Browsing by Author "Wu, Zhijie"

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    Identification and Quantification of Proteoforms by Mass Spectrometry
    (Wiley, 2019-05) Schaffer, Leah V.; Millikin, Robert J.; Miller, Rachel M.; Anderson, Lissa C.; Fellers, Ryan T.; Ge, Ying; Kelleher, Neil L.; LeDuc, Richard D.; Liu, Xiaowen; Payne, Samuel H.; Sun, Liangliang; Thomas, Paul M.; Tucholski, Trisha; Wang, Zhe; Wu, Si; Wu, Zhijie; Yu, Dahang; Shortreed, Michael R.; Smith, Lloyd M.; BioHealth Informatics, School of Informatics and Computing
    A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, we outline some recent advances and discuss current challenges and future directions for the field.
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    MASH Explorer: A Universal Software Environment for Top-Down Proteomics
    (ACS, 2020-08) Wu, Zhijie; Roberts, David S.; Melby, Jake A.; Wenger, Kent; Wetzel, Molly; Gu, Yiwen; Ramanathan, Sudharshanan Govindaraj; Bayne, Elizabeth F.; Liu, Xiaowen; Sun, Ruixiang; Ong, Irene M.; McIlwain, Sean J.; Ge, Ying; BioHealth Informatics, School of Informatics and Computing
    Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.