悟空云第49期---最新发表《PTMoreR》介绍-Cell Reports Methods

原创 omicsolution omicsolution

国庆都过了11个小时了，该起来干活了！

本工具近期发表在Cell子刊Cell Reports Methods期刊上(https://doi.org/10.1016/j.crmeth.2024.100859)，其可以辅助科研人员对不同物种的翻译后修饰（PTM）进行motif比对、富集和注释，旨在推动跨物种PTM映射和磷酸化蛋白组学的研究。该工具的推出为生物医学研究提供了新的视角，尤其是在理解不同哺乳动物之间的磷酸化差异及其生物学意义方面。欢迎各位老师同学使用。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。

使用悟空云平台，可在文章中如下描述：

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：

(2024) Shisheng Wang, Yi Di, Yin Yang, Barbora Salovska, Wenxue Li, Liqiang Hu, Jiahui Yin, Wenguang Shao, Dong Zhou, Jingqiu Cheng, Dan Liu, Hao Yang, Yansheng Liu, PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals, Cell Reports Methods
(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).
(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).
(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).
(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).
(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).
(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).
(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).
(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).
(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.
(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.
(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

而围绕上游质谱数据解析和下游组学应用，易算近期也发表了多篇文章：

Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species Wen-Feng Zeng, Guoquan Yan, Huan-huan Zhao, Chao Liu & Weiqian Cao Nature Communications IF18,2024
Deep Learning Powers Protein Identification from Precursor MS Information Y Dai, Y Yang, E Wu, C Shen, L Qiao Journal of Proteome Research 2024
Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics E Wu, V Mallawaarachchi, J Zhao, Y Yang, H Liu, X Wang, C Shen, Y Lin, ... Microbiome 12 (1), 2024
High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics E Wu, Y Yang, J Zhao, J Zheng, X Wang, C Shen, L Qiao Analytical Chemistry 2024
Metaproteomics profiling of the microbial communities in fermentation starters (Daqu) during multi-round production of Chinese liquor J Zhao, Y Yang, M Teng, J Zheng, B Wang, V Mallawaarachchi, Y Lin, ... Frontiers in Nutrition 2023
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 IF8,2023
Circulating 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, IF10,2021
Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao*, Y. Wang*, Talanta, IF5,2021
Proteomic and Metabolic Elucidation of Solar-Powered Biomanufacturing by Bio-Abiotic Hybrid System Rutan Zhang, ..., Chengpin Shen, ..., Liang Qiao Chem IF26,2020
In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics
Yi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF18,2020
Metaproteomics characterizes human gut microbiome function in colorectal cancer
Shuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF8,2020

如有您进一步咨询需求和合作意向。

欢迎和我们联系

www.omicsolution.com

若有任何疑问，欢迎邮件或来电咨询：

marketing@omicsolution.com

support@omicsolution.com

+86-18221381405

阅读原文

悟空云第49期---最新发表《PTMoreR》介绍-Cell Reports Methods

(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).

(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).

(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).

(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).

(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).

(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).

(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).

(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).

(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.

(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.

(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.

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 IF8,2023

Circulating 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, IF10,2021

Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao, Y. Wang, Talanta, IF5,2021

Proteomic and Metabolic Elucidation of Solar-Powered Biomanufacturing by Bio-Abiotic Hybrid System Rutan Zhang, ..., Chengpin Shen, ..., Liang Qiao Chem IF26,2020

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics
Yi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF18,2020

Metaproteomics characterizes human gut microbiome function in colorectal cancer
Shuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF8,2020

悟空云第49期---最新发表《PTMoreR》介绍-Cell Reports Methods

(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).

(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).

(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).

(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).

(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).

(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).

(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).

(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).

(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.

(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.

(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.

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiotaJ. Zhao, Y.Yang, H.Xu,..., Chengpin Shen,.. Xia Li* and Liang Qiao* npj Biofilms and Microbiomes IF8,2023

Circulating 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, IF10,2021

Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao*, Y. Wang*, Talanta, IF5,2021

Proteomic and Metabolic Elucidation of Solar-Powered Biomanufacturing by Bio-Abiotic Hybrid System Rutan Zhang, ..., Chengpin Shen, ..., Liang Qiao Chem IF26,2020

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomicsYi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF18,2020

Metaproteomics characterizes human gut microbiome function in colorectal cancerShuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF8,2020

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 IF8,2023

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, IF10,2021

Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao, Y. Wang, Talanta, IF5,2021

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics
Yi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF18,2020

Metaproteomics characterizes human gut microbiome function in colorectal cancer
Shuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF8,2020