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Molecular & Cellular Proteomics

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Protein array

  • TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic Data
    You have access
    TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic Data
    Mei-Ju May Chen, Jun Li, Yumeng Wang, Rehan Akbani, Yiling Lu, Gordon B. Mills and Han Liang
    Molecular & Cellular Proteomics August 9, 2019, First published on June 14, 2019, 18 (8 suppl 1) S15-S25; https://doi.org/10.1074/mcp.RA118.001260

    Reverse-phase protein arrays represent a powerful functional proteomics approach. Using this platform, we have characterized ∼8,000 patient samples of 32 cancer types through The Cancer Genome Atlas and built a widely used, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA). Here we have developed a new module called “TCGA Pan-Cancer Analysis,” which provides comprehensive protein-centric, pan-cancer analyses in rich context of TCGA data. This upgraded TCPA (v3.0) provides a more valuable tool for studying functional proteomics and making translational impacts.

  • Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors
    You have access
    Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors
    Guang Song, Li Chen, Bai Zhang, Qifeng Song, Yu Yu, Cedric Moore, Tian-Li Wang, Ie-Ming Shih, Hui Zhang, Daniel W. Chan, Zhen Zhang and Heng Zhu
    Molecular & Cellular Proteomics March 1, 2019, First published on December 6, 2018, 18 (3) 448-460; https://doi.org/10.1074/mcp.RA118.000851

    A systematic, multiplexed approach interrogating enzyme-substrate relationships in context of PTMs is fundamental in understanding the dynamics of these pathways in disease processes. Multiplexed PTM reactions on HuProt arrays were developed and applied to 102 TCGA ovarian tumor samples. Data integration and networks analysis led to the prediction that 19 tyrosine kinases were elevated and potentially responsible for the dysregulated pTyr signaling pathways in ovarian tumors. Elevated kinase activities of PTK2 and PTK2B were confirmed in several ovarian cancer cell lines.

  • Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass Spectrometry
    Open Access
    Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass Spectrometry
    Zachary Klamer, Peter Hsueh, David Ayala-Talavera and Brian Haab
    Molecular & Cellular Proteomics January 1, 2019, First published on September 26, 2018, 18 (1) 28-40; https://doi.org/10.1074/mcp.RA118.000906

    A new method is presented to decipher information about the isomeric variants of the glycans attached to purified proteins. The method takes advantage of the specificities of glycosidases and lectins, combined with computational integration of the data with information from glycan arrays and mass spectrometry. The application to microspots of proteins makes it compatible with analyzing low-abundance proteins, providing the potential for studying proteins derived from clinical specimens.

  • You have access
    Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation
    Ran Wei, Tomonori Kaneko, Xuguang Liu, Huadong Liu, Lei Li, Courtney Voss, Eric Liu, Ningning He and Shawn S.-C. Li
    Molecular & Cellular Proteomics November 1, 2018, First published on December 7, 2017, 17 (11) 2216-2228; https://doi.org/10.1074/mcp.RA117.000114
  • You have access
    Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks
    Li Cheng, Cheng-xi Liu, Shuangying Jiang, Sha Hou, Jin-guo Huang, Zi-qing Chen, Yang-yang Sun, Huan Qi, He-wei Jiang, Jing-fang Wang, Yi-ming Zhou, Daniel M. Czajkowsky, Junbiao Dai and Sheng-ce Tao
    Molecular & Cellular Proteomics September 1, 2018, First published on June 5, 2018, 17 (9) 1720-1736; https://doi.org/10.1074/mcp.RA117.000550
  • You have access
    Antigen Analysis of Pre-Eclamptic Plasma Antibodies Using Escherichia Coli Proteome Chips
    Te-Yao Hsu, Jyun-Mu Lin, Mai-Huong T. Nguyen, Feng-Hsiang Chung, Ching-Chang Tsai, Hsin-Hsin Cheng, Yun-Ju Lai, Hsuan-Ning Hung and Chien-Sheng Chen
    Molecular & Cellular Proteomics August 1, 2018, First published on December 28, 2017, 17 (8) 1457-1469; https://doi.org/10.1074/mcp.RA117.000139
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    Credentialing Individual Samples for Proteogenomic Analysis
    Wei Zhao, Jun Li, Rehan Akbani, Han Liang and Gordon B. Mills
    Molecular & Cellular Proteomics August 1, 2018, First published on May 1, 2018, 17 (8) 1515-1530; https://doi.org/10.1074/mcp.RA118.000645
  • You have access
    Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies
    Jinho Lee, Gary K. Geiss, Gokhan Demirkan, Christopher P. Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y. Bogatzki, Warren Carter, Rhonda K. Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M. Beechem and Gordon B. Mills
    Molecular & Cellular Proteomics June 1, 2018, First published on March 12, 2018, 17 (6) 1245-1258; https://doi.org/10.1074/mcp.RA117.000291

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