms and Microbiomes IF8,2023Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture
Yueting Xiong, ...,Xiaohui Liu*
EMBO Mol Med, IF12.3,2022 Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer
Runqiu Yi, Liying Xie, Xiaoqing Wang, Chengpin Shen, Xiaojun Chen*, Liang Qiao*，Frontiers in Oncology，IF6.3,2022
Mesoporous Silica as Sorbents and Enzymatic Nanoreactors for Microbial Membrane Proteomics
J. Zhao, R. Jian, Y. Wang, B. Yang, D. Zhao, C. Shen, L. Qiao*, B. Liu*, ACS Applied Materials & Interfaces, IF10,2021Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis
J. Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao*, Y. Wang*, Talanta, IF5,2021Proteomic and Metabolic Elucidation of Solar-Powered Biomanufacturing by Bio-Abiotic Hybrid System
Rutan Zhang, ..., Chengpin Shen, ..., Liang Qiao Chem IF26,2020In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics
Yi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF18,2020Metaproteomics characterizes human gut microbiome function in colorectal cancer
Shuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF8,2020